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At least 217 records · Page 12Linked to original sources
PubMed2006

AB-QTL analysis in spring barley: II. Detection of favourable exotic alleles for agronomic traits introgressed from wild barley (H. vulgare ssp. spontaneum).

The objective of the present study was to identify favourable exotic Quantitative Trait Locus (QTL) alleles for the improvement of agronomic traits in the BC2DH population S42 derived from a cross between the spring barley cultivar Scarlett and the wild barley accession ISR42-8 (Hordeum vulgare ssp. spontaneum). QTLs were detected as a marker main effect and/or a marker x environment interaction effect (M x E) in a three-factorial ANOVA. Using field data of up to eight environments and genotype data of 98 SSR loci, we detected 86 QTLs for nine agronomic traits. At 60 QTLs the marker main effect, at five QTLs the M x E interaction effect, and at 21 QTLs both the effects were significant. The majority of the M x E interaction effects were due to changes in magnitude and are, therefore, still valuable for marker assisted selection across environments. The exotic alleles improved performance in 31 (36.0%) of 86 QTLs detected for agronomic traits. The exotic alleles had favourable effects on all analysed quantitative traits. These favourable exotic alleles were detected, in particular on the short arm of chromosome 2H and the long arm of chromosome 4H. The exotic allele on 4HL, for example, improved yield by 7.1%. Furthermore, the presence of the exotic allele on 2HS increased the yield component traits ears per m2 and thousand grain weight by 16.4% and 3.2%, respectively. The present study, hence, demonstrated that wild barley does harbour valuable alleles, which can enrich the genetic basis of cultivated barley and improve quantitative agronomic traits.

Alleles↗
PubMed2005

GENEHUNTER versus SimWalk2 in the context of an extended kindred and a qualitative trait locus.

GENEHUNTER and SimWalk2 are among the most commonly used software for parametric multipoint linkage analysis. In the context of extended kindred analysis, GENEHUNTER has a limitation in terms of the number of individuals it can handle. One solution is to manually split the kindred into smaller pedigrees. SimWalk2 can handle a much larger number of individuals. However, its major drawback is the time it takes to process the data when compared to GENEHUNTER. Aside from the limitations of each program, when studying extended kindreds researchers are typically confronted with missing data. In this work we used simulated genotype data based on the structure of a real extended pedigree in order to compare the results obtained through GENEHUNTER and SimWalk2, evaluate the effect of discarding individuals and splitting the kindred on the logarithm of odds (lod) score, and to assess how missing data affect the performance of each program. Our results show that (1) for pedigrees of a moderate size, GENEHUNTER and SimWalk2 produce nearly the same results; (2) when using GENEHUNTER, either splitting the kindred into smaller sub-pedigrees or discarding individuals has an adverse effect when compared to the results obtained when using SimWalk2 with the whole pedigree; and (3) the performance of both programs is qualitatively similar in the missing data scenario. These conclusions are based on the sample distributions of the lod score values and of the estimates of the recombination fraction.

Computer Simulation↗
PubMed2004

Molecular epidemiology of hepatitis B and C virus infections in Asia.

The present paper provides a review of the current literature regarding the molecular-based epidemiology of hepatitis B virus (HBV) and hepatitis C virus (HCV), which are very important viruses underlying the etiology of blood-borne infectious diseases worldwide. Particularly, both HBV and HCV are widespread on the Asian continent and are associated with acute and chronic liver diseases, including hepatocellular carcinoma. HBV has been classified into genotypes A through G and shown to have a distinct geographic distribution. In Asia, genotypes B and C of HBV prevail, and genotype C has been shown to cause more serious liver disease than genotype B. High prevalence of HBV mutants with various forms, such as the pre-S mutant, basal core promoter mutant, YMDD motif mutant and vaccine escape mutant, were seen in Asia and these were found to be related to the severity of liver disease and sensitivity to therapy. HCV has also been classified into multiple genotypes and associated with geographic distribution. HCV genotype 1 is less sensitive to interferon therapy and may be associated with the presence of more serious liver disease than the other genotypes. Data on the relation among the HBV/HCV genotypes, their pathogenicity in chronic liver diseases including hepatocellular carcinoma and their effect on therapy are awaited with great interest, especially in Asia, which is an endemic region of blood-borne hepatitis viruses.

Asia↗
PubMed2005

KORA-gen--resource for population genetics, controls and a broad spectrum of disease phenotypes.

KORA-gen is a resource for genetic epidemiological research, based on the KORA platform (Cooperative Health Research in the Region of Augsburg). Biosamples and phenotypic characteristics as well as environmental parameters of 18,000 adults from Augsburg and the surrounding counties are available. The age range of the participants was 25 to 74 years of recruitment and is 30 to 90 years in 2005. KORA-gen can be used by external partners. Interested parties can inform themselves interactively via internet about the available data and the rules of access. The genotypic data base is a common resource of all partners.

Adult↗
PubMed2006

Statistical analysis for haplotype-based matched case-control studies.

Using unphased genotype data, we studied statistical inference for association between a disease and a haplotype in matched case-control studies. Statistical inference for haplotype data is complicated due to ambiguity of genotype phases. An estimating equation-based method is developed for estimating odds ratios and testing disease-haplotype association. The method potentially can also be applied to testing haplotype-environment interaction. Simulation studies show that the proposed method has good performance. The performance of the method in the presence of departures from Hardy-Weinberg equilibrium is also studied.

Biometry↗
PubMed2007

Large-scale population-based study shows no association between common polymorphisms of the TGFB1 gene and BMD in women.

UNLABELLED: The TGFB1 gene is a strong functional candidate for regulating genetic susceptibility to osteoporosis. We studied five common polymorphisms of TGFB1 in relation to osteoporosis-related phenotypes in a population-based cohort of 2975 British women, but found no significant association with bone mass, bone loss, bone markers, or fracture. INTRODUCTION: The gene encoding TGFB1 is a strong functional candidate for genetic susceptibility to osteoporosis. Several polymorphisms have been identified in TGFB1, and previous work has suggested that allelic variants of TGFB1 may regulate BMD and susceptibility to osteoporotic fracture. MATERIALS AND METHODS: We studied the relationship between common polymorphisms of TGFB1 and several osteoporosis-related phenotypes including BMD at the lumbar spine and femoral neck, measured by DXA; bone loss over a 6-year period; biochemical markers of bone turnover (urinary free deoxypyridinoline and free pyridinoline/creatinine ratio and serum N-terminal propeptide of type 1 collagen), and fractures in a population-based study of 2975 women from the United Kingdom. Participants were genotyped for single nucleotide polymorphisms (SNPs) in the TGFB1 promoter (G-800A; rs1800468; C-509T; rs1800469), exon 1 (T29C; rs1982073 and G74C; rs1982073); and exon 5 (C788T; rs1800471) on PCR-generated fragments of genomic DNA. Haplotypes were constructed from genotype data using the PHASE software program, and genotypes and haplotypes were related to the phenotypes of interest using general linear model ANOVA, with correction for confounding factors including age, height, weight, menopausal status, hormone replacement therapy (HRT) use, physical activity score, and dietary calcium intake. RESULTS: The polymorphisms were in strong linkage disequilibrium, and four common haplotypes accounted for >95% of alleles at the locus. There was no association between individual SNPs and BMD, bone loss, or biochemical markers of bone turnover. Haplotype analysis showed a nominally significant association with femoral neck BMD (p = 0.042) and with incident osteoporotic fracture (p = 0.013), but these were not significant after correcting for multiple testing. CONCLUSIONS: Common polymorphic variants of the TGFB1 gene did not influence BMD or bone loss in this population.

Absorptiometry, Photon↗
PubMed1998

Evaluation of the ovine callipyge locus: II. Genotypic effects on growth, slaughter, and carcass traits.

A resource flock of 362 F2 lambs provided phenotypic and genotypic data to estimate effects of callipyge (CLPG) genotypes on growth, slaughter, and carcass traits. Lambs were serially slaughtered in six groups at 3-wk intervals starting at 23 wk of age to allow comparisons at different end points. Probabilities of CLPG genotypes were calculated at a position 86 cM from the most centromeric marker of chromosome 18. A contrast of CLPG genotypic effects, based on the paternal polar overdominance model, was used to evaluate callipyge and normal phenotypes. Relationships of traits with slaughter age, carcass weight, or 12th-rib fat depth for callipyge and normal phenotypic groups were estimated by regression. Callipyge and normal lambs did not differ for growth traits measured from birth to slaughter. Callipyge lambs produced 55.9% of live weight as chilled carcass weight compared with 51.7% for normal lambs at the same mean live weight of 48.32 kg. Lighter pelt, kidney-pelvic fat, and liver weights contributed to this advantage of callipyge lambs for dressing percentage (P < .001). Estimated accretion rates of carcass protein at the mean slaughter age were 12.5 and 10.2 g/d for callipyge and normal carcasses, respectively. Corresponding values for carcass fat were 35.2 and 42.1 g/d. Compositional differences in favor of callipyge carcasses were detected at constant values of slaughter age, carcass weight, and 12th-rib fat depth. Callipyge carcasses had 2.56 kg greater fat-free lean and 1.39 kg less fat than normal carcasses at the same mean age of 214.9 d (P < .001). The majority of these differences were established before the initial group was slaughtered and were maintained as age increased. Callipyge carcasses consisted of 24.3% fat and 71.3% fat-free lean, compared with 31.5 and 64.0% for normal carcasses at 25.6 kg of carcass weight. When evaluated at .49 cm of 12th-rib fat depth, callipyge lambs were 15.4 d older and produced 4.1 kg heavier carcasses with 4.3% less fat (P < .001). Effects of CLPG genotypic groups on carcass composition were greater than virtually all reported breed substitution effects. Use of the CLPG mutant allele in structured mating systems can dramatically increase production of lean lamb.

Age Factors↗
PubMed2005

Quantitative trait loci mapping for meat quality and muscle fiber traits in a Japanese wild boar x Large White intercross.

Three generations of a swine family produced by crossing a Japanese wild boar and three Large White female pigs were used to map QTL for various production traits. Here we report the results of QTL analyses for skeletal muscle fiber composition and meat quality traits based on phenotypic data of 353 F(2) animals and genotypic data of 225 markers covering almost the entire pig genome for all of the F(2) animals as well as their F(1) parents and F(0) grandparents. The results of a genome scan using least squares regression interval mapping provided evidence that QTL (<1% genome-wise error rate) affected the proportion of the number of type IIA muscle fibers on SSC2, the number of type IIB on SSC14, the relative area (RA) of type I on SSCX, the RA of type IIA on SSC6, the RA of type IIB on SSC6 and SSC14, the Minolta a* values of loin on SSC4 and SSC6, the Minolta b* value of loin on SSC15, and the hematin content of the LM on SSC6. Quantitative trait loci (<5% genome-wise error rate) were found for the number of type I on SSC1, SSC14, and SSCX, for the number of type IIA on SSC14, for the number of type IIB on SSC2, for the RA of type IIA on SSC2, for the Minolta b* value of loin on SSC3, for the pH of loin on SSC15, and for the i.m. fat content on SSC15. Twenty-four QTL were detected for 11 traits at the 5% genome-wise level. Some traits were associated with each other, so the 24 QTL were located on 11 genomic regions. In five QTL located on SSC2, SSC6, and SSC14, each wild boar allele had the effect of increasing types I and IIA muscle fibers and decreasing type IIB muscle fibers. These effects are expected to improve meat quality.

Animals↗
PubMed2006

Collaborative analysis of alpha-synuclein gene promoter variability and Parkinson disease.

CONTEXT: Identification and replication of susceptibility genes for Parkinson disease at the population level have been hampered by small studies with potential biases. Alpha-synuclein (SNCA) has been one of the most promising susceptibility genes, but large-scale studies have been lacking. OBJECTIVE: To determine whether allele-length variability in the dinucleotide repeat sequence (REP1) of the SNCA gene promoter is associated with Parkinson disease susceptibility, whether SNCA promoter haplotypes are associated with Parkinson disease, and whether REP1 variability modifies age at onset. DESIGN, SETTING, AND PARTICIPANTS: We performed a collaborative analysis of individual-level data on SNCA REP1 and flanking markers in patients with Parkinson disease and controls. Study site recruitment, data collection, and analyses were performed between April 5, 2004, and December 31, 2005. Eighteen participating sites of a global genetics consortium provided clinical data. Genotyping was performed for SNCA REP1, -770, and -116 markers at individual sites; however, each site also provided 20 DNA samples for regenotyping centrally. MAIN OUTCOME MEASURES: Measures included estimations of Hardy-Weinberg equilibrium in controls; a test of heterogeneity; analyses for association of single variants or haplotypes; and survival analyses for age at onset. RESULTS: Of the 18 sites, 11 met stringent criteria for concordance with Hardy-Weinberg equilibrium and low genotyping error rate. These 11 sites provided complete data for 2692 cases and 2652 controls. There was no heterogeneity across studies (P>.60). The SNCA REP1 alleles differed in frequency for cases and controls (P<.001). Genotypes defined by the 263 base-pair allele were associated with Parkinson disease (odds ratio, 1.43; 95% confidence interval, 1.22-1.69; P<.001 for trend). Multilocus haplotypes differed in frequency for cases and controls (global score statistic, P<.001). Two-loci haplotypes were associated with Parkinson disease only when they included REP1 as one of the loci. However, genotypes defined by REP1 alleles did not modify age at onset (P = .55). CONCLUSION: This large-scale collaborative analysis demonstrates that SNCA REP1 allele-length variability is associated with an increased risk of Parkinson disease.

Adult↗
PubMed2006

Data and animal management software for large-scale phenotype screening.

The mouse N-ethyl-N-nitrosourea (ENU) mutagenesis program at the Genomics Institute of the Novartis Research Foundation (GNF) uses MouseTRACS to analyze phenotype screens and manage animal husbandry. MouseTRACS is a Web-based laboratory informatics system that electronically records and organizes mouse colony operations, prints cage cards, tracks inventory, manages requests, and reports Institutional Animal Care and Use Committee (IACUC) protocol usage. For efficient phenotype screening, MouseTRACS identifies mutants, visualizes data, and maps mutations. It displays and integrates phenotype and genotype data using likelihood odds ratio (LOD) plots of genetic linkage between genotype and phenotype. More detailed mapping intervals show individual single nucleotide polymorphism (SNP) markers in the context of phenotype. In addition, dynamically generated pedigree diagrams and inventory reports linked to screening results summarize the inheritance pattern and the degree of penetrance. MouseTRACS displays screening data in tables and uses standard charts such as box plots, histograms, scatter plots, and customized charts looking at clustered mice or cross pedigree comparisons. In summary, MouseTRACS enables the efficient screening, analysis, and management of thousands of animals to find mutant mice and identify novel gene functions. MouseTRACS is available under an open source license at http://www.mousetracs.sourceforge.net.

Animals↗
PubMed1996

Effect of polymorphism in the insulin gene region on IDDM susceptibility and insulin secretion. The Childhood Diabetes in Finland (DiMe) Study Group.

In addition to the major genetic determinants of insulin-dependent diabetes mellitus (IDDM) in the major histocompatibility complex (MHC) on chromosome 6, there are also minor genetic risk markers, e.g. in the insulin gene region on chromosome 11p15.5 (IDDM2). We studied the significance of the-23 HphI polymorphism in the insulin gene region (-23 HphI INS) in the Finnish population in combination with HLA genotyping data. The frequency of the-23 HphI INS +/+ genotype was higher in diabetic subjects with a low risk HLA DQB1 genotype than in control subjects (P = 0.05). Diabetic children in multiple-case families also had a higher frequency of the INS risk genotype than the controls (P < 0.05), and this difference was independent of the HLA genotype. Furthermore, we studied siblings positive for islet cell antibodies (ICAs) and/or insulin autoantibodies (IAAs) to evaluate the impact of the-23 HphI INS +/+ genotype on their beta-cell function assessed by sequential intravenous glucose tolerance tests and on their progression to IDDM. When analysing siblings with a low-risk HLA DQB1 genotype, those with the-23 HphI INS +/+ genotype had lower first phase insulin responses (P < 0.02) on several occasions than the remaining sibling. Six siblings (26.1%) in the former group progressed to clinical disease during the observation period, whereas none in the latter group presented with IDDM (P = 0.01). These observations suggest that the-23 HphI INS +/+ polymorphism is associated with an increased risk of IDDM in subjects without predisposing genes in the MHC region. The enhanced susceptibility may be related to a reduced insulin secretory capacity.

Adolescent↗
PubMed2003

PCR detection of virulence genes in Yersinia enterocolitica and Yersinia pseudotuberculosis and investigation of virulence gene distribution.

PCR-based assays were developed for the detection of plasmid- and chromosome-borne virulence genes in Yersinia enterocolitica and Yersinia pseudotuberculosis, to investigate the distribution of these genes in isolates from various sources. The results of PCR genotyping, based on 5 virulence-associated genes of 140 strains of Y. enterocolitica, were compared to phenotypic tests, such as biotyping and serotyping, and to virulence plasmid-associated properties such as calcium-dependent growth at 37 degrees C and Congo red uptake. The specificity of the PCR results was validated by hybridization. Genotyping data correlated well with biotype data, and most biotypes resulted in (nearly) homogeneous genotypes for the chromosomal virulence genes (ystA, ystB, and ail); however, plasmid-borne genes (yadA and virF) were detected with variable efficiency, due to heterogeneity within the bacterial population for the presence of the virulence plasmid. Of the virulence genes, only ystB was present in biotype 1A; however, within this biotype, pathogenic and apathogenic isolates could not be distinguished based on the detection of virulence genes. Forty Y. pseudotuberculosis isolates were tested by PCR for the presence of inv, yadA, and lcrF. All isolates were inv positive, and 88% of the isolates contained the virulence plasmid genes yadA and lcrF. In conclusion, this study shows that genotyping of Yersinia spp., based on both chromosome- and plasmid-borne virulence genes, is feasible and informative and can provide a rapid and reliable genotypic characterization of field isolates.

Animals↗
PubMed2004

Molecular genotyping of a large, multicentric collection of tubercle bacilli indicates geographical partitioning of strain variation and has implications for global epidemiology of Mycobacterium tuberculosis.

Tuberculosis continues to be a major killer disease, despite an all-out effort launched against it in the postgenomic era. We describe here the population structure of Mycobacterium tuberculosis strains, as revealed by a chromosome-wide scan of fluorescent amplified fragment length polymorphisms (FAFLPs), for more than 1,100 independent isolates from 11 different countries. The bacterial strains were genotyped based on a total of 136 +/- 1 different FAFLP markers at the genome sequence interface, with details on IS6110 profiles, drug resistance status, clinicopathological observations, and host status integrated into the analysis process. The strains were found to cluster with possible geographic affinities, including the parameters of host species type, IS6110 profile, and drug susceptibility status. Of the five most commonly amplified fragment sets (or amplitypes), type A predominated in strains of mixed origin, deposited in The Netherlands; type B was exclusively observed for Indian isolates; type C was found mainly in strains from Peru and Australia; and types D and E predominated in European strains from France and Italy. The amplitypes were independent of certain large sequence polymorphisms representing two important deletions, TbD1 and Rd9. It appears that M. tuberculosis has a high genomic diversity with a possible geographic evolution. This may have occurred due to specific genomic deletions and synonymous substitutions selected rigorously against host defenses and environmental stresses on an evolutionary timescale. The genotypic data reported here are additionally significant for genotype-phenotype correlations and for determining whether pathogen diversity is a reflection f the host population diversity.

DNA Transposable Elements↗
PubMed2006

Effect of NAT1 and NAT2 genetic polymorphisms on colorectal cancer risk associated with exposure to tobacco smoke and meat consumption.

N-Acetyltransferases 1 and 2 (NAT1 and NAT2), both being highly polymorphic, are involved in the metabolism of aromatic and heterocyclic aromatic amines present in cigarette smoke and red meat cooked by high-temperature cooking techniques. We investigated the effect of differences in acetylation capacity, determined by NAT1 and NAT2 genotypes, on colorectal cancer risk associated with exposure to tobacco smoke or red meat consumption. In this population-based case-control study in Germany, 505 patients with incident colorectal cancer and 604 age- and sex-matched control individuals with genotyping data and detailed risk factor information were included. Genotyping of NAT1 and NAT2 genetic polymorphisms was done using a fluorescence-based melting curve analysis method. The association between genotypes, environmental exposures, and colorectal cancer risk was estimated using multivariate logistic regression. Colorectal cancer risk associated with active smoking was elevated after accumulation of 30(+) pack-years of smoking [odds ratio (OR), 1.4; 95% confidence interval (95% CI), 0.9-2.2] but not significantly modified by either NAT1 or NAT2 genotype. Exposure to environmental tobacco smoke was associated with an increased risk for colorectal cancer only among NAT2 fast acetylators (OR, 2.6; 95% CI, 1.1-5.9 for exposure in childhood and adulthood). Frequent consumption of red meat significantly increased colorectal cancer risk for the group comprising all NAT2 fast acetylators or carriers of the NAT1*10 allele (OR, 2.6; 95% CI, 1.1-6.1) but not among those with "slow" NAT1 and NAT2 genotypes. Our findings indicate that NAT1 and NAT2 genotypes may contribute jointly to individual susceptibility and that heterocyclic aromatic amines may play an important role in colorectal cancer associated with red meat and possibly also exposure to environmental tobacco smoke.

Acetylation↗
PubMed2005

Haplotype sharing correlation of alcohol dependence on chromosomes 1-6 in 93 nuclear families.

Haplotype data contain signatures of ancestral alleles and increased information for mapping genes associated with complex traits. The motivation of this paper is to test the feasibility of a recently developed haplotype reconstruction algorithm and to perform haplotype-sharing correlation (HSC) analysis in nuclear families using data provided by the Genetic Analysis Workshop 14 and the Collaborative Study of the Genetics of Alcoholism. As an exemplary analysis, haplotype data on chromosomes 1-6 were reconstructed from genotype data in 93 nuclear families by minimizing both the recombinants in within-family haplotypes and the tree distance in between-family haplotypes. HSC analysis was performed using the best set of reconstructed haplotypes, and chromosome-wide significance was evaluated using a permutation procedure. Three markers were found to have significant haplotype associations with DSM-IV alcohol dependence that exceeded the 0.05 level of chromosome-wide significance: marker rs895941 at 36.7 cM on chromosome 3 (p = 0.03), marker rs1631833 at 109.1 cM on chromosome 4 (p = 0.008), and marker rs953887 at 74.2 cM on chromosome 6 (p = 0.02). These results indicated the usefulness of HSC analysis and provided further evidence on chromosome regions associated with alcohol dependence.

Alcoholism↗
PubMed2025

vcfgl: a flexible genotype likelihood simulator for VCF/BCF files.

MOTIVATION: Accurate quantification of genotype uncertainty is pivotal in ensuring the reliability of genetic inferences drawn from NGS data. Genotype uncertainty is typically modeled using Genotype Likelihoods (GLs), which can help propagate measures of statistical uncertainty in base calls to downstream analyses. However, the effects of errors and biases in the estimation of GLs, introduced by biases in the original base call quality scores or the discretization of quality scores, as well as the choice of the GL model, remain under-explored. RESULTS: We present vcfgl, a versatile tool for simulating genotype likelihoods associated with simulated read data. It offers a framework for researchers to simulate and investigate the uncertainties and biases associated with the quantification of uncertainty, thereby facilitating a deeper understanding of their impacts on downstream analytical methods. Through simulations, we demonstrate the utility of vcfgl in benchmarking GL-based methods. The program can calculate GLs using various widely used genotype likelihood models and can simulate the errors in quality scores using a Beta distribution. It is compatible with modern simulators such as msprime and SLiM, and can output data in pileup, Variant Call Format (VCF)/BCF, and genomic VCF file formats, supporting a wide range of applications. The vcfgl program is freely available as an efficient and user-friendly software written in C/C++. AVAILABILITY AND IMPLEMENTATION: vcfgl is freely available at https://github.com/isinaltinkaya/vcfgl.

Software↗
PubMed2005

CYP2C9 and CYP2C19 genetic polymorphisms: frequencies in the south Indian population.

The aim of the study was to establish the frequencies of CYP2C9*1, *2, *3 and CYP2C19*1, *2 and *3 in the south Indian population and to compare them with the inter-racial distribution of the CYP2C9 and CYP2C19 genetic polymorphisms. Genotyping analyses of CYP2C9 and CYP2C19 were conducted in unrelated, healthy volunteers from the three south Indian states of Andhra Pradesh, Karnataka and Kerala, by the polymerase chain reaction-restriction fragment-length polymorphism (PCR-RFLP). The allele frequencies of the populations of these three states were then pooled with our previous genotyping data of Tamilians (also in south India), to arrive at the distribution of CYP2C9 and CYP2C19 alleles in the south Indian population. Frequencies of CYP2C9 and CYP2C19 alleles and genotypes among various populations were compared using the two-tailed Fisher's exact test. The frequencies of CYP2C9*1, *2 and *3 in the south Indian population were 0.88 (95% CI 0.85-0.91), 0.04 (95% CI 0.02-0.06) and 0.08 (95% CI 0.06-0.11), respectively. The frequencies of CYP2C9 genotypes *1/*1, *1/*2, *1/*3, *2/*2, *2/*3 and *3/*3 were 0.78 (95% CI 0.74-0.82), 0.05 (95% CI 0.03-0.07), 0.15 (95% CI 0.12-0.18), 0.01 (95% CI 0.0-0.02), 0.01 (95% CI 0.0-0.02) and 0.0, respectively. CYP2C19*1, *2 and *3 frequencies were 0.64 (95% CI 0.60-0.68), 0.35 (95% CI 0.31-0.39) and 0.01 (95% CI 0.0-0.03), respectively. As a result of a significant heterogeneity, the data on CYP2C19 genotype frequencies were not pooled. The frequency of CYP2C9*2 mutant alleles in south Indians was higher than in Chinese and Caucasians, while CYP2C9*3 was similar to Caucasians. CYP2C19*2 was higher than in other major populations reported so far. The relatively high CYP2C19 poor-metabolizer genotype frequency of 12.6% indicates that over 28 million south Indians are poor metabolizers of CYP2C19 substrates.

Adult↗
PubMed1993

Genetic structure of Trypanosoma cruzi populations from Argentina estimated from enzyme polymorphism.

Isolates of Trypanosoma cruzi from human patients, domestic and sylvatic animals and vector insects were obtained in different areas of Argentina. Electrophoretic patterns of enzymes from extracts of 95 isolates were analysed. On the basis of zymograms providing information on 10 loci, 12 zymodemes are described according to their genotypes. Data presented show fixed heterozygosity, absence of segregation of genotypes, significant departures from Hardy-Weinberg equilibrium, and over-represented genotypes. This evidence supports the hypothesis that sexual reproduction is very restricted or absent in this parasite. The proportion of polymorphic loci is 80%. The expected mean heterozygosity per locus (He) is 0.43, while the observed value (Ho) is 0.24. Differences between these values may be explained by accepting a basically clonal structure for T. cruzi. The data matrix of 12 zymodemes using 28 characters was analysed using a Wagner parsimony algorithm. Two equally most parsimonious unrooted trees were generated; both have 39 steps. The results show clusters clearly separated according to the geographical origin of the stocks. There are some indications of some correlations between genetic composition of the parasite and the clinical picture of the infection in human patients.

Animals↗