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2,336,200 |
Screening of antibiotics resistance to Enterobacteriaceae, Pseudomonas aeruginosa, and Acinetobacter baumannii by an advanced expert system.
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The VITEK2 advanced expert system (AES) gives information about the antibiotics-resistance mechanisms based on the biological validation derived from the VITEK2 susceptibility result. In this study, we investigated whether or not this system correctly categorized the beta-lactamase resistance mechanism data derived from the VITEK2 susceptibility result using the testing card, AST-N025, with Enterobacteriaceae, Pseudomonas aeruginosa, and Acinetobacter baumannii. We used 131 strains, and their phenotypes were determined according to the biological and genetic screening. The AES analysis result matched the phenotype testing in 120 (91.6%) of the 131 strains. Incorrect findings were found in six strains, including three strains of Serratia marcescens. The resistance mechanism could not be determined in five strains, including three strains of Providencia rettgeri. The analysis of those phenotypes agreed in 34 (97.1%) among 35 strains with extended spectrum beta-lactamase (ESBL), and in 27 (96.4%) among 28 strains with high-level cephalosporinase. The agreement ratio in the phenotype was very high as we expected. The incorrect and nondeterminable samples were strains with relatively high cephalosporinase that has variation of outer membrane protein. The AES was able to detect the phenotype for carbapenemase. The AES is a clinically useful system that allows taking prompt measures to treat patients because it can provide information about the resistance mechanism in less than half a day after starting the analysis.
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2,336,201 |
Accurate prediction of HIV-1 drug response from the reverse transcriptase and protease amino acid sequences using sparse models created by convex optimization.
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Genotype-phenotype modeling problems are often overcomplete, or ill-posed, since the number of potential predictors-genes, proteins, mutations and their interactions-is large relative to the number of measured outcomes. Such datasets can still be used to train sparse parameter models that generalize accurately, by exerting a principle similar to Occam's Razor: When many possible theories can explain the observations, the most simple is most likely to be correct. We apply this philosophy to modeling the drug response of Type-1 Human Immunodeficiency Virus (HIV-1). Owing to the decreasing expense of genetic sequencing relative to in vitro phenotype testing, a statistical model that reliably predicts viral drug response from genetic data is an important tool in the selection of antiretroviral therapy (ART). The optimization techniques described will have application to many genotype-phenotype modeling problems for the purpose of enhancing clinical decisions.</AbstractText>We describe two regression techniques for predicting viral phenotype in response to ART from genetic sequence data. Both techniques employ convex optimization for the continuous subset selection of a sparse set of model parameters. The first technique, the least absolute shrinkage and selection operator, uses the l(1) norm loss function to create a sparse linear model; the second, the support vector machine with radial basis kernel functions, uses the epsilon-insensitive loss function to create a sparse non-linear model. The techniques are applied to predict the response of the HIV-1 virus to 10 reverse transcriptase inhibitor and 7 protease inhibitor drugs. The genetic data are derived from the HIV coding sequences for the reverse transcriptase and protease enzymes. When tested by cross-validation with actual laboratory measurements, these models predict drug response phenotype more accurately than models previously discussed in the literature, and other canonical techniques described here. Key features of the methods that enable this performance are the tendency to generate simple models where many of the parameters are zero, and the convexity of the cost function, which assures that we can find model parameters to globally minimize the cost function for a particular training dataset.</AbstractText>Results, tables and figures are available at ftp://ftp.genesecurity.net.</AbstractText>An Appendix to accompany this article is available at Bioinformatics online.</AbstractText>
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2,336,202 |
Multiplex fluorescent analysis of four short tandem repeats for rapid haemophilia A molecular diagnosis.
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Indirect molecular diagnosis of hemophiliaA (HA) is carried out by analyzing intragenic polymorphic markers described along the coagulation factorVIII (FVIII) gene. Several studies have demonstrated that the two commonly used intronic short tandem repeats (STR13 and STR22) located in the FVIII gene are highly informative for this task. Two extragenic markers closely linked to FVIII (DXS1073 and DXS1108) have also been described as valuable tools for gene tracking. The objective of the present work was to develop a rapid, single-tube automated method to simultaneously analyze these four STRs. Consistent amplification was achieved by quadruplex fluorescent PCR and the products were analyzed by capillary electrophoresis. Validation of the method included DNA analysis of 88 individuals from a control population, 45 HA patients and 32 individuals from 10 HA-affected families. Statistical study showed that the STR13, STR22 and DXS1108 loci were in significant linkage disequilibrium, whereas DXS1073 was not. Nevertheless, the combination of the four markers offered a high heterozygosity rate (>90%) that improved tracing of FVIII gene inheritance. Optimal results with application to single cells in a HA preimplantation genetic diagnosis (PGD) protocol demonstrated the sensitivity of the technique. In conclusion, the automated fluorescent method described is an extremely rapid, simple and highly informative one that is easy to standardize and allows direct comparison of results among different groups working with genetic counseling, prenatal diagnosis and PGD in HA-affected families.
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2,336,203 |
Large deletions of the PROS1 gene in a large fraction of mutation-negative patients with protein S deficiency.
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Protein S deficiency is an autosomal dominant disorder that results from mutations in the PROS1 gene. Conventional mutation detection techniques fail to detect a pathogenic PROS1 mutation in approximately 50% of cases. The present study investigates whether large deletions of PROS1 are found in families where mutations in the PROS1 gene have not been found despite sequencing. For this purpose,a dense set of SNP and microsatellite markers were used in segregation analysis to identify deletions. Large deletions were identified by this technique in three out of eight investigated families (38%). The deletions encompassed at least 35 kb, 437 kb and 449 kb respectively. The deletions were confirmed by quantitative PCR. Haplotype analysis showed that the three large deletions and the five other disease haplotypes were all different. All of the eight disease haplotypes co-segregated with protein S deficiency, but each of the five non-deletion haplotypes were present also in normal individuals.</AbstractText>Large deletions of PROS1 are relatively common in protein S deficiency patients and screening for large deletions in PROS1 mutation-negative individuals are therefore warranted.</AbstractText>
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2,336,204 |
Novel and recurrent rearrangements in the CFTR gene: clinical and laboratory implications for cystic fibrosis screening.
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Because standard techniques used to detect mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene do not detect single or multiple exonic rearrangements, the importance of such rearrangements may be underestimated. Using an in-house developed, single-tube, semi-quantitative fluorescent PCR (SQF PCR) assay, we analyzed 36 DNA samples submitted for extensive CFTR sequencing and identified ten samples with rearrangements. Of 36 patients with classic CF, 10 (28%) harbored various deletions in the CFTR gene, accounting for 14% of CF chromosomes. A deletion encompassing the CFTR promoter and exons 1 and 2 was detected in a sample from one proband, and in the maternal DNA as well. In another family, a deletion of the promoter and exon 1 was detected in three siblings. In both of these cases, the families were African American and the 3120+1G > A splice site mutation was also identified. These promoter deletions have not been previously described. In a third case, a deletion of exons 17a, 17b, and 18 was identified in a Caucasian female and the same mutation was detected in the paternal DNA. In the other seven cases, we identified the following deletions: exons 2 and 3 (n = 2); exons 4, 5, and 6a; exons 17a and 17b; exons 22 and 23; and exons 22, 23, and 24 (n = 2). In our series, the frequency of CFTR rearrangements in classic CF patients, when only one mutation was identified by extensive DNA sequencing, was >60% (10/16). Screening for exon deletions and duplications in the CFTR gene would be beneficial in classic CF cases, especially when only one mutation is identified by standard methodologies.
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2,336,205 |
Inferring candidate genes for attention deficit hyperactivity disorder (ADHD) assessed by the World Health Organization Adult ADHD Self-Report Scale (ASRS).
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The present study tests the psychometric properties and validity of the German version of the World Health Organization Adult Attention Deficit Hyperactivity Disorder (ADHD) Self-Report Scale (ASRS), which is a short screening instrument for use in the general population. Furthermore, two candidate genes for ADHD, the COMT VAL158MET and the 5-HT2a T102C polymorphisms, were tested for associations with the ASRS subscales inattention and hyperactivity/impulsivity in N = 203 healthy subjects. The ordinal CFA yielded a two-factorial model corroborating the structure of the official English WHO version. Genetic analysis revealed an association between the VAL allele of COMT and the inattention scale (F(1, 201) = 7.20, p = 0.008), the hyperactivity/impulsivity scale (F(1, 201) = 4.30, p = 0.039), and the total ASRS scale (F(2, 201) = 7.64, p = 0.006) with highest scores in carriers of the MET/MET genotype. The C-allele of 5-HT2a was significantly associated with the hyperactivity/impulsivity scale (F(1, 201) = 5.52, p = 0.020) and the total ASRS scale (F(1, 201) = 4.21, p = 0.042) with highest scores in carriers of the TT genotype. The data provide evidence for the structural as well as for the external validity of the ASRS.
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2,336,206 |
Reversible nitrous oxide myelopathy and a polymorphism in the gene encoding 5,10-methylenetetrahydrofolate reductase.
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We present a case of a patient who received nitrous oxide on two occasions within a period of 8 weeks and who subsequently developed a diffuse myelopathy, characterized by upper extremity paresis, lower extremity paraplegia and neurogenic bladder. Laboratory testing revealed hyperhomocysteinaemia and low levels of vitamin B(12). Because of this uncommon clinical presentation, we analysed the patient's DNA, and found a polymorphism in the MTHFR gene that is associated with the thermolabile isoform of the 5,10-methylenetetrahydrofolate reductase enzyme, which explained the myelopathy experienced by the patient after being exposed to nitrous oxide. Soon after initiating supplementary therapy with folic acid and vitamin B(12), the neurological symptoms subsided.
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2,336,207 |
Chromosome segment duplications in Neurospora crassa and their effects on repeat-induced point mutation and meiotic silencing by unpaired DNA.
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The size and extent of four Neurospora crassa duplications, Dp(AR17), Dp(IBj5), Dp(OY329), and Dp(B362i), was determined by testing the coverage of RFLP markers. The first three duplications were all > approximately 350 kb and have been shown in earlier studies to act as dominant suppressors of repeat-induced point mutation (RIP) in gene-sized duplications, possibly via titration of the RIP machinery. Dp(B362i), which is only approximately 117 kb long, failed to suppress RIP. RIP suppression in gene-sized duplications by large duplications was demonstrated using another test gene, dow, and supposedly applies generally. Crosses homozygous for Dp(AR17) or Dp(IBj5) were as barren as heterozygous crosses. Barrenness of the heterozygous but not the homozygous crosses was suppressible by Sad-1, a semidominant suppressor of RNAi-dependent meiotic silencing by unpaired DNA. A model is proposed in which large duplications recessively suppress semidominant Sad-1 mutations. The wild-isolated Sugartown strain is hypothesized to contain a duplication that confers not only dominant suppression of RIP but also a barren phenotype, which is linked (9%) to supercontig 7.118 in LG VII.
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2,336,208 |
Quantification of mitochondrial DNA using real-time polymerase chain reaction in patients with premature ovarian failure.
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To quantify mitochondrial DNA using real-time PCR in women with premature ovarian failure (POF) and a control group.</AbstractText>Prospective study.</AbstractText>Genome Research Center for Reproductive Medicine and Infertility, Korea Ministry of Health & Welfare.</AbstractText><AbstractText Label="PATIENT(S)" NlmCategory="METHODS">Thrity patients with POF and 30 control individuals.</AbstractText><AbstractText Label="INTERVENTION(S)" NlmCategory="METHODS">The mitochondrial DNA content was quantified using real-time PCR. The effectiveness of the assay was determined by relative quantification using the comparative threshold cycle (CT) method.</AbstractText><AbstractText Label="MAIN OUTCOME MEASURE(S)" NlmCategory="METHODS">Relative quantification of mitochondrial DNA content.</AbstractText><AbstractText Label="RESULT(S)" NlmCategory="RESULTS">The mitochondrial DNA content was significantly lower in the POF group than in the control group (0.58 +/- 0.38 vs. 1.15 +/- 0.67; P < .01). In both groups, there was a significant positive correlation between the mitochondrial DNA/28S rRNA ratio and mitochondrial DNA CT (control group: r = 0.774; P < .001; POF group: r = 0.556; P = .001) and a significant negative correlation between the mitochondrial DNA/28S rRNA ratio and 28S rRNA CT (control group: r = -0.677; P < .001; POF group: r = -0.627; P = .001).</AbstractText><AbstractText Label="CONCLUSION(S)" NlmCategory="CONCLUSIONS">This study has established the clinical feasibility of quantifying amounts of mitochondrial DNA, relative to an internal standard, using real-time PCR. Further studies are warranted to elucidate the roles of apoptosis and mitochondrial function in the pathogenesis of POF.</AbstractText>
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2,336,209 |
Pregnancies and live births after trophectoderm biopsy and preimplantation genetic testing of human blastocysts.
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To compare multiple-cell trophectoderm biopsy for preimplantation genetic diagnosis (PGD) from day-5 blastocysts with previously published experience with day-3 cleavage-stage embryos.</AbstractText>Retrospective review of laboratory and clinical experience.</AbstractText>Sydney IVF, a private clinic in Australia.</AbstractText><AbstractText Label="PATIENT(S)" NlmCategory="METHODS">Preimplantation genetic diagnosis (PGD) patients age < 44 years with at least one IVF blastocyst suitable for biopsy, recruited from January 2002 through August 2004.</AbstractText><AbstractText Label="INTERVENTION(S)" NlmCategory="METHODS">Biopsy of trophectoderm from blastocysts on day 5 or 6, with same-day PGD for mutation testing, translocation testing, aneuploidy screening or sex selection. Spare, normal biopsied blastocysts were cryostored for possible later transfer.</AbstractText><AbstractText Label="MAIN OUTCOME MEASURE(S)" NlmCategory="METHODS">Fetal heart-positive pregnancy rate and accumulating live birth rate after adding results from biopsied fresh and frozen blastocysts for particular couples.</AbstractText><AbstractText Label="RESULT(S)" NlmCategory="RESULTS">In 231 started PGD treatment cycles, unambiguous results were obtained from 974 of 1,050 biopsied blastocysts (93%); all blastocysts survived the biopsy procedure by reconstitution of their blastocele. One hundred nineteen women (median age, 36 years) have had 127 blastocysts transferred fresh (fetal heart-positive implantation rate, 41%). Of 146 blastocysts cryostored, 27 have been thawed (all with > 50% cell survival) and 24 transferred (implantation rate, 26%). To date, 53 pregnancies have been delivered or are ongoing, with an additional 4 clinical miscarriages (7%) and 6 subclinical miscarriages (total miscarriage rate, including biochemical pregnancies, 16%). There were no twin pregnancies.</AbstractText><AbstractText Label="CONCLUSION(S)" NlmCategory="CONCLUSIONS">With technically appropriate blastocyst culture and freezing, blastocyst biopsy and cryostorage and later transfer of biopsied blastocysts is shown to be a practical and probably preferable path to preimplantation genetic testing of embryos compared with cleavage-stage embryo biopsy, being accompanied by a high implantation rate (and hence more conducive to elective single embryo transfer) and by a low rate of twinning and miscarriage.</AbstractText>
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2,336,210 |
Comprehensive screening of CREB-binding protein gene mutations among patients with Rubinstein-Taybi syndrome using denaturing high-performance liquid chromatography.
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Mutations in the CREBBP (CREB-binding protein gene) cause Rubinstein-Taybi syndrome (RSTS). At present, however, genetic testing of CREBBP is not commonly applied in clinical settings because the currently available assays are technically and financially demanding, mainly because of the size of the gene. In the present study, we took advantage of a highly sensitive and specific, automated denaturing high-performance liquid chromatography (DHPLC) technique. First, we developed a DHPLC-based protocol to analyze the entire coding region of CREBBP. Second, we analyzed genetic samples from 21 RSTS patients using DHPLC. The coding region was amplified by 41 primer pairs, all of which have the same cycling conditions, aliquoted on a 96-well format PCR plate. In this manner, all the exons were simultaneously amplified using a single block in a PCR machine. We then wrote a computer script to analyze all the PCR amplicons generated from various portions of the CREBBP gene in a serial manner at optimized conditions determined individually for each amplicon. Heterozygous CREBBP mutations were identified in 12 of the 21 patients: five frameshift mutations, three nonsense mutations, two splice-site mutations, and two missense mutations. The resulting detection rate of 57% was comparable to the outcome of previous studies. The relatively high detection rate in the present study demonstrates the enhanced sensitivity of the DHPLC-based mutation analysis, as exemplified by mutation analyses of other genes. The implementation of similar methodologies for other dysmorphic syndromes will help medical geneticists to confirm their clinical impressions and to provide accurate genetic counseling for patients and their families.
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2,336,211 |
CMfinder--a covariance model based RNA motif finding algorithm.
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The recent discoveries of large numbers of non-coding RNAs and computational advances in genome-scale RNA search create a need for tools for automatic, high quality identification and characterization of conserved RNA motifs that can be readily used for database search. Previous tools fall short of this goal.</AbstractText>CMfinder is a new tool to predict RNA motifs in unaligned sequences. It is an expectation maximization algorithm using covariance models for motif description, featuring novel integration of multiple techniques for effective search of motif space, and a Bayesian framework that blends mutual information-based and folding energy-based approaches to predict structure in a principled way. Extensive tests show that our method works well on datasets with either low or high sequence similarity, is robust to inclusion of lengthy extraneous flanking sequence and/or completely unrelated sequences, and is reasonably fast and scalable. In testing on 19 known ncRNA families, including some difficult cases with poor sequence conservation and large indels, our method demonstrates excellent average per-base-pair accuracy--79% compared with at most 60% for alternative methods. More importantly, the resulting probabilistic model can be directly used for homology search, allowing iterative refinement of structural models based on additional homologs. We have used this approach to obtain highly accurate covariance models of known RNA motifs based on small numbers of related sequences, which identified homologs in deeply-diverged species.</AbstractText>
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2,336,212 |
Biological, cellular, and molecular characteristics of an inducible transgenic skin tumor model: a review.
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The genetically initiated Tg.AC transgenic mouse carries a transgene consisting of an oncogenic v-Ha-ras coding region flanked 5' by a mouse zeta-globin promoter and 3' by an SV-40 polyadenylation sequence. Located on chromosome 11, the transgene is transcriptionally silent until activated by chemical carcinogens, UV light, or full-thickness wounding. Expression of the transgene is an early event that drives cellular proliferation resulting in clonal expansion and tumor formation, the unique characteristics now associated with the Tg.AC mouse. This ras-dependent phenotype has resulted in the widespread interest and use of the Tg.AC mouse in experimental skin carcinogenesis and as an alternative carcinogenesis assay. This review examines the general biology of the tumorigenic responses observed in Tg.AC mice, the genetic interactions of the ras transgene, and explores the cellular and molecular regulation of zeta-globin promoted transgene expression. As a prototype alternative model to the current long-term rodent bioassays, the Tg.AC has generated a healthy discussion on the future of transgenic bioassays, and opened the doors for subsequent models for toxicity testing. The further exploration and elucidation of the molecular controls of transgene expression will enhance the usefulness of this mouse and enable a better understanding of the Tg.AC's discriminate response to chemical carcinogens.
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2,336,213 |
A genetic screen for mutations that affect cranial nerve development in the mouse.
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Cranial motor and sensory nerves arise stereotypically in the embryonic hindbrain, act as sensitive indicators of general and region-specific neuronal development, and are directly or indirectly affected in many human disorders, particularly craniofacial syndromes. The molecular genetic hierarchies that regulate cranial nerve development are mostly unknown. Here, we describe the first mouse genetic screen that has used direct immunohistochemical visualization methods to systematically identify genetic loci required for cranial nerve development. After screening 40 pedigrees, we recovered seven new neurodevelopmental mutations. Two mutations model human genetic syndromes. Mutation 7-1 causes facial nerve anomalies and a reduced lower jaw, and is located in a region of conserved synteny with an interval associated with the micrognathia and mental retardation of human cri-du-chat syndrome. Mutation 22-1 is in the Pax3 gene and, thus, models human Waardenburg syndrome. Three mutations cause global axon guidance deficits: one interferes with initial motor axon extension from the neural tube, another causes overall axon defasciculation, and the third affects general choice point selection. Another two mutations affect the oculomotor nerve specifically. Oculomotor nerve development, which is disrupted by six mutations, appears particularly sensitive to genetic perturbations. Phenotypic comparisons of these mutants identifies a "transition zone" that oculomotor axons enter after initial outgrowth and in which new factors govern additional progress. The number of interesting neurodevelopmental mutants revealed by this small-scale screen underscores the promise of similar focused genetic screens to contribute significantly to our understanding of cranial nerve development and human craniofacial syndromes.
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2,336,214 |
Concordance, disease progression, and heritability of coeliac disease in Italian twins.
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We adopted the twin method to disentangle the genetic and environmental components of susceptibility to coeliac disease (CD). We estimated disease concordance rate by zygosity and HLA genotypes, discordance times, progression rates to disease, and heritability.</AbstractText>We crosslinked the Italian Twin Registry with the membership lists of the Italian Coeliac Disease Association and recruited 23 monozygotic (MZ) and 50 dizygotic (DZ) twin pairs with at least one affected member. Zygosity was assigned by DNA fingerprinting, and HLA-DQ and DR alleles were genotyped. Disease status was ascertained by antiendomysial, anti-human tissue transglutaminase antibodies, and bowel biopsy.</AbstractText>Concordance was significantly higher in MZ (83.3% probandwise, 71.4% pairwise) than in DZ (16.7% probandwise, 9.1% pairwise) pairs. Concordance was not affected by sex or HLA genotype of the co-twin and being MZ was significantly associated with the occurrence of CD (Cox adjusted hazard ratio 14.3 (95% confidence interval 4.0-50.3)). In 90% of concordant pairs the discordance time was <or=2 years. MZ and DZ co-twins had 70% and 9% cumulative probability of having symptomatic or silent forms of CD, respectively, within five years. Under ACE (additive genetic, common, and unshared environmental factors) models, with CD population prevalences of 1/91 and 1/1000, heritability estimates were 87% and 57%, respectively.</AbstractText>MZ pairs have a high probability of being concordant, regardless of sex or HLA genotype. Most of the affected co-twins receive a diagnosis within two years. A remarkable proportion of phenotypic variance is due to genetic factors.</AbstractText>
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2,336,215 |
Genetic and environmental influences on skin pattern deterioration.
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Sun exposure has been known to cause histological changes in the dermal layer of the skin. Using deterioration in the fine reticular patterning of the epidermal stratum corneum (skin pattern, as measured on the Beagley-Gibson scale) as a proxy measure of histological changes in the dermal layer, previous studies have typically assumed that degradation of skin pattern is largely caused by sun exposure. A twin study comprising 332 monozygotic twin pairs and 488 dizygotic twin pairs at ages 12, 14, and 16 was used to investigate the etiology of variation in skin pattern, particularly in relation to measured sun exposure and skin color. Our results indicate that although self-reported sun exposure is a significant contributor to variation in skin pattern, its effect is small, explaining only 3.4% of variation in skin pattern at age 14. Additive genetic effects explain 86% of variation in skin pattern at age 12 but these effects reduce with age so that 75% of variation is due to additive genetic effects at age 14 and 72% at age 16. This trend of diminishing genetic influences continues into adulthood, with 62% of variation due to non-additive genetic factors in a smaller adult sample (aged 32-86). Skin color explains 10.4% of variation in skin pattern at age 12, which is due to additive genetic influences common to both. Melanin content appears to provide a protective effect against skin pattern deterioration, perhaps because of the structural differences in melanosomes between different skin types or the free radical scavenging properties of melanin.
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2,336,216 |
Molecular mechanisms of junctional epidermolysis bullosa: Col 15 domain mutations decrease the thermal stability of collagen XVII.
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Mutations in the collagen XVII gene, COL17A1, are associated with junctional epidermolysis bullosa. Most COL17A1 mutations lead to a premature termination codon (PTC), whereas only a few mutations result in amino acid substitutions or deletions. We describe here two novel glycine substitutions, G609D and G612R, and a splice site mutation resulting in a deletion of three Gly-X-Y amino acid triplets. In order to investigate the molecular pathomechanisms of non-PTC mutations, G609D and G612R and two previously known substitutions, G627V and G633, and deletion of the amino acids 779-787 were introduced into recombinant collagen XVII. The thermal stability of the mutated collagens was assessed using trypsin digestions at incremental temperatures. All the four glycine substitutions significantly destabilized the ectodomain of collagen XVII, which manifested as 16 degrees C-20 degrees C lower T(m) (midpoint of the helix-to-coil transition). These results were supported by secondary structure predictions, which suggested interruptions of the collagenous triple helix within the largest collagenous domain, Col15. In contrast, deletion of the three full Gly-X-Y triplets, amino acids 779-787, had no overall effect on the stability of the ectodomain, as the deletion was in register with the triplet structure and also generated compensatory changes in the NC15 domain.
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2,336,217 |
Something not quite right: Gardner syndrome diagnosed by multiple cutaneous lesions and genetic testing.
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Gardner syndrome is a variant of familial adenomatous polyposis characterized by intestinal adenomatous polyps, which can progress to adenocarcinoma, and a variety of extraintestinal manifestations, including skin cysts, osteomas, soft tissue fibrous tumours and a characteristic ocular lesion. The extraintestinal manifestations are often the presenting feature but are usually not sufficiently characteristic on their own to trigger recognition of the syndrome. We report a case of a 17-year-old female who had been treated by a number of specialists over a 13-year period for a variety of cutaneous lesions without a hereditary condition being suspected. Gardner syndrome was considered only after excision of subcutaneous fibrous tumours from the mastoid region and paraspinal area and was confirmed by genetic testing in spite of the patient's refusal to undergo colonic endoscopic examination. Subsequent resection revealed approximately 70 adenomatous colonic polyps in the colon and rectum but no invasive tumour, highlighting the benefits of genetic testing in treatment planning.
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2,336,218 |
Genetic relatedness of a rarely isolated Salmonella: Salmonella enterica serotype Niakhar from NARMS animal isolates.
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In the United States, Salmonella enterica serotype Niakhar is infrequently isolated. Between 1997 and 2000, the animal arm of the National Antimicrobial Resistance Monitoring System-Enteric Bacteria (NARMS) assayed a total of 22,383 Salmonella isolates from various animal sources (swine, cattle, chickens, turkeys, cats, horses, exotics and dogs) for antimicrobial susceptibility. Isolates originated from diagnostic and non-diagnostic submissions.</AbstractText>To study the phenotypic and genotypic characteristics of Salmonella Niakhar.</AbstractText>Only five (0.02%) of the 22,383 isolates were identified as Salmonella Niakhar. Antimicrobial resistance testing indicated that three isolates were pan-susceptible, one isolate was resistant to ampicillin and one isolate was resistant to ampicillin, chloramphenicol, ciprofloxacin, kanamycin, nalidixic acid, streptomycin, sulfamethoxazole, tetracycline and trimethoprim/sulfamethoxazole. RAPD-PCR analysis, PFGE and ribotyping indicated that two pan-susceptible isolates were genetically similar, whereas the three remaining isolates were genetically different. The one Salmonella Niakhar isolate that was multiresistant harboured a class I integron, intI1 and two large plasmids.</AbstractText>This study represents the first report of a ciprofloxacin-resistant Salmonella isolate from the animal arm of NARMS.</AbstractText>
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2,336,219 |
Common HEXB polymorphisms reduce serum HexA and HexB enzymatic activities, potentially masking Tay-Sachs disease carrier identification.
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A DNA-proven Tay-Sachs disease (TSD) carrier and his brother were found to have serum percent Hexosaminidase A (%HexA) enzymatic activities in the non-carrier range, while the leukocyte %HexA profiles clearly identified them as TSD heterozygotes. Both their serum HexA and HexB enzymatic activities were below reference range, suggesting inheritance of mutations in both the HEXA (alpha-subunit) and HEXB (beta-subunit) genes. DNA sequencing revealed that both individuals, carried the common HEXA 1277_1278insTATC mutation, and two common HEXB polymorphisms: [619A>G (+) delTG]. To determine if these HEXB polymorphisms reduce HexA and HexB enzymatic activities, 69 DNA samples from subjects previously screened enzymatically in both serum and leukocytes for TSD carrier status were selected for either high, mid-range or low serum Total Hex (defined as the sum of HexA and HexB) activities and were tested for the HEXB mutations. Further, three additional TSD carriers ascertained by the atypical pattern of normal serum %HexA but carrier leukocyte %HexA, were found to have the [delTG (+) 619A>G] genotype. In addition, the frequency of the [delTG (+) 619A>G] genotype was significantly higher (P < 0.01) in subjects with low serum HexB enzymatic activities. Given the high frequency of the [delTG (+) 619A>G] haplotype in the Ashkenazi Jewish population (approximately 10%), up to 10% of TSD carriers may have normal serum %HexA values with low total Hex. Accordingly, serum %HexA should not be the sole criterion used for carrier status determination. Where total Hex activity is reduced, further testing with leukocyte Hex profiles is indicated.
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2,336,220 |
An analysis of genetic toxicity, reproductive and developmental toxicity, and carcinogenicity data: II. Identification of genotoxicants, reprotoxicants, and carcinogens using in silico methods.
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This study examined a novel method to identify carcinogens that employed expanded data sets composed of in silico data pooled with actual experimental genetic toxicity (genetox) and reproductive and developmental toxicity (reprotox) data. We constructed 21 modules using the MC4PC program including 13 of 14 (11 genetox and 3 reprotox) tests that we found correlated with results of rodent carcinogenicity bioassays (rcbioassays) [Matthews, E.J., Kruhlak, N.L., Cimino, M.C., Benz, R.D., Contrera, J.F., 2005b. An analysis of genetic toxicity, reproductive and developmental toxicity, and carcinogenicity data: I. Identification of carcinogens using surrogate endpoints. Regul. Toxicol. Pharmacol.]. Each of the 21 modules was evaluated by cross-validation experiments and those with high specificity (SP) and positive predictivity (PPV) were used to predict activities of the 1442 chemicals tested for carcinogenicity for which actual genetox or reprotox data were missing. The expanded data sets had approximately 70% in silico data pooled with approximately 30% experimental data. Based upon SP and PPV, the expanded data sets showed good correlation with carcinogenicity testing results and had correlation indicator (CI, the average of SP and PPV) values of 75.5-88.7%. Conversely, expanded data sets for 9 non-correlated test endpoints were shown not to correlate with carcinogenicity results (CI values <75%). Results also showed that when Salmonella mutagenic carcinogens were removed from the 12 correlated, expanded data sets, only 7 endpoints showed added value by detecting significantly more additional carcinogens than non-carcinogens.
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2,336,221 |
A family with McLeod syndrome and calpainopathy with clinically overlapping diseases.
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The authors describe a family with six patients with muscular dystrophy with a variable course. One is a compound heterozygote for CAPN3 mutations (calpainopathy) and the others have a single CAPN3 mutation. Linkage analysis and sequencing revealed a XK gene mutation (McLeod syndrome). This illustrates the variable phenotype of XK mutations and suggests the possibility that CAPN3 heterozygotes may have their condition caused by nonallelic mutations in other unrelated genes.
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2,336,222 |
Familial basilar migraine associated with a new mutation in the ATP1A2 gene.
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Basilar migraine (BM), familial hemiplegic migraine (FHM), and sporadic hemiplegic migraine (SHM) are phenotypically similar subtypes of migraine with aura, differentiated only by motor symptoms, which are absent in BM. Mutations in CACNA1A and ATP1A2 have been found in FHM. The authors detected a novel mutation in the ATP1A2 gene (R548H) in members of a family with BM, suggesting that BM and FHM may be allelic disorders.
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2,336,223 |
Comparison of family histories in FTLD subtypes and related tauopathies.
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Pedigrees from 269 patients with frontotemporal lobar degeneration (FTLD), including frontotemporal dementia (FTD), FTD with ALS (FTD/ALS), progressive nonfluent aphasia, semantic dementia (SD), corticobasal degeneration, and progressive supranuclear palsy were analyzed to determine the degree of heritability of these disorders. FTD/ALS was the most and SD the least heritable subtype. FTLD syndromes appear to have different etiologies and recurrence risks.
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2,336,224 |
Clinical and molecular features of encephalomyopathy due to the A3302G mutation in the mitochondrial tRNA(Leu(UUR)) gene.
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The mitochondrial DNA mutation A3302G in the tRNA(Leu(UUR)) gene causes respiratory chain complex I deficiency. The main clinical feature appears to be a progressive mitochondrial myopathy with proximal muscle weakness.</AbstractText>To report on clinical and molecular features in 4 novel patients with the A3302G mutation.</AbstractText>Case reports.</AbstractText>Four patients (3 of whom are from the same family) with a myopathy caused by the A3302G mitochondrial DNA mutation.</AbstractText>Identification of the A3302G mutation by DNA sequencing.</AbstractText>All 4 patients had an adult-onset progressive mitochondrial myopathy with proximal muscle weakness, resulting in exercise intolerance. In 2 unrelated patients, upper limb reflexes were absent with preservation of at least some lower limb reflexes. Other features including hearing loss, recurrent headaches, ptosis, progressive external ophthalmoplegia, and depression were present.</AbstractText>While the dominant clinical features of the A3302G mutation were exercise intolerance and proximal muscle weakness, other features of mitochondrial encephalomyopathies, previously not described for this mutation, were present.</AbstractText>
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2,336,225 |
Association of organic cation transporter risk haplotype with perianal penetrating Crohn's disease but not with susceptibility to IBD.
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<AbstractText Label="BACKGROUND & AIMS" NlmCategory="OBJECTIVE">Three years after the identification of NOD2/CARD15, 2 more genes for inflammatory bowel diseases (IBDs) were reported. The carnitine/organic cation transporter (OCTN) on 5q31 (IBD5) is associated with Crohn's disease (CD) and DLG5 (10q23), a member of membrane-associated guanylate kinase (MAGUK) family, with IBD. We studied mutation prevalence, assessed phenotypic expression, and performed conditional analysis to examine evidence for gene-gene interactions.</AbstractText>A cohort of 2032 individuals was genotyped for disease-associated OCTN and DLG5 variants, including 981 patients with IBD (CD, n = 769; ulcerative colitis, n = 186; indeterminate colitis, n = 26) followed up at a tertiary IBD center. For 373 patients, DNA from both parents was available (cohort 1) for transmission disequilibrium testing analysis; case-control analysis was performed in 608 patients and 305 controls (cohort 2).</AbstractText>There was no distortion of transmission toward affected offspring for any of the variant alleles. Case-control analysis also failed to shown an association. A higher frequency of DLG5 113A was observed in CARD15-positive patients (12.2%) compared with CARD15-negative patients (8.7%; P = .033). The OCTN-TC risk haplotype was associated with penetrating disease (odds ratio, 1.474; 95% confidence interval, 1.028-2.114; P = .035). For DLG5, there were no associations with a particular phenotype.</AbstractText>DLG5 and OCTN do not play a role in the susceptibility to IBD, CD, or ulcerative colitis in the Flemish population but play a role in the phenotypic expression of the disease. OCTN variants were associated with perianal and penetrating CD. More studies in independent populations are urgently needed to assess the validity of DLG5 and OCTN in the pathogenesis of IBD.</AbstractText>
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2,336,226 |
Heterogeneity in alpha-thalassemia interactions in Malays, Chinese and Indians in Malaysia.<Pagination><StartPage>540</StartPage><EndPage>546</EndPage><MedlinePgn>540-6</MedlinePgn></Pagination><Abstract><AbstractText Label="AIM" NlmCategory="OBJECTIVE">Interactions between different determinants of alpha-thalassemia raises considerable problems, particularly during pregnancies where antenatal diagnosis is necessary. This study aims to determine the different types of deletional alpha-thalassemia and Hemoglobin Constant Spring (HbCS), and their frequency in Malays, Chinese and Indians in Malaysia.</AbstractText><AbstractText Label="METHODS" NlmCategory="METHODS">DNA from 650 pregnant women from the Antenatal Clinic of the University of Malaya Medical Center in Kuala Lumpur, Malaysia who showed mean cell volume < or =89 fL and/or mean cell hemoglobin < or =28 pg were analyzed for the double alpha-globin gene South-East Asian deletion (--SEA), the -alpha3.7 and -alpha4.2 single alpha-globin gene deletions and HbCS.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">One hundred and three (15.8%) of the pregnant women were confirmed as alpha-thalassemia carriers: 25 (3.8%) were alpha-thalassemia-1 carriers with the --SEA/alphaalpha genotype, 64 (9.8%) were heterozygous for the -alpha3.7 rightward deletion (-alpha3.7/alphaalpha), four (0.6%) were heterozygous for the -alpha4.2 leftward deletion (-alpha4.2/alphaalpha), nine (1.4%) were heterozygous for HbCS (alphaCSalpha/alphaalpha) and one (0.2%) was compound heterozygous with the -alpha3.7/alphaCSalpha genotype. The double alpha-globin gene --SEA deletion was significantly higher in the Chinese (15%) compared to the Malays (2.5%) and not detected in the Indians studied. The -alpha3.7 deletion was distributed equally in the three races. HbCS and -alpha4.2 was observed only in the Malays.</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">The data obtained gives a better understanding of the interactions of the different alpha-thalassemia determinants in the different ethnic groups, thus enabling more rapid and specific confirmation of alpha-thalassemia in affected pregnancies where antenatal diagnosis is necessary.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Wee</LastName><ForeName>Yong-Chui</ForeName><Initials>YC</Initials><AffiliationInfo><Affiliation>Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia. [email protected]</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tan</LastName><ForeName>Kim-Lian</ForeName><Initials>KL</Initials></Author><Author ValidYN="Y"><LastName>Chow</LastName><ForeName>Teresa Wai-Ping</ForeName><Initials>TW</Initials></Author><Author ValidYN="Y"><LastName>Yap</LastName><ForeName>Sook-Fan</ForeName><Initials>SF</Initials></Author><Author ValidYN="Y"><LastName>Tan</LastName><ForeName>Jin-Ai Mary Anne</ForeName><Initials>JA</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D003160">Comparative Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>Australia</Country><MedlineTA>J Obstet Gynaecol Res</MedlineTA><NlmUniqueID>9612761</NlmUniqueID><ISSNLinking>1341-8076</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>9004-22-2</RegistryNumber><NameOfSubstance UI="D005914">Globins</NameOfSubstance></Chemical><Chemical><RegistryNumber>9007-49-2</RegistryNumber><NameOfSubstance UI="D004247">DNA</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000293" MajorTopicYN="N">Adolescent</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000328" MajorTopicYN="N">Adult</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D044466" MajorTopicYN="N">Asian People</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004247" MajorTopicYN="N">DNA</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005260" MajorTopicYN="N">Female</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006580" MajorTopicYN="N">Genetic Carrier Screening</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005914" MajorTopicYN="N">Globins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008296" MajorTopicYN="N" Type="Geographic">Malaysia</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011247" MajorTopicYN="N">Pregnancy</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011250" MajorTopicYN="N">Pregnancy Complications, Hematologic</DescriptorName><QualifierName UI="Q000175" MajorTopicYN="N">diagnosis</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017085" MajorTopicYN="N">alpha-Thalassemia</DescriptorName><QualifierName UI="Q000150" MajorTopicYN="Y">complications</QualifierName><QualifierName UI="Q000175" MajorTopicYN="N">diagnosis</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000517" MajorTopicYN="N">prevention & control</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2005</Year><Month>12</Month><Day>14</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2006</Year><Month>2</Month><Day>24</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2005</Year><Month>12</Month><Day>14</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">16343256</ArticleId><ArticleId IdType="doi">10.1111/j.1447-0756.2005.00333.x</ArticleId><ArticleId IdType="pii">JOG333</ArticleId></ArticleIdList></PubmedData></PubmedArticle><PubmedArticle><MedlineCitation Status="MEDLINE" Owner="KIE"><PMID Version="1">16342438</PMID><DateCompleted><Year>2006</Year><Month>04</Month><Day>25</Day></DateCompleted><DateRevised><Year>2013</Year><Month>06</Month><Day>07</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0362-4331</ISSN><JournalIssue CitedMedium="Print"><PubDate><Year>2005</Year><Month>Nov</Month><Day>20</Day></PubDate></JournalIssue><Title>The New York times on the Web</Title><ISOAbbreviation>N Y Times Web</ISOAbbreviation></Journal>The problem with an almost-perfect genetic world.<Pagination><StartPage>WK1</StartPage><EndPage>WK14</EndPage><MedlinePgn>WK1, WK14</MedlinePgn></Pagination><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Harmon</LastName><ForeName>Amy</ForeName><Initials>A</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D018431">Newspaper Article</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>N Y Times Web</MedlineTA><NlmUniqueID>9877126</NlmUniqueID><ISSNLinking>0362-4331</ISSNLinking></MedlineJournalInfo><MeshHeadingList><MeshHeading><DescriptorName UI="D000025" MajorTopicYN="N">Abortion, Eugenic</DescriptorName><QualifierName UI="Q000592" MajorTopicYN="N">standards</QualifierName><QualifierName UI="Q000639" MajorTopicYN="N">trends</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006233" MajorTopicYN="Y">Disabled Persons</DescriptorName><QualifierName UI="Q000523" MajorTopicYN="N">psychology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004314" MajorTopicYN="N">Down Syndrome</DescriptorName><QualifierName UI="Q000175" MajorTopicYN="N">diagnosis</QualifierName><QualifierName UI="Q000523" MajorTopicYN="N">psychology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005260" MajorTopicYN="N">Female</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005820" MajorTopicYN="Y">Genetic Testing</DescriptorName><QualifierName UI="Q000941" MajorTopicYN="N">ethics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011247" MajorTopicYN="N">Pregnancy</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011287" MajorTopicYN="N">Prejudice</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011296" MajorTopicYN="Y">Prenatal Diagnosis</DescriptorName><QualifierName UI="Q000941" MajorTopicYN="N">ethics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D015995" MajorTopicYN="N">Prevalence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012934" MajorTopicYN="N">Social Isolation</DescriptorName></MeshHeading></MeshHeadingList><OtherID Source="KIE">124885</OtherID><OtherID Source="NRCBL">VF 15.3</OtherID><KeywordList Owner="KIE"><Keyword MajorTopicYN="N">Genetics and Reproduction</Keyword><Keyword MajorTopicYN="N">Popular Approach/Source</Keyword></KeywordList><GeneralNote Owner="KIE">KIE Bib: genetic screening; prenatal diagnosis</GeneralNote></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2005</Year><Month>12</Month><Day>14</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2006</Year><Month>4</Month><Day>28</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2005</Year><Month>12</Month><Day>14</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">16342438</ArticleId></ArticleIdList></PubmedData></PubmedArticle><PubmedArticle><MedlineCitation Status="MEDLINE" Owner="KIE"><PMID Version="1">16342436</PMID><DateCompleted><Year>2006</Year><Month>03</Month><Day>21</Day></DateCompleted><DateRevised><Year>2013</Year><Month>06</Month><Day>07</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0362-4331</ISSN><JournalIssue CitedMedium="Print"><PubDate><Year>2005</Year><Month>Oct</Month><Day>10</Day></PubDate></JournalIssue><Title>The New York times on the Web</Title><ISOAbbreviation>N Y Times Web</ISOAbbreviation></Journal>I.B.M. to put genetic data of workers off limits.
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Interactions between different determinants of alpha-thalassemia raises considerable problems, particularly during pregnancies where antenatal diagnosis is necessary. This study aims to determine the different types of deletional alpha-thalassemia and Hemoglobin Constant Spring (HbCS), and their frequency in Malays, Chinese and Indians in Malaysia.</AbstractText>DNA from 650 pregnant women from the Antenatal Clinic of the University of Malaya Medical Center in Kuala Lumpur, Malaysia who showed mean cell volume < or =89 fL and/or mean cell hemoglobin < or =28 pg were analyzed for the double alpha-globin gene South-East Asian deletion (--SEA), the -alpha3.7 and -alpha4.2 single alpha-globin gene deletions and HbCS.</AbstractText>One hundred and three (15.8%) of the pregnant women were confirmed as alpha-thalassemia carriers: 25 (3.8%) were alpha-thalassemia-1 carriers with the --SEA/alphaalpha genotype, 64 (9.8%) were heterozygous for the -alpha3.7 rightward deletion (-alpha3.7/alphaalpha), four (0.6%) were heterozygous for the -alpha4.2 leftward deletion (-alpha4.2/alphaalpha), nine (1.4%) were heterozygous for HbCS (alphaCSalpha/alphaalpha) and one (0.2%) was compound heterozygous with the -alpha3.7/alphaCSalpha genotype. The double alpha-globin gene --SEA deletion was significantly higher in the Chinese (15%) compared to the Malays (2.5%) and not detected in the Indians studied. The -alpha3.7 deletion was distributed equally in the three races. HbCS and -alpha4.2 was observed only in the Malays.</AbstractText>The data obtained gives a better understanding of the interactions of the different alpha-thalassemia determinants in the different ethnic groups, thus enabling more rapid and specific confirmation of alpha-thalassemia in affected pregnancies where antenatal diagnosis is necessary.</AbstractText>
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2,336,227 |
Parent-of-origin, imprinting, mitochondrial, and X-linked effects in traits related to alcohol dependence: presentation Group 18 of Genetic Analysis Workshop 14.
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The participants of Presentation Group 18 of Genetic Analysis Workshop 14 analyzed the Collaborative Study on the Genetics of Alcoholism data set to investigate sex-specific effects for phenotypes related to alcohol dependence. In particular, the participants looked at imprinting (which is also known as parent-of-origin effect), differences between recombination fractions for the two sexes, and mitochondrial and X-chromosomal effects. Five of the seven groups employed newly developed or existing methods that take imprinting into account when testing for linkage, or test for imprinting itself. Single-marker and multipoint analyses were performed for microsatellite as well as single-nucleotide polymorphism markers, and several groups used a sex-specific genetic map in addition to a sex-averaged map. Evidence for paternal imprinting (i.e., maternal expression) was consistently obtained by at least two groups at genetic regions on chromosomes 10, 12, and 21 that possibly harbor genes responsible for alcoholism. Evidence for maternal imprinting (which is equivalent to paternal expression) was consistently found at a locus on chromosome 11. Two groups applied extensions of variance components analysis that model a mitochondrial or X-chromosomal effect to latent class variables and electrophysiological traits employed in the diagnosis of alcoholism. The analysis, without using genetic markers, revealed mitochondrial or X-chromosomal effects for several of these traits. Accounting for sex-specific environmental variances appeared to be crucial for the identification of an X-chromosomal factor. In linkage analysis using marker data, modeling a mitochondrial variance component increased the linkage signals obtained for autosomal loci.
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2,336,228 |
Fine mapping by linkage and association in nuclear family and case-control designs.
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This report summarizes the Genetic Analysis Workshop 14 contributions related to fine-mapping strategies, in which examining smaller regions by association with single-nucleotide polymorphisms (SNPs) can yield savings in genotyping and multiple-testing penalties. The aim of the analyses conducted in Group 7 contributions was to localize disease susceptibility loci from either the simulated or the Collaborative Study on the Genetics of Alcoholism (COGA) data within identified regions of linkage. Among the 10 contributions, most groups analyzed the simulated data, one group analyzed the COGA data only, and one group analyzed both data sets. The research questions included evaluation of new methods of analysis, as well as comparisons among alternative methods, analytic strategies, and study designs. Methods of interest included an algorithm for SNP marker ordering, a locally weighted transmission disequilibrium test statistic, a likelihood-ratio test statistic for family-based association in nuclear families, a robust test statistic for case-control association studies, and Bayesian spatial modeling methods for haplotype clustering and association. Evaluations included comparisons among confidence intervals for loci detected via linkage, effects of multiple testing adjustments and trade-offs between type I error and power, comparisons among haplotype-based (multilocus) and genotype-based (multilocus and single-locus) association analyses, and design of fine-mapping and replication studies. While several promising new approaches were identified, further development and evaluation of methods for multiple testing, regression modeling of association with multiple markers and haplotypes, and combined treatment of linkage and association data are necessary if we are to identify many of the genes that contribute to complex traits.
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2,336,229 |
Association mapping: methodologies, strategies, and issues.
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Recent advances in molecular genetic technology allow for detailed characterization of genetic variation and easy cost-efficient accumulation of such data, even for large human samples. One such advance that presents incredible opportunities for identifying associations between genetic polymorphisms and disease-related phenotypes is the ability to quickly type a large number of single-nucleotide polymorphisms (SNPs). Contributors to Group 10 of Genetic Analysis Workshop 14 explored the potential of SNP genotypes for the association mapping of disease-related genes in family-based studies. Using both real data involving alcoholism susceptibility, made available by the Collaborative Study on the Genetics of Alcoholism (COGA), and simulated data involving personality-disorder susceptibility, group members investigated specific methodological issues involved in association mapping, such as multiple testing, single SNPs vs. combinations and haplotypes, and the effect of linkage disequilibrium on SNP-based linkage; evaluated existing methodologies for association mapping using SNPs, short-tandem repeats (STRs), or a combination of the two; and introduced new or modified association-mapping methods, including a gamma random effects (GRE) model and the quantitative trait linkage disequilibrium (QTLD) test. These papers are unified by the application of association-based methods to analyze SNPs, microsatellite markers, or both, to identify chromosomal regions harboring genes that contribute to quantitative endophenotype variation, and thus to disease risk. Their diversity attests to the breadth and flexibility of association-mapping approaches to the genetics of complex disease.
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2,336,230 |
Summary of contributions to GAW Group 12: multivariate methods.
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Here we summarize the contributions to Group 12 of Genetic Analysis Workshop (GAW) 14, held in Noordwijkerhout, The Netherlands. The theme of this group, multivariate methods, covered a broad range of statistical applications. Most of the contributors considered Problem 1 of the GAW. However, one paper considered the bivariate analysis of two binary phenotypes generated by the simulated data in Problem 2. Some contributors focused on statistical issues involved in considering multiple variables, and others on extensions to the variance-components methodology for analysis of quantitative traits. Applications to the Collaborative Study on the Genetics of Alcoholism data identified a single-nucleotide polymorphism (SNP) on chromosome 4 associated with the ttth1-ttth4 phenotypes, and replicated previous findings of linkage on chromosome 4 for alcohol consumption, using microsatellite and SNP data.
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2,336,231 |
Summary of contributions to GAW Group 5: linkage mapping methods, Problem 2.
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Here I summarize the contributions to Group 5 of Genetic Analysis Workshop 14, held in Noordwijkerhout in The Netherlands. The theme of this group was linkage mapping methods applied to the simulated data (Problem 2). A variety of approaches were taken, and a number of questions were examined. In addition to testing for linkage in regions harboring known disease or modifying loci, or testing for linkage across the genome, the contributions addressed such issues as whether power/significance could be improved by making use of subphenotypes in addition to the primary disease phenotype, by modeling interactions between loci, or by using meta-analytic approaches to combine results from different populations. Most contributions were successful in identifying known disease loci D1 and D2, and for those contributions that examined the relevant regions, in identifying disease loci D3 and D4. The power to detect modifying loci D5 and D6 appeared to be lower. Some gain in power/significance was found from making use of subphenotypes and meta-analytic approaches.
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2,336,232 |
Genetic characterization of European-Zebu composite bovine using RFLP markers.
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A population of 370 European-Zebu composite beef heifers, consisting of six different breed compositions (A-F), were characterized genetically, using RFLP markers of luteinizing hormone receptor (LHR) and follicle-stimulating hormone receptor (FSHR) genes. Our objectives were to genetically characterize this population and to determine the structure and the genetic variability of this hybrid herd. The genotypes were determined through PCR, followed by digestion with restriction endonucleases. The PCR-RFLP analysis made it possible to identify the LHR and FSHR genotypes, as well as to characterize the degree of heterozygosis, which was high for all of the breed compositions, for both loci, except for two combinations for LHR (B and C). The observed heterozygosity (Ho) was lower than the expected heterozygosity (He) for compositions C (for LHR) and A and D (for FSHR); however, for the population as a whole, Ho was above He (with a mean of 57 versus 46%, respectively), reflecting the elevated genetic variability in this population and also the informative value of the RFLP markers, which could be useful for population genetic characterization studies. The analysis of the degree of genetic structure of this population, estimated by the Nei's statistic, for both loci, indicated an elevated total genetic diversity (HT = 47%), with most of this variability being due to intrapopulational diversity (HS = 46%), with a low degree of genetic differentiation among the six breed compositions (GST = 1.2%). The estimates generated by the Wright's F statistic indicated a non-endogamic population, with excess heterozygotes (FIT = -0.22), which was also observed at the intrapopulational level (FIS = -0.23). The results gave evidence that the genetic selection applied to this European-Zebu composite population did not affect the expected high genetic variability for this type of crossbreeding, which makes it possible to use these animals to obtain economically valuable productive and reproductive traits.
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2,336,233 |
Long term follow-up of HNPCC gene mutation carriers: compliance with screening and satisfaction with counseling and screening procedures.
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Hereditary non polyposis colorectal cancer (HNPCC) is a hereditary predisposition to colorectal and endometrial cancer, caused by mutations of the mismatch repair (MMR) genes MSH2, MLH1 and MSH6. Regular colonoscopy reduces the incidence of colorectal cancer in mutation carriers dramatically. The aim of this study was to evaluate the use of colonoscopy by proven HNPCC mutation carriers. We also evaluated the satisfaction with the counseling and screening procedures at the long term. A questionnaire survey was performed among 94 proven MMR gene mutation carriers. Data were analyzed using univariate and multivariate analysis. The average time of follow-up was 3,5 years (range 0.5-8.5 years). The response rate was 74%. The proportion of unaffected mutation carriers under colonoscopic screening increased from 31 to 88% upon genetic testing, and for gynecological screening from 17 to 69%. However, more than half of the responders experienced colonoscopy as unpleasant or painful. About 97% felt well informed during counseling, and 88% felt sufficiently supported. Ten percent of the responders reported a high cancer worry that was significantly (P = 0.007) associated with a high perceived cancer risk. Six responders (9%) regretted being tested. Remarkably, of 4 of these 6 a close relative died recently of cancer. Problems with obtaining a disability or life insurance or mortgage were experienced by 4 out 10 healthy carriers opting for these services. In conclusion, genetic testing for HNPCC considerably improves compliance for screening, which will result in a reduction of HNPCC-related cancer morbidity and mortality in mutation carriers. Most HNPCC gene mutation carriers cope well with their cancer susceptibility on the long term.
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2,336,234 |
Development and QTL assessment of Triticum aestivum-Aegilops tauschii introgression lines.
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A set of 84 bread wheat lines, each containing a single homozygous introgression of the Aegilops tauschii genome was produced in the 'Chinese Spring' background via backcrossing of the D-genome chromosome substitution lines 'Chinese Spring'/Sears's 'Synthetic 6x' with the recurrent parent and subsequent selfing. The development of the lines was accompanied by microsatellite marker assisted selection. With the exception of three telomeric regions at chromosomes 1DL, 4DL and 7DS, and a region of less than 24 cM on the chromosome arm 3DL, the genome of Ae. tauschii is fully represented in these lines. The newly developed lines were used for the discovery of morphological and agronomical quantitative trait loci (QTLs) from the wild species. Fifty-two introgression lines were grown in the field and evaluated for six traits including flowering time, plant height, ear length, spikelet number, fertility and grain weight per ear. Seventeen significant QTLs were detected, Ae. tauschii contributed favourable alleles at nine loci influencing five traits. The whole set of 84 homozygous lines provides a tool for further testing the effects and stability of the detected QTLs and for the evaluation of new traits.
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2,336,235 |
A catalog of nonsynonymous polymorphism on mouse chromosome 16.
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Numerous phenotypic traits differ among inbred mice, and the genetic diversity of inbred strains has been exploited in studies of quantitative trait loci (QTL). Sequencing the mouse genome has resulted in improved tools for the study of QTL, but a comprehensive catalog of sequence variants between strains would be of great value in identifying and testing potentially causative alleles. A/J DNA was included in the Celera shotgun sequence of the mouse genome and C57BL/6 DNA was sequenced by an international consortium. We have resequenced A/J and B6 DNA to cover nearly all of the protein-coding portions of mouse Chromosome 16, revealing that there are 106 nonsynonymous substitutions in 74 of the 779 genes on the chromosome. The pattern of substitution is more similar to the spectrum of benign polymorphism in the human population than it is to human disease-causing mutations. In mouse, polymorphic variants tend to be associated with one another on large haplotypes; this pattern also holds true for nonsynonymous polymorphism. However, sufficient fragmentation of haplotypes is present to suggest that only a very-high-resolution haplotype map will enable effective inference of alleles in additional strains.
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2,336,236 |
[Screening of the delta-F508 mutation and analysis of two Single Nucleotide Polymorphism of the CFTR gene, in a sample of the general population of Valparaíso, Chile].
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The Cystic Fibrosis (CF) carrier rate in Chile was estimated to be 1/40. CF is caused by mutations in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene. Delta F508 mutation is the most common in CF patients in Chile and worldwide. Delta F508 has linkage disequilibrium with two Single Nucleotide Polymorphisms (SNP), often used to define the haplotypic frameworks of CF mutations.</AbstractText>To know the frequency of the delta F508 mutation and to establish the SNPs, M470V and T854T, haplotypic frequency, in a Valparaiso general population sample.</AbstractText>Fifty subjects were studied. Genetic material was obtained from blood samples, amplified by PCR and analyzed by restriction fragment length polymorphism.</AbstractText>Two of the 100 chromosomes analyzed, carried the delta F508 mutation. Therefore, the observed frequency carrier rate (0.02) was higher than the expected (0.01). Both carrier chromosomes had the same SNPs haplotypic framework (1-2). In normal chromosomes, the haplotype 2-1 was the most common.</AbstractText>These results suggest that the chromosomes that bear delta F508 mutation have most likely a Mediterranean European origin, since this haplotypic framework has been reported in that region. We suggest that CF could be more common in Valparaiso than it was previously.</AbstractText>
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2,336,237 |
Population genetics of wild-type CAG repeats in the Machado-Joseph disease gene in Portugal.
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To gain insights on the molecular mechanisms of mutation that led to the emergence of expanded alleles in the MJD gene, by studying the behavior of wild-type alleles and testing the association of its distribution with the representation of the disease.</AbstractText>The number of CAG motifs in the MJD gene was determined in a representative sample of 1000 unrelated individuals. Associations between the repeat size and the epidemiological representation of MJD were tested.</AbstractText>The allelic profile of the total sample was in the normal range (13-41 repeats), with mode (CAG)23. No intermediate alleles were present. Allelic size distribution showed a negative skew. The correlation between the epidemiological representation of MJD in each district and the frequency of small, medium and large normal alleles was not significant. Further correlations performed grouping the districts also failed to produce significant results.</AbstractText>The absence of association between the size of the repeats and the representation of MJD demonstrates that prevalence is not an indirect reflection of the frequency of large normal alleles. Globally the results obtained are in accordance with a model that postulates the occurrence of a few mutations on the basis of most of the MJD cases worldwide.</AbstractText>Copyright (c) 2005 S. Karger AG, Basel.</CopyrightInformation>
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2,336,238 |
Prenatal diagnosis of hemoglobinopathies in Ontario, Canada.
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In 1989, the Province of Ontario established a molecular diagnostic laboratory for carrier detection and prenatal diagnosis of hemoglobinopathies. Over the past 15 years, the laboratory has provided prenatal diagnosis for 672 pregnancies at-risk for severe hemoglobinopathies: 276 (41%) for homozygous beta-thalassemia or hemoglobin (Hb) E/beta-thalassemia, 211 (31%) for homozygous alpha 0-thalassemia (Hb Bart's hydrops fetalis), and/or Hb H disease, and 185 (28%) for various sickling disorders (Hb SS, Hb SC, Hb S/beta-thalassemia). Despite the availability of services for carrier screening, genetic counseling, and prenatal diagnosis, there has been only a modest reduction in the overall incidence of hemoglobinopathies in Ontario.
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2,336,239 |
Preimplantation genetics: Improving access to stem cell therapy.
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There has been progress in the application of stem cell transplantation for treatment of an increasing number of severe congenital and acquired bone marrow disorders, currently restricted by the availability of human leukocyte antigen (HLA)-matched related donors. Preimplantation HLA typing has recently been introduced to improve the access to stem cell therapy for inherited bone marrow failures. Preimplantation genetic diagnosis (PGD) provides an option not only for avoiding an affected pregnancy with thalassemia and other inherited disorders but also for preselection of the HLA-compatible donors for affected siblings. Multiple short tandem repeat markers throughout the HLA region are applied for this purpose, allowing 100% accuracy of HLA typing, through picking up possible recombination in the HLA region, as well as the copy number of chromosome 6, which affect accuracy of preimplantation HLA typing. Present experience of preimplantation HLA typing includes preimplantation HLA typing in 180 cycles, 122 of which were done as part of PGD for Fanconi anemia, thalassemia, Wiscott-Aldrich syndrome, hyper-immunoglobulin M syndrome, hypohidrotic ectodermal dysplasia with immune deficiency, and X-linked adrenoleukodystrophy, and 58 for the sole purpose of HLA typing for leukemias and for aplastic and Diamond-Blackfan anemia. The applied method resulted in the accurate preselection and transfer of 100% HLA-matched embryos, yielding already three dozen clinical pregnancies and the birth of two dozen HLA-matched children to the siblings requiring stem cell transplantation. Successful therapy with HLA-matched stem cells, obtained from these PGD children, has been achieved already for Diamond-Blackfan anemia hypohidrotic ectodermal dysplasia with immune deficiency and thalassemia.
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2,336,240 |
Study of two markers of apoptosis and meiotic segregation in ejaculated sperm of chromosomal translocation carrier patients.
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To try to explain the infertility of chromosomal translocation carrier patients, we compared the expression of two markers of apoptosis in the sperm of patients and of fertile donors, and we studied the meiotic segregation in the ejaculated sperm of these translocation carriers.</AbstractText>Twenty semen samples of translocation carriers, [reciprocal (n=14) and Robertsonian translocations (n=6)], were compared with the semen samples of donors (n=20). Different tests were applied: annexin V binding assay; terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick end labelling (TUNEL); and fluorescence in situ hybridization (FISH).</AbstractText>The annexin V binding assay in sperm of patients with chromosomal translocation (n=17) showed a significantly increased proportion of sperm with externalized phosphatidylserine (PS) than in the control group (n=20, P<or=0.05). The rates of DNA fragmentation investigated by TUNEL reaction were higher in samples of translocation carriers (n=14) than in donors (n=20, P<0.0001). The measures by FISH technique showed that the proportions of balanced or normal gametes were predominant in the reciprocal translocation group (alternate: n=7; from 33.0 to 58.8%; adjacent I: n=7; from 4.6 to 43.8%) and in the Robertsonian translocation group (normal: n=5; from 76.0 to 88.5%).</AbstractText>Our data show a predominant proportion of balanced gametes in sperm of chromosomal translocation carrier patients. Moreover, PS externalization and DNA fragmentation rates are significantly higher in ejaculated sperm of these patients than in donor sperm. These tests could be used to predict the outcome of ICSI for these patients.</AbstractText>
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2,336,241 |
A method for using incomplete triads to test maternally mediated genetic effects and parent-of-origin effects in relation to a quantitative trait.
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The authors recently developed a semiparametric family-based test for linkage and association between markers and quantitative traits. This quantitative polytomous logistic regression test allows for analysis of families with incomplete information on parental genotype. In addition, it is not necessary to assume normality of the quantitative trait. Previous simulations have shown that the new test is as powerful as the other widely used tests for linkage disequilibrium in relation to a quantitative trait. Here the authors propose an extension to quantitative polytomous logistic regression that allows testing for maternally mediated effects and parent-of-origin effects in the same framework. Missing data on parental genotype are accommodated through an expectation-maximization algorithm approach. Simulations show robustness of the new tests and good power for detecting effects in the presence or absence of offspring effects. Methods are illustrated with birth weight and gestational length, two quantitative outcomes for which data were collected in a Montreal, Canada, study of intrauterine growth restriction between May 1998 and June 2000.
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2,336,242 |
Clinical trials with tumor antigen genetically modified dendritic cells.
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Tumor antigen genetically modified dendritic cells (DC) have been extensively tested as cancer vaccine approaches in preclinical models. This testing has provided evidence of their ability to generate coordinated antitumor CD8+ cytotoxic T lymphocyte (CTL) and CD4+ T-helper cell responses. Their antitumor activity compared favorably to multiple other vaccination strategies in mice. This approach has been brought to patients within nine pilot clinical trials reported to date. These clinical trials have tested both RNA and DNA as means to introduce the foreign genetic material into the DC. Administration to human subjects has proven to be both feasible and safe. There is clear evidence of the ability to activate both CD8+ CTL and CD4+ T-helper cells, which has been the major scientific endpoint in most of these trials. However, antitumor activity has been marginal thus far. In conclusion, tumor antigen genetically modified DC are a feasible strategy to activate tumor-specific T cells in humans.
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2,336,243 |
Pharmacogenomics of responsiveness to interferon IFN-beta treatment in multiple sclerosis: a genetic screen of 100 type I interferon-inducible genes.
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Interferon IFN-beta is indicated for the treatment of multiple sclerosis. A significant proportion of patients show a poor clinical response to therapy. Type I interferon exerts its effect at least partially through interaction of specific transcription factors with interferon-stimulated response elements (ISREs), mostly located in promoter regions of its target genes. We hypothesized that polymorphisms may occur within or close to ISRE elements, altering type I interferon inducibility and ultimately leading to a modified clinical response in carriers.</AbstractText>We selected 100 ISRE-containing genes and sequenced their promoter regions in small genomic deoxyribonucleic acid pools of responding and nonresponding patients, as well as healthy control subjects. A selection of polymorphisms discovered by this approach was scrutinized subsequently in a collection of individual deoxyribonucleic acid samples.</AbstractText>We identified 4 genes containing polymorphisms associated with response to recombinant IFN-beta: IFNAR1 (P = .036), LMP7 (P = .002; odds ratio [OR], 6.37 [95% confidence interval (CI), 1.84-24.1]), CTSS (P = .02; OR, 0.38 [95% CI, 0.18-0.84]), and MxA (P = .015; OR, 3.37 [95% CI, 1.11-11.4]). Logistic regression analysis with treatment outcome used as the dependent variable and genotype as the independent variable revealed 2 genes, LMP7 (OR, 0.55 [95% CI, 0.34-0.89]) and MxA (OR, 0.41 [95% CI, 0.19-0.88]), that were independently associated with treatment response.</AbstractText>Our work confirms and extends previous indications for a polygenic mechanism involved in bringing about responsiveness to recombinant IFN-beta. The identification of 2 genes active in the antigen processing and presentation cascade; that is, LMP7, coding for the proteasome subunit beta, and CTSS, coding for cathepsin S; as potential response modifiers may identify this pathway as being of particular relevance to phenotypic expression of response heterogeneity.</AbstractText>
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2,336,244 |
Truncation of the C-terminus of human MLH1 blocks intracellular stabilization of PMS2 and disrupts DNA mismatch repair.
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The human DNA mismatch repair (MMR) protein MLH1 has essential roles in the correction of replication errors and the activation of cell cycle checkpoints and cytotoxic responses to DNA damage that contribute to suppression of cancer risk. MLH1 functions as a heterodimer with the PMS2 protein, and steady state levels of PMS2 are very low in MLH1-deficient cells. Unique to MLH1 among MutL-homolog proteins, and conserved in identified eukaryotic MLH1 proteins, is the so-called C-terminal homology domain (CTH). The function of these C-terminal 20-30 amino acids is not known. We investigated the effect of a C-terminal truncation of human MLH1 (MLH1-L749X) on mammalian MMR by testing its activity in MLH1-deficient cells. We found the CTH to be essential for suppression of spontaneous mutation, activation of a cytotoxic response to 6-thioguanine, and maintenance of normal steady state levels of PMS2. Co-expression in doubly mutant Mlh1-/-; Pms2-/- fibroblasts showed that MLH1-L749X was unable to stabilize PMS2. Over-expression of MLH1-L749X did not reduce stabilization of PMS2 mediated by wild-type MLH1, indicating that truncation of the CTH reduces the ability to compete with wild-type MLH1 for interaction with PMS2. Lack of PMS2 stabilization also was observed with a previously reported pathogenic truncation (MLH1-Y750X), but not with two different point mutations in the CTH. Biochemical assays demonstrated that truncation of the CTH reduced the stability of heterodimers, although MLH1-L749X retained significant capacity for interaction with PMS2. Thus, the CTH of human MLH1 is necessary for error correction, checkpoint signaling, and for promoting interaction with, and the stability of, PMS2. Analysis of the CTH role in stabilizing PMS2 was facilitated by a novel intracellular assay for MLH1-PMS2 interaction. This assay should prove useful for identifying additional amino acids in MLH1 and PMS2 necessary for interaction in cells, and for determining the functional consequences of MLH1 mutations identified in human cancers.
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2,336,245 |
Triallelic patterns in STR loci used for paternity analysis: evidence for a duplication in chromosome 2 containing the TPOX STR locus.
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We report triallelic patterns in several short tandem repeat (STR) loci revealed by routine paternity testing using the commercial AMPFlSTR Profiler and AMPFlSTR SGMplus kits. One case where the TPOX-locus (2p25.3) produced three peaks from the blood sample of a child was analysed further. Quantitative polymerase chain reaction (QPCR) and STR typing of the DNAs of the family trio revealed a large (>1.59 Mb) duplication flanking the TPOX-locus in chromosome 2 in both the mother and child. The implications of such genetic anomalies for paternity testing are discussed.
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2,336,246 |
Elevated and similar urinary testosterone/epitestosterone ratio in all samples of a competition testing: suspicion of a manipulation.
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The case of seven urine samples collected for anti-doping purposes during a cycling stage race with moderately elevated testosterone and epitestosterone ratio (T/E) is reported. The very low probability of having all seven urine samples with such similar elevated T/E ratio (from 3.2 to 4.7) was very suspicious. Different pattern classification tools were tested to categorize the most similar steroid profiles, but none of the models enabled a clear classification of the different urine samples. Subsequently, genetic profiling of all urine samples was performed and demonstrated that three of the seven samples were collected from the same cyclist. Finally, the International Federation confirmed DNA profiling results. This suggests that urinary steroid data using several methodologies are not appropriate for identification purposes and to an extent not unique to individuals.
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2,336,247 |
Theatre as a public engagement tool for health-policy development.
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To explore theatre as a public engagement tool for health-policy development.</AbstractText>In a justice-based democracy, engagement of a large number of citizens of diverse perspectives is required for legitimate health-policy development. However, all current strategies of citizen participation are limited in their capacity to engage, either by lack of opportunity to educate citizens prior to soliciting their opinions or lack of large numbers of citizens.</AbstractText>A series of 12 nested case studies was conducted, with each case study consisting of a performance of a 70-min play, specifically written to educate citizens to scientific, clinical, and psychosocial issues of adult predictive genetic testing, and to foster empathy for persons immersed therein; and a 1-h audience discussion that was taped and transcribed for qualitative analysis (modified thematic). The script was based on key informant interviews, literature review, and six script readings for key informants and communities. Audience members were recruited through conference or educational event programs, posters, newsletters, and electronic announcements, as well as newspaper advertisements and other public, community and institutional postings.</AbstractText>More than 1,000 citizens were engaged. The analysis indicated that audience members were engaged emotionally and cognitively in the position of the characters and the health-policy issues. Audience members' comments forwarded from personal or professional lived experience confirmed the validity of the script and promoted further emotional and cognitive engagement of other audience members. Audience members offered informed and diverse opinions on policy issues, including resource allocation, patenting of genetic tests, research funding, genetic test-based insurance discrimination, and imperative for public education. The potential for harm to key informants and audience members (and those in relationships with them) were observed, usually related to learning or offering personal information regarding their genetic risk.</AbstractText>As many citizens can be engaged in theatre-based policy development as surveyed through public opinion polls, and many times the number that can be engaged in strategies that educate citizens prior to soliciting their opinions, likely at a similar cost per citizen engaged.</AbstractText>
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2,336,248 |
Chloroplast biogenesis 92: In situ screening for divinyl chlorophyll(ide) a reductase mutants by spectrofluorometry.
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Chlorophyll biosynthetic heterogeneity is rooted mainly in parallel divinyl (DV) and monovinyl (MV) biosynthetic routes interconnected by 4-vinyl reductases (4VRs) that convert DV tetrapyrroles to MV tetrapyrroles by conversion of the vinyl group at position 4 of the macrocycle to ethyl. What is not clear at this stage is whether the various 4VR activities are catalyzed by one enzyme of broad specificity or by a family of enzymes encoded by one gene or multiple genes with each enzyme having narrow specificity. Additional research is needed to identify the various regulatory components of 4-vinyl reduction. In this undertaking, Arabidopsis mutants that accumulate DV chlorophyllide a and/or DV chlorophyll [Chl(ide)] a are likely to provide an appropriate resource. Because the Arabidopsis genome has been completely sequenced, the best strategy for identifying 4VR and/or putative regulatory 4VR genes is to screen Arabidopsis Chl mutants for DV Chl(ide) a accumulation. In wild-type Arabidopsis, a DV plant species, only MV chlorophyllide (Chlide) a is detectable. However in Chl mutants lacking 4VR activity, DV Chl(ide) a may accumulate in addition to MV Chl(ide) a. In the current work, an in situ assay of DV Chl(ide) a accumulation, suitable for screening a large number of mutants lacking 4-vinyl Chlide a reductase activity with minimal experimental handling, is described. The assay involves homogenization of the tissues in Tris-HCl:glycerol buffer and the recording of Soret excitation spectra at 77K. DV Chlide a formation is detected by a Soret excitation shoulder at 459 nm over a wide range of DV Chlide a/MV Chl a ratios. The DV Chlide a shoulder became undetectable at DV Chlide a/MV Chl a ratios less than 0.049, that is, at a DV Chlide a content of less than 5%.
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2,336,249 |
Variation in conserved non-coding sequences on chromosome 5q and susceptibility to asthma and atopy.
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Evolutionarily conserved sequences likely have biological function.</AbstractText>To determine whether variation in conserved sequences in non-coding DNA contributes to risk for human disease, we studied six conserved non-coding elements in the Th2 cytokine cluster on human chromosome 5q31 in a large Hutterite pedigree and in samples of outbred European American and African American asthma cases and controls.</AbstractText>Among six conserved non-coding elements (> 100 bp, > 70% identity; human-mouse comparison), we identified one single nucleotide polymorphism (SNP) in each of two conserved elements and six SNPs in the flanking regions of three conserved elements. We genotyped our samples for four of these SNPs and an additional three SNPs each in the IL13 and IL4 genes. While there was only modest evidence for association with single SNPs in the Hutterite and European American samples (P < 0.05), there were highly significant associations in European Americans between asthma and haplotypes comprised of SNPs in the IL4 gene (P < 0.001), including a SNP in a conserved non-coding element. Furthermore, variation in the IL13 gene was strongly associated with total IgE (P = 0.00022) and allergic sensitization to mold allergens (P = 0.00076) in the Hutterites, and more modestly associated with sensitization to molds in the European Americans and African Americans (P < 0.01).</AbstractText>These results indicate that there is overall little variation in the conserved non-coding elements on 5q31, but variation in IL4 and IL13, including possibly one SNP in a conserved element, influence asthma and atopic phenotypes in diverse populations.</AbstractText>
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2,336,250 |
DNA barcoding: error rates based on comprehensive sampling.
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DNA barcoding has attracted attention with promises to aid in species identification and discovery; however, few well-sampled datasets are available to test its performance. We provide the first examination of barcoding performance in a comprehensively sampled, diverse group (cypraeid marine gastropods, or cowries). We utilize previous methods for testing performance and employ a novel phylogenetic approach to calculate intraspecific variation and interspecific divergence. Error rates are estimated for (1) identifying samples against a well-characterized phylogeny, and (2) assisting in species discovery for partially known groups. We find that the lowest overall error for species identification is 4%. In contrast, barcoding performs poorly in incompletely sampled groups. Here, species delineation relies on the use of thresholds, set to differentiate between intraspecific variation and interspecific divergence. Whereas proponents envision a "barcoding gap" between the two, we find substantial overlap, leading to minimal error rates of approximately 17% in cowries. Moreover, error rates double if only traditionally recognized species are analyzed. Thus, DNA barcoding holds promise for identification in taxonomically well-understood and thoroughly sampled clades. However, the use of thresholds does not bode well for delineating closely related species in taxonomically understudied groups. The promise of barcoding will be realized only if based on solid taxonomic foundations.
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2,336,251 |
Oculopharyngeal muscular dystrophy - an under-diagnosed disorder?
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Oculopharyngeal muscular dystrophy (OPMD) is an autosomal dominant muscle disorder, usually of late onset. OPMD is among the few triplet repeat diseases/ polyalanine (poly(A)) expansion diseases for which the function of the mutated gene is quite well established. The disease is characterised by slowly progressive bilateral ptosis, dysphagia and proximal limb weakness, appearing after the age of 40 years. Prevalence and incidence of OPMD are low, but the disease occurs all over the world. The pedigrees of two Swiss kindred have been previously reported in Switzerland. In the last 2 years, accumulation of newly diagnosed cases in North-West Switzerland have been observed, which suggests that OPMD may be more prevalent than previously thought. Primary care providers, opthalmologists and neurologists that are alert for the almost specific combination of clinical signs, together with the availability of reliable genetic testing may help to recognise currently undiagnosed patients. They can advance knowledge and the characterisation of the OPMD population in Switzerland. Since the number of disorders linked to poly(A) expansions is growing rapidly, the study of OPMD may contribute to the understanding of a large group of other developmental and degenerative diseases. On the basis of a patient with "classical" OPMD, this review summarises the clinical, therapeutic, epidemiological, pathomechanistic and genetic aspects of OPMD, provides practical information about the differential diagnosis of OPMD, and presents a survey of different investigational methods.
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2,336,252 |
Low prevalence of primary antiretroviral resistance mutations and predominance of HIV-1 clade C at polymerase gene in newly diagnosed individuals from south Brazil.
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We describe preliminary molecular characterization of HIV-1 pol from 108 consecutive HIV seropositive users of a Voluntary Counseling and Testing (VCT) site of Porto Alegre city, the major metropolitan area in the south of Brazil. Protease and partial reverse transcriptase regions were retrotranscribed from plasma HIV-1 RNA and sequenced after direct nested PCR. Principal antiretroviral resistance mutations (ARM) were observed in 3% of the samples, two cases with K103N and one with M41L, L210W and T215Y, all in HIV-1 clade B infected men. At protease region, no principal mutations were observed, but polymorphisms at secondary codons were frequent. Contrary to other areas in the country where clade B dominates, HIV-1 clade C genomes predominated in this study (58%), clade B (32%) and clade F1 (3%). Of the genomes clustering in clade C, almost half (43%) had a small clade B segment at reverse transcriptase, forming a sub-cluster within clade C with a similar recombinant structure and carrying new amino acid signatures. Other mosaic genomes were also observed (7%). The low prevalence of resistance mutations is consistent with previous observations at this geographical location but the high frequency of HIV-1 clade C and CB mosaics seems pre-eminent and warns close monitoring.
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2,336,253 |
PCR primers based on different portions of insertion elements can assist genetic relatedness studies, strain fingerprinting and species identification in rhizobia.
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Using the sequence of an insertion element originally found in Rhizobium sullae, the nitrogen-fixing bacterial symbiont of the legume Hedysarum coronarium, we devised three primer pairs (inbound, outbound and internal primers) for the following applications: (a) tracing genetic relatedness within rhizobia using a method independent of ribosomal inheritance, based on the presence and conservation of IS elements; (b) achieve sensitive and reproducible bacterial fingerprinting; (c) enable a fast and unambiguous detection of rhizobia at the species level. In terms of taxonomy, while in line with part of the 16S rRNA gene- and glutamine synthetase I-based clustering, the tools appeared nonetheless more coherent with the actual geographical ranges of origin of rhizobial species, strengthening the European-Mediterranean connections and discerning them from the asian and american taxa. The fingerprinting performance of the outward-pointing primers, designed upon the inverted repeats, was shown to be at least as sensitive as BOX PCR, and to be functional on a universal basis with all 13 bacterial species tested. The primers designed on the internal part of the transposase gene instead proved highly species-specific for R. sullae, enabling selective distinction from its most related species, and testing positive on every R. sullae strain examined, fulfilling the need of PCR-mediated species identification. A general use of other IS elements for a combined approach to rhizobial taxonomy and ecology is proposed.
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2,336,254 |
Investigating the evolutionary history of the Pacific Northwest mesic forest ecosystem: hypothesis testing within a comparative phylogeographic framework.
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We examine the evolution of mesic forest ecosystems in the Pacific Northwest of North America using a statistical phylogeography approach in four animal and two plant lineages. Three a priori hypotheses, which explain the disjunction in the mesic forest ecosystem with either recent dispersal or ancient vicariance, are tested with phylogenetic and coalescent methods. We find strong support in three amphibian lineages (Ascaphus spp., and Dicampton spp., and Plethodon vandykei and P. idahoensis) for deep divergence between coastal and inland populations, as predicted by the ancient vicariance hypothesis. Unlike the amphibians, the disjunction in other Pacific Northwest lineages is likely due to recent dispersal along a northern route. Topological and population divergence tests support the northern dispersal hypothesis in the water vole (Microtus richardsoni) and northern dispersal has some support in both the dusky willow (Salix melanopsis) and whitebark pine (Pinus albicaulis). These analyses demonstrate that genetic data sampled from across an ecosystem can provide insight into the evolution of ecological communities and suggest that the advantages of a statistical phylogeographic approach are most pronounced in comparisons across multiple taxa in a particular ecosystem. Genetic patterns in organisms as diverse as willows and salamanders can be used to test general regional hypotheses, providing a consistent metric for comparison among members of an ecosystem with disparate life-history traits.
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2,336,255 |
The analysis for identifying large DNA fragment aberrations of MSH2 and MLH1 genes from familial colorectal cancer in China.
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To investigate the frequency of large fragment aberrations of MSH2 and MLH1 genes from Chinese colorectal cancer (CRC) patients with family history.</AbstractText>Sixteen exons of MSH2, nineteen exons of MLH1 and seven DNA sequences from the other genes of the samples were screened and checked by multiplex ligation dependent probe amplification (MLPA). First, the methodology was confirmed by testing the positive and negative control samples. Then, 32 CRC or hereditary nonpolyposis colorectal cancer (HNPCC) patients with family history and 20 cases of sporadic CRC were applied to investigate for the large fragment aberrations of MSH2 and MLH1 genes.</AbstractText>The genomic DNA fragment deletions of all positive controls were identified and verified by MLPA. Three cases of 32 familial (hereditary) CRC/HNPCC were detected and identified to be the germline heterozygous deletions of MSH2 gene, of which exons 1-7 were deleted from patient No.3, exon 11 from No.25 and exons 2-6 from No.11. However, no genomic DNA fragment aberration of either MSH2 or MLH1 gene was uncovered from 20 sporadic CRC.</AbstractText>Large DNA fragment aberrations of MSH2 gene was a frequent cause of Chinese HNPCC and CRC patients with family history, and the identification of those aberrations should be included in the regular genetic analysis for CRC/HNPCC patients.</AbstractText>
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2,336,256 |
Quantitative studies on SMN1 gene and carrier testing of spinal muscular atrophy.
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To construct a method for detecting the copy number of survival of motor neuron 1 gene (SMN1) with single copy difference based on real-time fluorescence quantitative PCR, and to make practical use of the method for acquiring the data on SMN1 copy number in Chinese as well as for screening the carriers of spinal muscular atrophy (SMA) from healthy individuals and SMA families.</AbstractText>Exon 7 and flanking area of SMN1 gene were amplified by real-time fluorescence quantitative PCR in 264 healthy individuals, in 1 standard sample having 2 SMN1 but having no SMN2, and in 88 parents of SMA patients. The samples for detecting were diluted to 30 ng/microL and the standard sample was diluted to 15 ng/microL, 30 ng/microL, 45 ng/microL, 60 ng/microL; the unknown samples and 4 standard samples with different concentrations were amplified at the same time, a standard curve could be drawn out according to the results of the 4 standard samples, then the copy number of samples could be calculated.</AbstractText>Of 88 parents' samples, 84 samples each had 1 copy of SMN1, and the rest 4 each had 2 copies of SMN1. Of 264 healthy individuals' samples, 5 samples each had only 1 copy of SMN1 (an indicator of definite gene carriers), 232 samples each had 2 copies of SMN1, 25 samples each had 3 copies of SMN1, and 2 samples each had 4 copies of SMN1. Of the samples of 32 members of SMA families, 2 samples each had only 1 copy of SMN1 indicating definite gene carriers, 25 samples each had 2 copies of SMN1, and 5 samples each had 3 copies of SMN1.</AbstractText>SMN1 copy number could be detected precisely by real-time fluorescence quantitative PCR; the screening of gene carriers could provide essential data for genetic counseling.</AbstractText>
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2,336,257 |
Linkage analyses of event-related potential slow wave phenotypes recorded in a working memory task.
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Working memory is an essential component of wide-ranging cognitive functions. It is a complex genetic trait probably influenced by numerous genes that individually have only a small influence. These genes may have an amplified influence on phenotypes closer to the gene action. In this study, event-related potential (ERP) phenotypes recorded during a working-memory task were collected from 656 adolescents from 299 families for whom genotypes were available. Univariate linkage analyses using the MERLIN variance-components method were conducted on slow wave phenotypes recorded at multiple sites while participants were required to remember the location of a target. Suggestive linkage (LOD > 2.2) was found on chromosomes 4, 5, 6, 10, 17, and 20. After correcting for multiple testing, suggestive linkage remained on chromosome 10. Empirical thresholds were computed for the most promising phenotypes. Those on chromosome 10 remained suggestive. A number of genes reported to regulate neural differentiation and function (i.e. NRP1, ANK3, and CHAT) were found under these linkage peaks and may influence the levels of neural activity occurring in individuals participating in a spatial working-memory task.
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2,336,258 |
Characterization of Bison bison major histocompatibility complex class IIa haplotypes.
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American bison (Bison bison) and domestic cattle (Bos taurus and Bos indicus) evolved from a common ancestor 1-1.4 million years ago. Nevertheless, they show dramatic differences in their susceptibility to infectious diseases, including malignant catarrhal fever (MCF). Although bison are highly susceptible to ovine herpesvirus-2 (OvHV-2) associated MCF, about 20% of healthy domesticated and wild bison are positive for OvHV-2 antibody. We are interested in testing the hypothesis that, within the bison population, the polymorphism of major histocompatibility complex (MHC) class II genes influences resistance to MCF. However, since little was known about the MHC class II genes of bison, it was necessary to first characterize class II haplotypes present in Bi. bison (Bibi). Thus, the MHC class II haplotypes carried by 14 bison were characterized by the PCR-based cloning and sequencing of their DRB3, DQA, and DQB alleles. Twelve MHC class II haplotypes were identified in the 14 bison. These haplotypes comprised six previously reported and six new Bibi-DRB3 alleles, along with 11 Bibi-DQA and 10 Bibi-DQB alleles. For each bison class II allele, it was possible to identify closely related cattle sequences. The closest bison and bovine DQA, DQB, and DRB3 alleles, on average, differed by only 1.3, 3.5, and 5.8 amino acids, respectively. Furthermore, bison MHC haplotypes with both nonduplicated and duplicated DQ genes were identified; these haplotypes appear to have originated from the same ancestral haplotypes as orthologous cattle haplotypes.
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2,336,259 |
Immunologic significance of HLA class I genes in measles virus-specific IFN-gamma and IL-4 cytokine immune responses.
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The variability of immune responses modulated by human leukocyte antigen (HLA) genes and secreted cytokines is a significant factor in the development of a protective effect of measles vaccine. We studied the association between type 1 helper T cells (Th1)- and Th2-like cytokine immune responses and HLA class I alleles among 339 schoolchildren who previously received two doses of the measles vaccine. Median values for measles-specific interferon gamma (IFN-gamma) and interleukin-4 (IL-4) cytokines were 40.7 pg/ml [interquartile range (IQR) 8.1-176.7] and 9.7 pg/ml (IQR 2.8-24.3), respectively. Class I HLA-A (*0101 and *3101) and HLA-Cw (*0303 and *0501) alleles were significantly associated with measles-virus-induced IFN-gamma secretion. HLA-A*3101 and Cw*0303 were associated with a higher median IFN-gamma response, while A*0101 and Cw*0501 were associated with lower measles-specific IFN-gamma response. We found limited associations between HLA class I gene polymorphisms and Th2-like (IL-4) immune responses after measles vaccination, indicating that HLA class I molecules may have a limited effect on measles-vaccine-induced IL-4 secretion. Understanding the genetic factors that influence variations in cytokine secretion following measles vaccination will provide insight into the factors that influence both cell-mediated and humoral immunity to measles.
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2,336,260 |
Mitochondrial myopathies: diagnosis, exercise intolerance, and treatment options.
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Mitochondrial myopathies are caused by genetic mutations that directly influence the functioning of the electron transport chain (ETC). It is estimated that 1 of 8,000 people have pathology inducing mutations affecting mitochondrial function. Diagnosis often requires a multifaceted approach with measurements of serum lactate and pyruvate, urine organic acids, magnetic resonance spectroscopy (MRS), muscle histology and ultrastructure, enzymology, genetic analysis, and exercise testing. The ubiquitous distribution of the mitochondria in the human body explains the multiple organ involvement. Exercise intolerance is a common but often an overlooked hallmark of mitochondrial myopathies. The muscle consequences of ETC dysfunction include increased reliance on anaerobic metabolism (lactate generation, phosphocreatine degradation), enhanced free radical production, reduced oxygen extraction and electron flux through ETC, and mitochondrial proliferation or biogenesis (see article by Hood in current issue). Treatments have included antioxidants (vitamin E, alpha lipoic acid), electron donors and acceptors (coenzyme Q10, riboflavin), alternative energy sources (creatine monohydrate), lactate reduction strategies (dichloroacetate) and exercise training. Exercise is a particularly important modality in diagnosis as well as therapy (see article by Taivassalo in current issue). Increased awareness of these disorders by exercise physiologists and sports medicine practitioners should lead to more accurate and more rapid diagnosis and the opportunity for therapy and genetic counseling.
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2,336,261 |
A genome-wide linkage scan of familial benign recurrent vertigo: linkage to 22q12 with evidence of heterogeneity.
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Benign recurrent vertigo (BRV) is a common disorder affecting up to 2% of the adult population and may be etiologically related to migraine because of similarities in the clinical spectrum of the phenotypes and a high co-morbidity within families. Many families have multiple-affected genetically related individuals suggesting familial transmission of the disorder with moderate to high penetrance. While clinically similar to episodic ataxias, there are currently no genes identified that contribute to BRV and no systematic linkage studies performed. In an initial effort to genetically define BRV, we have selected from our Neurology Clinic population a subset of 20 multigenerational families with apparent autosomal dominant transmission, and performed genetic linkage mapping using both parametric and non-parametric linkage (NPL) approaches. The Affymetrix 10K SNP Mapping Assay was used for the genotyping. Heterogeneity LOD (HLOD) analysis reveals the evidence of genetic heterogeneity for BRV and evidence of linkage in a subset of the families to 22q12 (HLOD = 4.02). An additional region was identified by NPL analysis at 5p15 (LOD = 2.63). As migraine is observed substantially more commonly both within the BRV-affected individuals and the related family members, it is possible that a form of migraine is allelic to the BRV locus at 22q12. However, testing linkage or the chromosome 22q12 region to a broader migraine/vertigo phenotype by defining affectation status as either migrainous headaches or BRV greatly weakened the linkage signal, and no significant other peaks were detected. Thus, BRV and migraine does not appear to be allelic disorders within these families. We conclude that BRV is a heterogeneous genetic disorder, appears genetically distinct from migraine with aura and is linked to 22q12. Additional family and population-based linkage and association studies will be needed to determine the causative alleles.
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2,336,262 |
Mutations or exclusion: an unusual case in paternity testing.
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In an immigration case with the scope of family reunification, the DNA extracted from the saliva samples of the male child, the alleged mother and the putative father was typed with 22 autosomal short tandem repeat (STR) systems. In seven STR systems, the alleged mother could be excluded from maternity, and the case then had to be regarded as a deficiency case. Taking this fact into consideration, only two exclusions were found for the putative father, and the question arose whether there was an exclusion of the putative father or the existence of two mutations. Autosomal STR typing could not clarify the case, but the application of eight Y-chromosomal markers showed that the alleged father could be excluded from paternity.
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2,336,263 |
An intervention study of smoking cessation with feedback on genetic cancer susceptibility in Japan.
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To evaluate whether feedback of genetic information regarding an L-myc polymorphism, identified as impacting on tobacco-related cancer risk, has an influence on smoking cessation, an intervention study was conducted.</AbstractText>We recruited smokers from first-visit outpatients at Aichi Cancer Center Hospital. Six hundred and seventeen participated and were allocated into two groups: the biomarker feedback group (BF) and the follow-up smoking status group (FS). The subjects were asked for their smoking status at enrolment and at 3- and 9-month follow-ups. BF subjects were notified about their L-myc genotype.</AbstractText>The smoking cessation rate at 9-month follow-up was essentially the same for both BF and FS cases, at 18.8% and 17.0%, respectively (P = 0.798). However, a difference in the rate was evident with non-cancer subjects (12.7% and 8.4%, respectively, P = 0.237), especially in females (15.0% and 4.2%, respectively, P = 0.024). The non-cancer subjects informed of their genotype were more likely to quit smoking than the FS patients; particularly in those having a risky genotype, this was significant (odds ratio: 2.87, P = 0.003). Again it was most prominent in females.</AbstractText>Feedback regarding an L-myc polymorphism did not impact on smoking cessation overall but appeared to benefit smokers without cancer. In addition, gender could affect the response to the feedback.</AbstractText>
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2,336,264 |
High-throughput screen for genes predominantly expressed in the ICM of mouse blastocysts by whole mount in situ hybridization.
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Mammalian preimplantation embryos provide an excellent opportunity to study temporal and spatial gene expression in whole mount in situ hybridization (WISH). However, large-scale studies are made difficult by the size of the embryos ( approximately 60mum diameter) and their fragility. We have developed a chamber system that allows parallel processing of embryos without the aid of a microscope. We first selected 91 candidate genes that were transcription factors highly expressed in blastocysts, and more highly expressed in embryonic (ES) than in trophoblast (TS) stem cells. We then used the WISH to identify 48 genes expressed predominantly in the inner cell mass (ICM) and to follow several of these genes in all seven preimplantation stages. The ICM-predominant expressions of these genes suggest their involvement in the pluripotency of embryonic cells. This system provides a useful tool to a systematic genome-scale analysis of preimplantation embryos.
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2,336,265 |
Presymptomatic thyroidectomy in multiple endocrine neoplasia 2a.
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To evaluate the value of prophylactic total thyroidectomy in multiple endocrine neoplasia 2a (MEN 2a), based on results of genetic testing, in a presymptomatic early stage of the disease.</AbstractText>Fourteen presymptomatic patients genetically diagnosed and surgically treated at our centre. We analysed age, gender, location of the RET mutation, calcitonin tests, surgery, histologic findings, TNM classification, and postoperative follow-up.</AbstractText>The 14 patients belonged to two families with MTC (MEN 2a). Median age was 16 years. The RET mutation was located in codon 618 and 634. Basal calcitonin (CT) levels were normal in all patients. Twelve had pathologic peak CT measurements. Total thyroidectomy was performed in all and associated central neck dissection in 12 patients. Pathohistologic assessment showed C-cell hyperplasia in all specimens and 11 MTCs; the median size of the tumours was 0.2 cm; two patient had lymph-node metastases. According to TNM, three had stage 0, nine had stage I, one had stage II, and one had stage III disease. Postsurgery basal and peak CT values were normal in all but one patients, indicating a biochemical curative rate of 95%. Calcitonin determination did not distinguish between MTC and C-cell hyperplasia.</AbstractText>Prophylactic thyroidectomy based on genetic testing allows identification and treatment of patients at an early stage of the disease. Pathologic peak CT values are markers for the presence of microscopic MTC and should be considered in selecting operative procedures for these patients.</AbstractText>
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2,336,266 |
[Mutational analysis of BRCA1 and BRCA2 genes in early-onset breast cancer patients in Shanghai].
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To investigate the prevalence of BRCA1 and BRCA2 mutations among early-onset breast cancer patients in Shanghai.</AbstractText>Fifty patients unselected for family history, who were diagnosed with breast cancer before the age of 40 years were analyzed. Among them, 13 patients have at least one first-degree relative affected with breast cancer. Mutation screening of BRCA1 and BRCA2 was performed in the whole coding sequence through Denaturing High Performance Liquid Chromatography (DHPLC) and subsequent DNA direct sequencing.</AbstractText>Six deleterious mutations, including 2 novel frameshift mutations (3449insA, 5587-1del8) and 2 novel splice-site mutations (IVS17-1G > T, IVS21 + 1G > C) in BRCA1 were identified. Two deleterious mutations detected in BRCA2, including one frameshift mutation (5950delCT) and one novel missense mutation (5911G > C), all occurring on exon 11 adjacently. Additional 12 novel sequence variants were also detected including one unclassified variant and 7 intronic variants in BRCA1, and 4 novel intronic variants in BRCA2, all causing no alteration of amino acid coding. The prevalence of BRCA1 and BRCA2 mutations in the patients with early-onset breast cancer was 12% and 4%, respectively.</AbstractText>Four novel mutations in BRCA1 and one novel mutation in BRCA2 may be mutations characterized of early-onset breast cancer in Chinese population. Germline mutations in BRCA2 may contribute less than mutations in BRCA1 to early-onset breast cancer in Shanghai. These data contribute to information on spectrum of BRCA gene in Chinese population and also offer a recommended screening mode for clinical genetic testing programme in China.</AbstractText>
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2,336,267 |
[Clinical symptoms, diagnosis and treatment of multiple endocrine neoplasia type 1. Results of genetic screening in Hungarian patients].
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Multiple endocrine neoplasia type 1 syndrome is an autosomal dominant disorder characterized by endocrinopathies involving the parathyroid glands, anterior pituitary gland, and pancreas. Also, it may be associated with foregut carcinoid, adrenocortical tumors and non-endocrine tumors. After reviewing the prevalence, genetic background, clinical symptoms, diagnosis and treatment of the disorder, the authors present their genetic screening method used for the detection of mutations of the MEN1 gene (prescreening of polymerase chain reaction amplified exons using temporal temperature gradient gel electrophoresis followed by direct DNA sequencing). Using this method, the authors identified disease-causing MEN1 gene mutations in 9 probands (small deletions in 2 cases, insertion in 2 cases, nonsense mutations in 2 cases and missense mutations in 3 cases). Of the 9 mutations, 4 proved to be novel mutation not reported in the literature. Family screening indicated de novo mutations in 2 probands. In addition to mutations, several sequence polymorphisms were also detected. The authors conclude that one of the major advantages of genetic screening in families with MEN1 syndrome was the identification of family members carrying the mutation who should be regularly screened for disease manifestations and those not carrying the mutation in whom clinical screening is unnecessary. Also, genetic screening may be useful in cases when MEN1 syndrome is suspected, but the clinical manifestations do not fully establish the diagnosis of MEN1 syndrome.
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2,336,268 |
Comparison of sequence analysis and INNO-LiPA HBV DR line probe assay in patients with chronic hepatitis B.
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The aim of this study was to compare direct sequence analysis of partial HBV pol gene and Inno-LiPA HBV DR in serum samples of 120 chronic hepatitis B patients sent to the Clinical Microbiology Laboratory of Ege University Hospital because of lamivudine resistance. Sequence analysis was performed on ABI Prism 310 Genetic Analyzer. Comparison of Inno-LiPA and sequence results obtained by double-blind evaluation showed full agreement (both at rt180 and rt204) in 58.8% of samples. Visually rechecking of the electropherograms increased this rate to 68.3% Codon based rates are 81.7% and 75.8% at rt180 and rt204 respectively. LiPA detected variants in additional 12 (10%) samples, but missed one variant sample (both rt180 and rt204) and one sample was indeterminate due to poor probe binding. LiPA allows determination of mixed variants and seems to be more sensitive and simple for routine testing even though sequence analysis is still the gold standard for detecting new variants.
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2,336,269 |
Molecular evaluation of foetuses with holoprosencephaly shows high incidence of microdeletions in the HPE genes.
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Holoprosencephaly (HPE), the most common structural malformation of the forebrain in humans, can be detected early during pregnancy using prenatal ultrasonography . Among foetuses with a normal karyotype, 14% have mutations in the four main HPE genes (SHH, ZIC2, SIX3 and TGIF). Genomic rearrangements have now been implicated in many genetic diseases, so we hypothesized that microdeletions in the major HPE genes may also be common in HPE foetuses with severe phenotype or other associated malformations. We screened the DNA obtained from 94 HPE foetuses with a normal karyotype for the presence of microdeletions involving the four major HPE genes (SHH, ZIC2, SIX3 and TGIF). Thirteen of the foetuses had a point mutation in one of the 4 genes and 81 had no known mutations. Quantitative multiplex PCR of short fluorescent fragments (QMPSF) analysis was used for rapid determination of HPE genes copy numbers and the identified microdeletions were confirmed by real time quantitative PCR, or fluorescent in situ hybridization (FISH) (if a cell line was available). Microdeletions were detected in 8 of 94 foetuses (8.5%) (2 in SHH, 2 in SIX3, 3 in ZIC2 and 1 in TGIF genes), and only among the 81 foetuses with a normal karyotype and no point mutations. These data suggest that microdeletions in the four main HPE genes are a common cause of prenatal HPE, as well as point mutations, and increase the total diagnosis rate close to approximately 22.3% of foetuses with normal karyotype. Detection can be achieved by the QMPSF testing method that proved to be efficient for testing several genes in a single assay.
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2,336,270 |
Triple gene-deleted oncolytic herpes simplex virus vector double-armed with interleukin 18 and soluble B7-1 constructed by bacterial artificial chromosome-mediated system.
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Conditionally replicating herpes simplex virus type 1 (HSV-1) vectors are promising therapeutic agents for cancer. Certain antitumor functions may be added to oncolytic activities of recombinant HSV-1 vectors by inserting transgenes into the viral genome. Because conventional homologous recombination techniques had required time-consuming processes to create "armed" oncolytic HSV-1 vectors, we established an innovative construction system using bacterial artificial chromosome and two recombinase systems (Cre/loxP and FLPe/FRT). Using G47Delta, a safe and efficacious oncolytic HSV-1 with triple gene mutations, as the backbone, this system allowed a rapid generation of multiple vectors with desired transgenes inserted in the deleted ICP6 locus. Four oncolytic HSV-1 vectors, expressing murine interleukin 18 (mIL-18), soluble murine B7-1 [B7-1-immunoglobulin (B7-1-Ig)], both, or none, were created simultaneously within 3 months. In vitro, all newly created recombinant vectors exhibited virus yields and cytopathic effects similar to the parental G47Delta. In two immunocompetent mouse tumor models, TRAMP-C2 prostate cancer and Neuro2a neuroblastoma, the vector expressing both mIL-18 and B7-1-Ig showed a significant enhancement of antitumor efficacy via T-cell-mediated immune responses. The results show that "arming" with multiple transgenes can improve the efficacy of oncolytic HSV-1 vectors. The use of our system may facilitate the development and testing of various armed oncolytic HSV-1 vectors.
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2,336,271 |
Clinical and genetic features of Hungarian achromatopsia patients.
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To describe the clinical features and molecular genetic findings in a collection of Hungarian achromatopsia patients.</AbstractText>Twelve patients with congenital achromatopsia from nine Hungarian families were analyzed in this study. The patients underwent standard ophthalmological examination including detailed full-field electroretinography and color vision testing. In two patients, dark adaptation and spectral luminosity tests were also performed. PCR/RFLP analysis and DNA sequencing was applied for mutation screening of CNGA3 and CNGB3. Heterologous minigene expression was used to evaluate transcript splicing of a new intronic mutation in CNGB3.</AbstractText>Mutations in CNGA3 were present in four families and mutations in CNGB3 in the remaining five families, including mutations known from Western European patient samples and two new CNGB3 mutations: c.112C>T/Gln38X and c.1663-5T>G. Heterologous expression in COS7 cells shows that the latter induces a splicing defect through the activation of a cryptic splice site 4 bases upstream of the genuine splice site. The patients presented with a clinical picture typical for congenital achromatopsia and there was no significant difference in the phenotype of subjects with either CNGA3 or CNGB3 mutations based on standard ophthalmological examination. However, we assume residual cone function in a subject homozygous for the Phe547Leu mutation in CNGA3 based on prior detailed psychophysical testing (i.e., dark adaptation and spectral luminosity).</AbstractText>Mutations in CNGA3 and CNGB3 account for achromatopsia in Hungarian patients including known mutations and a few new CNGB3 mutations. While standard ophthalmological examination revealed a phenotype of complete achromatopsia, we show that thorough psychophysical testing can help to identify subjects with some minute cone function.</AbstractText>
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2,336,272 |
A novel logistic model based on clinicopathological features predicts microsatellite instability in colorectal carcinomas.
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High-frequency microsatellite instability has been reported to be associated with good prognosis in colorectal adenocarcinoma. However, methods to assess microsatellite instability (MIN) are based on genetic assays and are not ideally suited to most histopathology laboratories. The aim of the present study was to develop a model for prediction of MIN status in colorectal cancer based on phenotypic characteristics. Clinicopathological features of a cohort of 204 patients with primary colon cancer were retrospectively reviewed following predetermined criteria. Genetic assessment of MIN status was performed on DNA extracted from sections of formalin-fixed, paraffin-embedded specimens by testing a panel of 11 microsatellite markers. Logistic regression analysis generated a mathematical tool capable of identifying colorectal tumors displaying MIN status with a sensitivity of 77.8% and a specificity of 96.8%. Features associated with instability included the proximal location of the lesions, occurrence of solid and/or mucinous differentiation, absence of cribriform structures, presence of peritumoral Crohn-like reaction, expansive growth pattern, high Ki67 proliferative index, and p53-negative phenotype. This approach predicts microsatellite instability in colorectal carcinoma with an overall assigned accuracy of 95.1% and a negative predictive value of 97.8%. Implementation of this tool to routine histopathological studies could improve the management of patients with colorectal cancer, especially those presenting with stage II and III of the disease. It will also assist in identifying a subset of patients likely to benefit from adjuvant chemotherapy.
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2,336,273 |
ACOG Committee Opinion. Number 325, December 2005. Update on carrier screening for cystic fibrosis.
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In 2001, the American College of Obstetricians and Gynecologists and the American College of Medical Genetics introduced guidelines for prenatal and preconception carrier screening for cystic fibrosis. The American College of Obstetricians and Gynecologists has updated current guidelines for cystic fibrosis screening practices among obstetrician-gynecologists.
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2,336,274 |
BRCA-mutation-associated fallopian tube carcinoma: a distinct clinical phenotype?
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To compare clinical and histologic features between fallopian tube cancers in women with germline BRCA mutations and sporadic cases.</AbstractText>Twenty-eight patients with fallopian tube cancer had BRCA mutation testing using multiplex polymerase chain reaction and protein truncation testing. Histologic slides were reviewed by 2 pathologists, and immunohistochemical staining for p53, ki67, estrogen receptor, and progesterone receptor was performed on carcinomas and dysplastic and benign tubal epithelia.</AbstractText>Twelve of 28 (43%) women had BRCA mutations: 11 BRCA1, 1 BRCA2. Excluding 4 cases found at prophylactic surgery, the median age of diagnosis of BRCA mutation carriers was 57 years compared with 65 years among sporadic cases (P = .09). Patients with BRCA-associated fallopian tube cancer had a median survival time of 68 months compared with 37 months when compared with sporadic cases (P = .14). Both groups had predominantly advanced stage, high grade, serous fallopian tube cancers. No patient had exclusively proximal disease. Occult fallopian tube cancer diagnosed at prophylactic surgery in BRCA mutation carriers was exclusively distal. "Skip" areas of high-grade dysplasia were only seen in 2 patients, both of whom were BRCA mutation carriers. There were no differences in the immunohistochemical staining for p53, ki67, estrogen receptor or progesterone receptor in carcinomas and dysplastic or benign epithelia of patients with or without BRCA mutations. Overexpression of p53 was commonly seen in fallopian tube cancers and dysplastic epithelium, but rarely noted in benign epithelium.</AbstractText>Fallopian tube cancer is part of the BRCA mutation phenotype and seems to share many clinical features with sporadic fallopian tube cancers, including no exclusively proximal disease. The presentation of BRCA-associated fallopian tube cancers may, however, occur at a younger age and have an improved survival.</AbstractText>
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2,336,275 |
The heritability of preterm delivery.
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To study the heritability of preterm delivery.</AbstractText>Women who delivered a singleton infant at less than 36 weeks of gestation were asked about their family history. Twenty-eight families were identified in which the proband had at least five first- or second-degree relatives with preterm delivery. An extensive genealogy database (GenDB) was constructed using more than 9,000 genealogy sources in the public domain (records before 1929). GenDB documents the relationships between more than 17.5 million ancestors and 3.5 million descendants of approximately 10,000 individuals who moved to Utah in the mid 1800s. This database was searched for the names, birth dates, and birthplaces of the four grandparents for each of the 28 probands. Pairwise coefficients of kinship were determined for the 93 preterm delivery grandparents identified, and for sets of 100 individuals born in the 1920s who were randomly selected from the population database.</AbstractText>Probands had a mean of 3.3 grandparents included in this database. The average coefficient of kinship for controls was 1.5 x 10(6) (standard deviation = 0.6 x 10(6)). This measure agrees with previous calculations for the Utah population. The coefficient of kinship for familial preterm delivery grandparents was more than 50 standard deviations higher (3.4 x 10(5) [P < .001]).</AbstractText>This study confirms the familial nature of preterm delivery. On average, gravidae randomly selected from our population are 23rd degree relatives, while these preterm delivery probands are eighth-degree relatives. A genome-wide scan using these affected families is underway.</AbstractText>
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2,336,276 |
Fetal cells in a transcervical cell sample collected at 5 weeks of gestation.
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Transcervical cell (TCC) sampling is being investigated as a promising method for obtaining fetal cells for prenatal genetic diagnosis. The present case report describes the identification of fetal cells by both fluorescent in situ hybridisation (FISH) and quantitative fluorescent polymerase chain reaction (QF-PCR) analyses in a TCC sample collected by intrauterine lavage at 5 + 0 weeks. This finding underscores the possible relevance of TCC sampling for extremely early prenatal genetic diagnosis.
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2,336,277 |
Reducing pain with genetic amniocentesis-A randomized trial of subfreezing versus room temperature needles.
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To determine whether pain associated with second trimester genetic amniocentesis is decreased by using subfreezing rather than room temperature needles.</AbstractText>Subjects were randomized to a -14 degrees C or room temperature (20-22 degrees C) 22-gauge spinal needle. Patients, blinded to allocation, recorded anticipated and actual pain before and after the procedure, respectively, using a 0-10 visual analog scale with 0 = no pain and 10 = excruciating pain.</AbstractText>Thirty-three subjects were randomized to room temperature and 29 subjects to subfreezing needles. Anticipated pain was similar in room temperature, 5.1 +/- 1.7, and subfreezing groups, 4.9 +/- 2.0, respectively (p = 0.6). Actual pain was also similar in the room temperature, 3.6 +/- 2.0, and subfreezing groups, 2.8 +/- 2.0, respectively (p = 0.14). Similar numbers of subjects in the room temperature and subfreezing groups reported less actual pain (20 vs. 18), greater actual pain (4 vs. 4) or no difference in pain (9 vs. 5) than anticipated (p = 0.6).</AbstractText>A subfreezing 22-gauge spinal needle does not decrease perceived pain associated with second trimester genetic amniocentesis.</AbstractText>
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2,336,278 |
Identification of significant periodic genes in microarray gene expression data.
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One frequent application of microarray experiments is in the study of monitoring gene activities in a cell during cell cycle or cell division. A new challenge for analyzing the microarray experiments is to identify genes that are statistically significantly periodically expressed during the cell cycle. Such a challenge occurs due to the large number of genes that are simultaneously measured, a moderate to small number of measurements per gene taken at different time points, and high levels of non-normal random noises inherited in the data.</AbstractText>Based on two statistical hypothesis testing methods for identifying periodic time series, a novel statistical inference approach, the C&G procedure, is proposed to effectively screen out statistically significantly periodically expressed genes. The approach is then applied to yeast and bacterial cell cycle gene expression data sets, as well as to human fibroblasts and human cancer cell line data sets, and significantly periodically expressed genes are successfully identified.</AbstractText>The C&G procedure proposed is an effective method for identifying statistically significant periodic genes in microarray time series gene expression data.</AbstractText>
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2,336,279 |
Are amniotic fluid C-reactive protein and glucose levels, and white blood cell counts at the time of genetic amniocentesis related with preterm delivery?
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To compare women with spontaneous preterm delivery before 37 weeks and women who delivered at term with respect to amniotic fluid C-reactive protein (CRP), glucose levels, and white blood cell counts at the time of genetic amniocentesis.</AbstractText>The study was conducted on 216 pregnant women who underwent genetic amniocentesis between the 15th and 18th weeks of gestation at Baskent University Obstetrics and Gynecology Department. All patients were followed until delivery for the occurrence of pregnancy complication. Indications for amniocentesis included abnormal triple test results showing increased risk for Down's syndrome, advanced maternal age and sonographic findings indicative for chromosomal abnormalities. The samples were carried immediately to the laboratory for cytogenetic and biochemical examination. Women with spontaneous preterm delivery before 37 weeks (n = 20) and those who delivered at term (n = 196) were compared with respect to some maternal and infant characteristics, amniotic fluid C-reactive protein, glucose levels, and amniotic fluid white blood cell counts.</AbstractText>During the study period 244 patients underwent amniocentesis. A chromosomal abnormality was present in 11 patients. 1 patient had a spontaneous pregnancy loss within 3 weeks after the procedure and 16 patients were delivered for fetal or maternal indications (preeclampsia, fetal growth restriction, placenta previa). The remaining 216 women were included in the study and investigated for the risk of preterm delivery. The prevalence of spontaneous preterm delivery before 37 weeks was 9.3% (20/216). There were no significant differences between the preterm delivery and the term delivery groups with respect to C-reactive protein levels and white blood cell counts. Mean amniotic glucose levels were significantly lower in the preterm delivery group (P<0.05). Amniotic fluid glucose levels of < or = 46 mg/dL had a sensitivity of 100% and NPV of 100%.</AbstractText>Amniotic fluid glucose levels at the time of genetic amniocentesis are lower in women with spontaneous preterm delivery before 37 weeks compared to those who delivered at term. Amniotic fluid glucose levels of < or = 46 mg/dL at the time of genetic amniocentesis may be more sensitive, cheaper and have higher negative predictive value than C-reactive protein levels and white blood cell counts for the prediction of patients in spontaneous preterm labor. The greatest benefit of amniotic fluid glucose testing might be when the physician judges the patient to be at low risk for preterm delivery.</AbstractText>
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2,336,280 |
Isolation and Characterization of Burkholderia gladioli from Orchids in Hawaii.
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Bacterial diseases of orchids continue to be serious problems. Bacterial strains were isolated from orchid plants exhibiting disease symptoms in Hawaii. Small to large leaf spots with or without water-soaking or soft rots were observed on various orchid genera, including Dendrobium, Oncidium, and Miltonia spp. and hybrids. Bacteria isolated and cultured from the lesions were tentatively identified using analytical profile index (API) strips and standard physiological and biochemical tests, and confirmed by species-specific polymerase chain reaction and sequencing of the 16S rRNA gene. The variation in pathogenic, morphological, cultural, and molecular characteristics of the orchid isolates also was evaluated. In our studies, a gramnegative, aerobic, rod-shaped bacterium that produced pale yellow, opaque, round colonies with entire margins on nutrient broth yeast extract agar (NBY) was isolated consistently from diseased orchid plants. On yeast dextrose calcium carbonate agar, the isolates produced brownishyellow, nonmucoid colonies, with the majority of the strains secreting a diffusible yellow or tan pigment into the media. The bacterium was identified as Burkholderia gladioli. Molecular analysis indicated very little diversity in the 16S rDNA gene. Testing B. gladioli isolates using media containing copper or streptomycin indicated varying levels of resistance (copper resistant = Cu<sup>r</sup>; streptomycin resistant, Sm<sup>r</sup>), with approximately 75% of the strains resistant to copper and 94% of the strains resistant to streptomycin. The minimum inhibitory concentration (MIC) of cupric sulfate among Cu<sup>r</sup> strains ranged from 50 to 1,000 μg/ml and the MIC of streptomycin was 50 to 100 μg/ml for all Sm<sup>r</sup> B. gladioli strains tested. Field and laboratory data suggest the frequent use of these chemicals in nurseries may have inadvertently resulted in the development of copper and streptomycin resistance in B. gladioli from orchids.
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2,336,281 |
Emerging technologies for identifying superior dairy cows in New Zealand.
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The performance of animals is determined by the interaction of their genes with environmental circumstances. Accordingly, animals exhibiting superior performance are not necessarily the animals with the best genes nor are they the best choice of parents. Statistical analyses of production records for repeated traits, e.g. lactation yields and reproductive performance, show that part of the variation in performance among animals in the same herd and year is due to genetic differences, and the remainder is due to so-called residual or environmental factors that are not passed on to offspring. These within-herd environmental factors can be partitioned into a component that affects performance throughout an animal's lifetime, and a part that is unique to each observation. The process of animal evaluation from pedigree and performance records partitions the superiority of each cow into these three components. Reliable assessment of the genetic merit of bulls has required progeny testing, and for cows has required observation of their own individual performance. Selection on the genetic or breeding value component has systematically improved animal performance over recent decades, but has been limited by the age at which assessments of genetic merit are available. Emerging molecular technologies can read DNA sequences or measure RNA expression and have allowed the identification of a number of chromosome regions, and a few specific genes in those regions, that influence economic performance. This information allows better characterisation of the relationships between animals and more accurate predictions of genetic merit in bulls without progeny information and in cows that have yet to produce their own performance record. At some stage, enough genes responsible for variation in performance will be identified to allow faster genetic progress through selection of animals at young ages and therefore more rapid turnover of the generations. Mechanisms that modify gene expression have been identified and these may ultimately allow animals to be selected at an early age for lifetime productivity, accounting for processes that modify gene expression and lead to differences in performance that are not reflected by DNA sequence information. This review describes the status of these emerging technologies and their likely role in the improvement of dairy cattle.
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2,336,282 |
Breeding dairy cows for the future in New Zealand.
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A brief history of the breeding of dairy cattle in New Zealand is provided. Dairy farming in New Zealand is unique compared with the majority of dairy systems in the developed world. New Zealand has a dependence on grass-based diets and a strict requirement for a 365-day calving interval. Four main areas are discussed: future traits to evaluate, advances in genetic evaluation technologies, impacts of crossbreeding, and future progeny testing schemes. These areas are not independent, e.g. the trend of increasing numbers of crossbred cattle in the national herd will have major impacts on the design of breeding schemes. It is foreseeable that in the future there will be improvements in the national breeding goal to better reflect on-farm profitability, and in the definition of traits and methods of data capture within the national breeding goal. Methods of selection and genetic evaluation that are currently feasible for a small population will become feasible for large populations as computing power improves. Genetic improvement of cows in New Zealand will continue to be a critical component of the increased economic efficiency achieved on dairy farms in this country.
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2,336,283 |
Clinical presentation and penetrance of pheochromocytoma/paraganglioma syndromes.
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The identification of mutations in genes encoding peptides of succinate dehydrogenase (SDH) in pheochromocytoma/paraganglioma syndromes has necessitated clear elucidation of genotype-phenotype associations.</AbstractText>Our objective was to determine genotype-phenotype associations in a cohort of patients with pheochromocytoma/paraganglioma syndromes and succinate dehydrogenase subunit B (SDHB) or subunit D (SDHD) mutations.</AbstractText><AbstractText Label="DESIGN, SETTING, AND PARTICIPANTS" NlmCategory="METHODS">The International SDH Consortium studied 116 individuals (83 affected and 33 clinically unaffected) from 62 families with pheochromocytoma/paraganglioma syndromes and SDHB or SDHD mutations. Clinical data were collected between August 2003 and September 2004 from tertiary referral centers in Australia, France, New Zealand, Germany, United States, Canada, and Scotland.</AbstractText>Data were collected on patients with pheochromocytomas and/or paragangliomas with respect to onset of disease, diagnosis, genetic testing, surgery, pathology, and disease progression. Clinical features were evaluated for evidence of genotype-phenotype associations, and penetrance was determined.</AbstractText>SDHB mutation carriers were more likely than SDHD mutation carriers to develop extraadrenal pheochromocytomas and malignant disease, whereas SDHD mutation carriers had a greater propensity to develop head and neck paragangliomas and multiple tumors. For the index cases, there was no difference between 43 SDHB and 19 SDHD mutation carriers in the time to first diagnosis (34 vs. 28 yr, respectively; P = 0.3). However, when all mutation carriers were included (n = 112), the estimated age-related penetrance was different for SDHB vs. SDHD mutation carriers (P = 0.008).</AbstractText>For clinical follow-up, features of SDHB mutation-associated disease include a later age of onset, extraadrenal (abdominal or thoracic) tumors, and a higher rate of malignancy. In contrast, SDHD mutation carriers, in addition to head and neck paragangliomas, should be observed for multifocal tumors, infrequent malignancy, and the possibility of extraadrenal pheochromocytoma.</AbstractText>
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2,336,284 |
Nerve growth factor expression by PLG-mediated lipofection.
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Biomaterials capable of efficient gene delivery provide a fundamental tool for basic and applied research models, such as promoting neural regeneration. We developed a system for the encapsulation and sustained release of plasmid DNA complexed with a cationic lipid and investigated their efficacy using in vitro models of neurite outgrowth. Sustained lipoplex release was obtained for up to 50 days, with rates controlled by the fabrication conditions. Released lipoplexes retained their activity, transfecting 48.2+/-8.3% of NIH3T3 cells with luciferase activity of 3.97x10(7)RLU/mg. Expression of nerve growth factor (NGF) was employed in two models of neurite outgrowth: PC12 and primary dorsal root ganglia (DRG) co-culture. Polymer-mediated lipofection of PC12 produced bioactive NGF, eliciting robust neurite outgrowth. An EGFP/NGF dual-expression vector identified transfected cells (GFP-positive) while neurite outgrowth verified NGF secretion. A co-culture model examined the ability of NGF secretion by an accessory cell population to stimulate DRG neurite outgrowth. Polymer-mediated transfection of HEK293T with an NGF-encoding plasmid induced outgrowth by DRG neurons. This system could be fabricated as implants or nerve guidance conduits to support cellular and tissue regeneration. Combining this physical support with the ability to locally express neurotrophic factors will potentiate regeneration in nerve injury and disease models.
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2,336,285 |
p16INK4a and p14ARF methylation as a potential biomarker for human bladder cancer.
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Promoter hypermethylation is one of the putative mechanisms underlying the inactivation of negative cell-cycle regulators. We examined whether the methylation status of p16(INK4a) and p14(ARF), genes located upstream of the RB and p53 pathway, is a useful biomarker for the staging, clinical outcome, and prognosis of human bladder cancer. Using methylation-specific PCR (MSP), we examined the methylation status of p16(INK4a) and p14(ARF) in 64 samples from 45 bladder cancer patients (34 males, 11 females). In 19 patients with recurrent bladder cancer, we examined paired tissue samples from their primary and recurrent tumors. The methylation status of representative samples was confirmed by bisulfite DNA sequencing analysis. The median follow-up duration was 34.3 months (range 27.0-100.1 months). The methylation rate for p16(INK4a) and p14(ARF) was 17.8% and 31.1%, respectively, in the 45 patients. The incidence of p16(INKa) and p14(ARF) methylation was significantly higher in patients with invasive (>or=pT2) than superficial bladder cancer (pT1) (p=0.006 and p=0.001, respectively). No MSP bands for p16(INK4a) and p14(ARF) were detected in the 8 patients with superficial, non-recurrent tumors. In 19 patients with tumor recurrence, the p16(INK4a) and p14(ARF) methylation status of the primary and recurrent tumors was similar. Of the 22 patients who had undergone cystectomy, 8 (36.4%) manifested p16(INKa) methylation; p16(INK4a) was not methylated in 23 patients without cystectomy (p=0.002). Kaplan-Meier analysis revealed that patients with p14(ARF) methylation had a significantly poorer prognosis than those without (p=0.029). This is the first study indicating that MSP analysis of p16(INK4a) and p14(ARF) genes is a useful biomarker for the pathological stage, clinical outcome, and prognosis of patients with bladder cancer.
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2,336,286 |
[The significance of elbow dysplasia (ED) for breeding in Bernese Mountain Dogs in Germany].
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Results from the elbow dysplasia screening program in Bernese Mountain Dogs of Germany were analysed in respect to its relevance for genetic evaluation and breeding. In total 2677 gradings were used. The grading was performed radiographically according to the recommendations of the International Elbow Working Group (IEWG). 75.8% of the dogs were free from visible dysplastic signs, 10.8%, 6.8% and 5.5% were classified to be of Grade 1, 2 and 3, respectively. 1.1% were classified as a borderline case between ED-free and Grade 1. A slight reduction of ED could be observed over years. Males had a 3.1 higher rate of dysplasia than females. Treating ED as a numerical trait, coded proportional to the severity of clinical relevant signs, gave a heritability estimation of 0.188 and a maternal effect of 0.07. From different mating combinations it was found, that ED average was higher in the progeny if one mate was affected but there was no increase in the prevalence with increasing grade of ED in the affected mates. About 10% more affected dogs could be observed, if one mate is affected. Heritability for dichotomic coding the trait was found to be 0.20. From these results can be suggested, that the differentiation in various grades of ED to describe the clinical relevance for the specific dog is helpfull, however, from a breeders point of view, dogs with ED should be treated equally for genetic evaluation.
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2,336,287 |
NOD2/CARD15 gene polymorphisms in idiopathic pulmonary fibrosis.
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Micro-organisms, behaving in a non-infectious fashion, may be among the exogenous factor(s) believed to trigger idiopathic pulmonary fibrosis (IPF). One possible strategy to identify an individual's susceptibility to such microbial triggers, which are likely to be ubiquitous, is to investigate the molecular processes involved in their recognition. NOD2/CARD15 is a specific pattern recognition receptor protein, whose genetic variants have been previously associated with susceptibility to Crohn's disease.</AbstractText>The aim of this work was to determine the frequencies of the three major NOD2/CARD 15 gene mutations (R702W, G908R and 1007fsinC) in a series of 76 subjects affected by IPF, and to compare them with those found in three groups of controls: a group with sarcoidosis (a disorder in which an involvement of the NOD2/CARD15 gene has already been investigated and rejected in different ethnic groups; 67 subjects) and two groups of healthy subjects (218 and 208 subjects, respectively), matched for gender, age, and ethnicity.</AbstractText>We found no differences in frequencies of NOD2/CARD15 gene polymorphisms among the four groups investigated.</AbstractText>We conclude that the NOD2/CARD15 gene is not likely to be involved in susceptibility to IPF in Italians.</AbstractText>
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2,336,288 |
From single cell gene-based diagnostics to diagnostic genomics: current applications and future perspectives.
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Molecular diagnostics is a branch of clinical diagnostics that uses primarily DNA or RNA as a biomarker for clinical testing. It combines various gene-based amplification technologies with highly sophisticated detection methods for the clinical diagnosis of a vast variety of diseases including infectious diseases, cancer, and inherited diseases. The principal application of gene-based amplification technology is to identify pathogen or gene-specific nucleic acid sequences that are used as surrogate markers for the identification of either infectious pathogens or alteration of disease-related genes. There are generally three classes of gene-based amplification technologies: target-based, e.g., PCR; probe-based, e.g., LCR; and signal-based, e.g., bDNA. Real-time detection of PCR allows us to quantify amplified amplicons with a broad dynamic range and it offers a unique way to detect genetic mutations. Other technologies such as immuno-PCR and bio-barcode assay (BCA) combine different amplification tactics offering extreme detection sensitivity ranging from femtogram (10(-15)) to zeptogram (10(-21)). Even though quantum dots technology is in its infant stage, its potential to further increase diagnostic sensitivity and specificity is likely beyond our current imagination. Future diagnostic technologies include the use of genomic and proteomic approaches especially in pure cell types or even in the single-cell level, which open up endless new possibilities for gene-based diagnostics at entirely different levels. In this article, principles of various current gene-based amplification and detection technologies along with their clinical applications are discussed. New technologies that could potentially be used in future gene-based diagnosis are introduced.
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2,336,289 |
Screening for HFE and iron overload.
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Type 1 hereditary hemochromatosis is a common disorder of iron overload occurring in individuals homozygous for the C282Y HFE gene mutation. It can be a progressive and fatal condition. Early detection and phlebotomy prior to the onset of cirrhosis can reduce morbidity and normalize life expectancy. It is readily identified through biochemical testing for iron overload using serum transferrin saturation and genetic testing for C282Y homozygosity. General population screening has been waived in preference to targeting high-risk groups such as first-degree relatives of affected individuals and those with clinical features suggestive of iron loading. This screening strategy is likely to continue until uncertainties regarding the natural history of the disease, age-related penetrance, and management of asymptomatic individuals are clarified. Potential ethical, legal, and psychosocial issues arising through application of genetic screening programs also must be resolved prior to implementation of general population screening programs.
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2,336,290 |
Genetic testing in pheochromocytoma or functional paraganglioma.
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To assess the yield and the clinical value of systematic screening of susceptibility genes for patients with pheochromocytoma (pheo) or functional paraganglioma (pgl).</AbstractText>We studied 314 patients with a pheo or a functional pgl, including 56 patients having a family history and/or a syndromic presentation and 258 patients having an apparently sporadic presentation. Clinical data and blood samples were collected, and all five major pheo-pgl susceptibility genes (RET, VHL, SDHB, SDHD, and SDHC) were screened. Neurofibromatosis type 1 was diagnosed from phenotypic criteria.</AbstractText>We have identified 86 patients (27.4%) with a hereditary tumor. Among the 56 patients with a family/syndromic presentation, 13 have had neurofibromatosis type 1, and germline mutations on the VHL, RET, SDHD, and SDHB genes were present in 16, 15, nine, and three patients, respectively. Among the 258 patients with an apparently sporadic presentation, 30 (11.6%) had a germline mutation (18 patients on SDHB, nine patients on VHL, two patients on SDHD, and one patient on RET). Mutation carriers were younger and more frequently had bilateral or extra-adrenal tumors. In patients with an SDHB mutation, the tumors were larger, more frequently extra-adrenal, and malignant.</AbstractText>Genetic testing oriented by family/sporadic presentation should be proposed to all patients with pheo or functional pgl. We suggest an algorithm that would allow the confirmation of suspected inherited disease as well as the diagnosis of unexpected inherited disease.</AbstractText>
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2,336,291 |
Creutzfeldt-Jakob disease (CJD) with a mutation at codon 148 of prion protein gene: relationship with sporadic CJD.
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Creutzfeldt-Jakob disease (CJD), the most common human prion disease, includes sporadic (s) and familial (f) forms. Regardless of etiology, both forms are thought to share the pathogenic mechanism whereby the cellular prion protein (PrP(C)) converts into its pathogenic isoform (PrP(Sc)). While PrP(C) conversion is thought to be random in sCJD, conversion in fCJD is facilitated by the congenital presence of mutated PrP. Differences in PrP genotype (PRNP) and in conversion circumstances lead to PrP(Sc) with distinct characteristics that elicit different disease phenotypes. Here, we describe a case of fCJD with a substitution of histidine (H) for arginine (R) at codon 148 (R148H) and heterozygosity of the methionine/valine (M/V) polymorphic codon 129, with the 129M allele coupled with the mutation. The disease phenotype and all major characteristics of PrP(Sc) of fCJD(R148H) were virtually indistinguishable from those of sCJDMV2, which has features different from those of any other sCJD. Therefore, despite the differences in etiology, PRNP, and conversion process, the two forms of PrP(Sc) had similar characteristics. Furthermore, comparison of fCJD(R148H) with a recently reported case carrying R148H and homozygosity at codon 129 suggests that codon 129 coupled with the mutation as well as that located on the normal allele can modify major phenotypic and PrP(Sc) features of fCJD(R148H).
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2,336,292 |
Participation of autophagy in storage of lysosomes in neurons from mouse models of neuronal ceroid-lipofuscinoses (Batten disease).
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In cathepsin D-deficient (CD-/-) and cathepsins B and L double-deficient (CB-/-CL-/-) mice, abnormal vacuolar structures accumulate in neurons of the brains. Many of these structures resemble autophagosomes in which part of the cytoplasm is retained but their precise nature and biogenesis remain unknown. We show here how autophagy contributes to the accumulation of these vacuolar structures in neurons deficient in cathepsin D or both cathepsins B and L by demonstrating an increased conversion of the molecular form of MAP1-LC3 for autophagosome formation from the cytosolic form (LC3-I) to the membrane-bound form (LC3-II). In both CD-/- and CB-/-CL-/- mouse brains, the membrane-bound LC3-II form predominated whereas MAP1-LC3 signals accumulated in granular structures located in neuronal perikarya and axons of these mutant brains and were localized to the membranes of autophagosomes, evidenced by immunofluorescence microscopy and freeze-fracture-replica immunoelectron microscopy. Moreover, as in CD-/- neurons, autofluorescence and subunit c of mitochondrial ATP synthase accumulated in CB-/-CL-/- neurons. This suggests that not only CD-/- but also CB-/-CL-/- mice could be useful animal models for neuronal ceroid-lipofuscinosis/Batten disease. These data strongly argue for a major involvement of autophagy in the pathogenesis of Batten disease/lysosomal storage disorders.
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2,336,293 |
Saccadic eye movement task identifies cognitive deficits in children with schizophrenia, but not in unaffected child relatives.
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The delayed oculomotor response (DOR) task requires response inhibition followed by movement of gaze towards a known spatial location without a current stimulus. Abnormalities in response inhibition and in the spatial accuracy of the eye movement are found in individuals with schizophrenia and in many of their relatives, supporting the use of these saccadic abnormalities as endophenotypes in genetic studies. It is unknown whether school-age children, either with psychosis or as relatives of a schizophrenic proband, can be included.</AbstractText>One hundred eighty-seven children, ages 5.8-16.0 years - 45 children with childhood-onset schizophrenia, 64 children with a first-degree relative with schizophrenia, and 84 typically developing children - completed DOR tasks with 1 and 3 second delays.</AbstractText>Children with childhood-onset schizophrenia demonstrated impaired response inhibition and impaired spatial accuracy compared to both relatives and typicals; however, relatives and typicals did not differ from each other.</AbstractText>Children with childhood-onset schizophrenia have saccadic abnormalities similar to those found in adults with schizophrenia, supporting the continuity of executive function deficits in childhood-onset with adolescent and adult-onset schizophrenia. However, saccadic tasks are not sensitive to genetic risk in non-psychotic children and 6-15-year-old children should not be included in genetic studies utilizing this endophenotype.</AbstractText>
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2,336,294 |
HLA and eye disease: a synopsis.
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Human leukocyte antigen (HLA) gene products have been implicated in the pathogenesis of an increasing number of eye diseases, mainly inflammatory in nature. This perspective reviews the current hypotheses for why HLA polymorphisms are associated with specific eye diseases. Statistical problems in studies involving HLA associations are discussed, and possible solutions outlined. The relevance of HLA testing in routine ophthalmic practice, its practical and cost implications is also assessed.
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2,336,295 |
Coincidence of atopy and its profile (monosensitization/polysensitization) between sibling pairs.
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Results of epidemiologic studies have shown that childhood atopy is probably a hereditary disorder. In the atopic population, some individuals are sensitized to only 1 class of allergens (monosensitized), whereas others are sensitized to more than 1 class of allergens (polysensitized).</AbstractText>To investigate whether atopy and its profile (monosensitization/polysensitization) tend to coincide in sibling pairs.</AbstractText>We evaluated sensitization to 5 classes of aeroallergens (house dust mites, animal danders, pollens, molds, and cockroach) using skin prick testing in 564 children with symptoms suggestive of allergic diseases (index children) and their paired siblings.</AbstractText>The frequency of sibling atopy was highest (56.8%) for polysensitized index children (n=222), intermediate (45.4%) for monosensitized index children (n=196), and lowest (30.8%) for nonsensitized index children (n=146). The proportion of polysensitization among atopic siblings was significantly higher for polysensitized (47.6%) than for monosensitized (32.6%) index children. Polysensitized index children were found to more frequently have polysensitized siblings (27.0%) than were monosensitized index children (14.8%), with an odds ratio of 2.13 (95% confidence interval, 1.30-3.49), whereas the likelihood of having a monosensitized sibling was similar for monosensitized and polysensitized index children.</AbstractText>These data suggest a coincidence of atopy and its profile in terms of monosensitization and polysensitization in sibling pairs, although the relative importance of genetic and environmental influences requires further study.</AbstractText>
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2,336,296 |
[Treatment of Familial Adenomatous Polyposis and family screening].
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To reduce the mortality associated to Familial Adenomatous Polyposis (FAP), screening of close relatives of patients with the disease is crucial.</AbstractText>To analyze the results of the surgical treatment of patients with FAP, and to evaluate the family screening.</AbstractText>Clinical records of patients operated in our institution since 1977, were reviewed analyzing surgical and pathological results, and follow up. In their family members, we evaluated and analyzed the performance of screening tests, former surgeries, history of disease-related cancer and mortality, all due to FAP.</AbstractText>Between January 1977 and August 2002, 15 patients were operated on. Of these, only 33% consulted on the setting of a familial screening. A proctocolectomy and terminal ileostomy was performed in 27% of patients; 20% had a proctocolectomy and ileal pouch, and 53% underwent a total colectomy with ileo-rectal anastomosis. Morbidity and mortality were 7% and 0%, respectively. Twenty percent had a colorectal cancer. During a median of 68 months follow-up, the disease-related survival was 92%; no cancer of the rectal stump was detected. Of the 122 family members identified, only 33% with clear indication of screening underwent a colonoscopy. Twenty-nine percent had a confirmed FAP and were operated: in 61% of them a colorectal cancer was found, and 91% of these died.</AbstractText>The results of the surgical treatment of FAP are satisfactory. Nevertheless, family screening should be improved to reduce the high rates of mortality revealed in the study of other family members.</AbstractText>
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2,336,297 |
[Prophylactic thyroidectomy in children and young people with hereditary medullary thyroid carcinoma: a Chilean experience].
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With the availability of the RET proto-oncogene genetic testing, it is possible to perform prophylactic total thyroidectomy among carriers of RET mutation.</AbstractText>To evaluate the histological findings and the effects of the prophylactic total thyroidectomy in first-degree relatives of Chilean patients with multiple endocrine neoplasia type 2 (MEN 2) based on the Ret proto-oncogene analysis.</AbstractText>Nineteen patients belonging to 11 MEN 2 families underwent total thyroidectomy. Of these, 16 either with C cell hyperplasia (CCH) or microscopic medullary thyroid carcinoma (MTC) were selected for the final analysis.</AbstractText>The age at the moment of thyroidectomy ranged from 3 to 24 years (median 9.5). The most common mutation was located in codon 634 (69%) followed by codon 620 (25%). Histopathology revealed MTC in 13 patients (81%, youngest 3 years, oldest ones 19 and 24 years) and CCH in 3. A significant correlation was observed between basal preoperative serum calcitonin/tumor size (r = 0.53, P < 0.05) and age/tumor size (r = 0.56, P < 0.03), but not between basal preoperative serum calcitonin and age. Stimulated preoperative calcitonin levels were confounding and not useful for differentiating CCH from MTC. None of patients in whom cervical dissection was done (9/16) presented lymph node metastases, including the oldest ones. All patients but the older ones were biochemically cured after a mean of 5 years of follow-up.</AbstractText>Prophylactic total thyroidectomy should be done early in life because there is an age-dependent progression from HCC to MTC. MTC often precedes biochemical detection of the disease.</AbstractText>
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2,336,298 |
Prenatal diagnosis of beta-thalassemia in the West Bank and Gaza.
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This study focuses on the genetic aspect of beta-thalassemia among 88 at risk couples from the West Bank and Gaza, and the attitude of these couples toward prenatal diagnosis and its outcome as a preventive method.</AbstractText>We tested 130 prenatal samples for beta-thalassemia during the period from January 1999 to July 2005. We performed prenatal diagnosis in these cases using the amplification refractory mutation system, as well as beta-globin gene sequencing as a conformational method. We drew a chorionic villus sample (CVS) for 1st trimester pregnant women and amniotic fluid (AF) for those in the 2nd trimester depending on the stage the pregnant woman contacted our lab.</AbstractText>The DNA analysis of 130 prenatal samples revealed 25 (19.2%) cases of beta-thalassemia major and 67 (51.5%) cases of beta-thalassemia carriers, while the remaining 38 (29.2%) were normal. The 25 affected fetuses were aborted according to the wishes of the parents. In the tested 88 couples, 14 mutations of beta-thalassemia were identified. These mutations and their frequencies were: IVSI-110 (22.2%), IVSI-6 (13.6%), Cd37 (12%), IVSI-I (9.7%), IVSII-1 (6.2%), Cd39 (9%), Cd6 (sickle cell mutation) (8.5%), Cd5 (8%), Cd8/9 (2.8%), Cd106/107 (2.8%), -30 promoter (1.1%), -88 promoter (1.1%), IVSI (-1) (2.3%) and IVSI-5 (0.6%). We found that in 77.3% of the couples, both the mother and the father carry the same type of mutation while 22.7% of them carry different mutations. We found 77.9% consanguinity among the couples</AbstractText>We found very good acceptability for prenatal diagnosis in beta-thalassemia afflicted families. All couples with affected fetuses opted for abortion. The spectrum of mutations in the tested couples revealed several similarities to neighboring countries with -88 promoter mutation reported for the first time in our region.</AbstractText>
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2,336,299 |
Breast cancer in an MSH2 gene mutation carrier.
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A 49-year-old woman presented with breast cancer. She is a member of a family with the hereditary nonpolyposis colorectal cancer syndrome for which a 2-base pair deletion in exon 11 of the mismatch repair gene MSH2 (c1705_1706 delGA) had been identified. Breast cancer is rare in the hereditary nonpolyposis colorectal cancer syndrome. Microsatellite analysis of the tumor showed a microsatellite instable pattern for markers Bat25, Bat26, and Bat40, and no changes for markers D2S123 and D5S346, a so-called microsatellite instability-high pattern. Immunohistochemical staining for the mismatch repair enzymes MSH2 and MSH6 was negative, whereas the tumor cells were positive for MLH1, a pattern suggestive for biallelic MSH2 gene inactivation. We tested the tumor for loss of heterozygosity of the MSH2 gene and found loss of the wild-type MSH2 allele. These data strongly suggest that the MSH2 gene was involved in the development of this breast tumor.
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