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PubMed2005

Allele and genotype frequencies of CYP2C9 in a Korean population.

AIMS: To determine the frequencies of the variant alleles and the genotypes of CYP2C9 in a Korean population. METHODS: Three hundred and fifty-eight healthy Korean subjects were studied. CYP2C9 alleles were detected by polymerase chain reaction-restriction fragment length polymorphism assays and direct sequencing assays. RESULTS: The allele frequencies were 0.934 for CYP2C9*1, 0.060 for CYP2C9*3 and 0.006 for CYP2C9*13. The CYP2C9*2,*4,*5 and *11 alleles were not detected. The frequencies of the CYP2C9*1/*1, *1/*3 and *1/*13 genotypes were 0.869, 0.120 and 0.011, respectively. CONCLUSION: The frequency of the CYP2C9*3 allele in the Korean population studied was significantly higher than reported elsewhere, and a novel allele, CYP2C9*13, was found at a frequency of 0.006 (95% confidence interval 0, 0.012). Only three genotypes of CYP2C9, CYP2C9*1/*1,*1/*3 and *1/*13 were observed in this Korean population.

Adult↗
PubMed2000

Analysis of genotype frequencies and interlocus association for the PM, DQA1, and D1S80 loci in four populations.

Allele frequencies of the LDLR, HBGG, GYPA, D7S8, GC, DQA1, and D1S80 loci are presented and genotypes are analyzed for each of four ethnic groups: African Americans (n = 200), US Caucasians (n = 200), US Hispanics (n = 200), and Japanese (n = 89). Hardy-Weinberg genotypic proportions were observed in all but two of the 28 population-locus tests undertaken. Those two instances are attributable to type I statistical error. Gametic equilibrium among loci is an assumption invoked for application of the product rule to utilize the discriminatory power from two or more loci simultaneously. Two statistical methods, a genotype matching statistic and log-linear modeling, were used to evaluate gametic disequilibrium. The match statistic, comparing observed to expected likelihood of genotypic identity for seven loci among pairs of individuals within the database, revealed only one statistically significant deviation among 20 tests. As expected, the probability of match was generally lowest in the test on all ethnic groups combined, indicating that allele frequencies differ among ethnic groups for some of the loci. This was confirmed with the statistic theta to measure ethnic stratification, in which about 0.10 of the genetic variation is apportioned among the four ethnic groups for four of the structural loci (LDLR, HBGG, GC, and DQA1), while for GYPA, D7S8, and D1S80, variation is more uniformly distributed among ethnic groups. Log-linear modeling was also applied to the five PM loci. The most parsimonious log-linear model included only three higher order terms: the two-way interactions of three of the PM loci with ethnic group. These three instances (LDLR, HBGG, and GC) indicated differences in allele frequencies between ethnic groups. No two or higher way interaction (disequilibrium) was observed among loci. In summary, the assumptions of Hardy-Weinberg and gametic equilibrium that facilitate the use of the five PM loci, DQA1 and D1S80 in forensic applications are consistent with the allele and genotype frequencies observed in these populations.

Asian People↗
PubMed2003

Allele and genotype frequency of CYP2C9 in Tamilnadu population.

OBJECTIVES: To identify the frequency of CYP2C9*1, *2 and *3 alleles and the genotype of CYP2C9 gene in the Tamilian population. METHODS: The study was conducted on 135 unrelated healthy human volunteers. DNA was extracted from the peripheral leukocytes samples and was analyzed using the polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) protocol. The PCR products were digested with AvaII, KpnI or NsiI restriction enzymes. The digested products were separated using 8% polyacrylamide gel and stained by ethidium bromide. Genotyping of the subjects was done based on DNA fragment size. RESULTS: The frequencies of CYP2C9*1, *2 and *3 alleles in the Tamilian population were 0.907, 0.026 and 0.067, respectively. The distribution of CYP2C9*1/*1, *1/*2, *1/*3 and *2/*3 genotypes were 0.823, 0.044, 0.126 and 0.007, respectively. CONCLUSION: CYP2C9*3 is the most frequent mutant allele found in the Tamilian population. The distribution of this mutant allele in the Tamilian population was found to be lesser than in Caucasians but higher than in Chinese.

Adult↗
PubMed2004

Allele and genotype frequencies of CYP2C9, CYP2C19 and CYP2D6 in an Italian population.

The polymorphic cytochrome P450 isoenzymes (CYPs) 2C9, 2C19 and 2D6 metabolise many important drugs, as well as other xenobiotics. Their polymorphism gives rise to important interindividual and interethnic variability in the metabolism and disposition of several therapeutic agents and may cause differences in the clinical response to these drugs. In this study, we determined the genotype profile of a random Italian population in order to compare the CYP2C9, CYP2C19 and CYP2D6 allele frequencies among Italians with previous findings in other Caucasian populations. Frequencies for the major CYP2C9, CYP2C19 and CYP2D6 mutated alleles and genotypes have been evaluated in 360 unrelated healthy Italian volunteers (210 males and 150 females, aged 19-52 years). Genotyping has been carried out on peripheral leukocytes DNA by molecular biology techniques (PCR, RFLP, long-PCR). CYP2C9, CYP2C19 and CYP2D6 allele and genotype frequencies resulted in equilibrium with the Hardy-Weinberg equation. One hundred and fourteen subjects (31.7%) carried one and 23 subjects (6.4%) carried two CYP2C9 mutated alleles. Sixty-eight (18.9%) volunteers were found to be heterozygous and six (1.7%) homozygous for the CYP2C19*2, while no CYP2C19*3 was detected in the evaluated population. Volunteers could be divided into four CYP2D6 genotypes groups: 192 subjects (53.3%) with no mutated alleles (homozygous extensive metabolisers, EM), 126 (35.0%) with one mutated allele (heterozygous EM), 12 (3.4%) with two mutated alleles (poor metabolisers, PM) and 30 (8.3%) with extracopies of a functional gene (ultrarapid metabolisers, UM). Frequencies of both CYP2C9 and CYP2C19 allelic variants, as well as CYP2D6 detrimental alleles, in Italian subjects were similar to those of other Caucasian populations. Conversely, the prevalence of CYP2D6 gene duplication among Italians resulted very high, confirming the higher frequency of CYP2D6 UM in the Mediterranean area compared to Northern Europe.

Adult↗
PubMed2001

Mamu-DQA1 allele and genotype frequencies in a randomly sampled breeding colony of rhesus macaques (Macaca mulatta).

We studied the allelic and genotypic distribution of the major histocompatibility class-II locus DQA1 observed in a random sample of Indian rhesus macaques (Macaca mulatta) from a major breeding facility in the United States. The DNA was isolated from whole blood samples collected between 1991 and 1994 from 65 Indian rhesus monkeys. Polymerase chain reaction-restriction fragment length polymorphism analysis (PCR-RFLP), which involves use of specific amplification of DQA1 exon 2 and subsequent restriction digestion of the 242-base pair fragment, was used to genotype the animals for the 20 known macaque (Mamu)-DQA1 alleles. Frequencies for four alleles (DQA1*240x, *2502, *2503 and *0102) differed significantly from those reported in a smaller sample of rhesus macaques from the German Primate Center. The modest genetic survey of Mamu-DQA1 genotypes presented here will be particularly useful in designing epidemiologic studies that investigate associations between immunogenetic background and disease susceptibility in macaque models of human disease.

Alleles↗
PubMed1999

Allele and genotype frequencies for the STR locus D18S51 in a western German population.

Genetic marker typing based on DNA amplification by the polymerase chain reaction (PCR) increasingly is being employed in forensic casework and for paternity testing. Allele frequencies were determined using PCR for 102 unrelated Germans (Rhine area) for the locus D18S51. Twelve alleles were observed, with frequencies ranging from 0.005 (allele 11) to 0.191 (allele 14). The observed heterozygosity was 0.867, and the power of discrimination was 0.968. There was no deviation from expectations under Hardy-Weinberg assumptions (P = 0.451).

Gene Frequency↗
PubMed1997

Italian population allele and genotype frequencies for the AmpliType PM and the HLA-DQ-alpha loci.

The distribution of six genetic loci analyzed by PCR using the commercial AmpliType PM (PolyMarker) kit (Perkin Elmer, Norwalk, CT) was evaluated in 200 unrelated Italian individuals. The examined loci included: Group-specific component (Gc) (1), D7S8 (2), hemoglobin G gammaglobin (HBGG) (3), glycophorin A (GYPA) (4), low density lipoprotein receptor (LDLR) (5), and HLA DQ-alpha (6). The AmpliType PM Kit analysis is based on the reverse dot blot format and the results are interpreted by reading the pattern of blue dots which determine the alleles present at each locus. The population data collected allow the implementation of AmpliType PM into routine casework.

Alleles↗
PubMed2001

Allele and genotype frequencies of polymorphic cytochromes P4502D6, 2C19 and 2E1 in aborigines from western Australia.

The polymorphisms of the important xenobiotic metabolizing enzymes CYP2D6, CYP2C19 and CYP2E1 have been studied extensively in a large number of populations and show significant heterogeneity in the frequency of different alleles/genotypes and in the prevalence of the extensive and poor metabolizer phenotypes. Understanding of inter-ethnic differences in genotypes is important in prediction of either beneficial or adverse effects from therapeutic agents and other xenobiotics. Since no data were available for Australian Aborigines, we investigated the frequencies of alleles and genotypes for CYP2D6, CYP2C19 and CYP2E1 in a population living in the far north of Western Australia. Because of its geographical isolation, this population can serve as a model to study the impact of evolutionary forces on the distribution of different alleles for xenobiotic metabolizing enzymes. Twelve CYP2D6 alleles were analysed. The wild-type allele *1 was the most frequent (85.81%) and the non-functional alleles (*4, * 5, * 16) had an overall frequency of less than 10%. Only one subject (0.4%) was a poor metabolizer for CYP2D6 because of the genotype *5/*5. For CYP2C19, the frequencies of the *1 (wild-type) and the non-functional (*2 and *3) alleles were 50.2%, 35.5% and 14.3%, respectively. The combined CYP2C19 genotypes (*2/*2, *2/*3 or *3/*3) correspond to a predicted frequency of 25.6% for the CYP2C19 poor metabolizer phenotype. For CYP2EI, only one subject had the rare c2 allele giving an overall allele frequency of 0.2%. For CYP2D6 and CYP2C19, allele frequencies and predicted phenotypes differed significantly from those for Caucasians but were similar to those for Orientals indicating a close relationship to East Asian populations. Differences between Aborigines and Orientals in allele frequencies for CYP2D6* 10 and CYP2E1 c2 may have arisen through natural selection, or genetic drift, respectively.

Alleles↗
PubMed2005

Differential cytokine genotype frequencies among Canadian Aboriginal and Caucasian populations.

Genetic diversity related to the human immune response is a key factor in individual and population survival throughout human history. Population diversity in disease susceptibility and resistance have been identified and linked to differences in cytokine mRNA and protein expression levels. Polymorphisms in the regulatory regions of cytokine genes can influence gene transcription levels and they have been associated with susceptibility to, and/or severity of, autoimmune disorders such as rheumatoid arthritis, meningococcus and sepsis. It is reported here that in two study populations, Canadian Aboriginal individuals have a higher frequency of cytokine single-nucleotide polymorphisms favouring a low production of TNFalpha, IFNgamma and IL-10 and high production of IL-6 as compared to a Caucasian population. We postulate that the evolution of this unique cytokine genotype profile may be linked to the Aboriginal adaptation to selection pressures related to an environment in which helminthic, parasitic and fungal infections predominated.

Cytokines↗
PubMed2002

Increased genotype frequency of N-acetyltransferase 2 slow acetylation in patients with rheumatoid arthritis.

OBJECTIVES: Acetylation polymorphism can alter therapeutic responses and toxicity to certain xenobiotics and may also be a factor that influences a patient's susceptibility to certain diseases. We investigated whether patients with rheumatoid arthritis (RA) differed from healthy individuals with regard to genotype of the polymorphic enzyme N-acetyltransferase 2 (NAT2). METHODS: NAT2 polymorphism was compared in 118 healthy subjects and 82 patients with RA. NAT2 alleles (*4, *5, *6, and *7) were determined by polymerase chain reaction-restriction fragment length polymorphism methods with deoxyribonucleic acid extracted from peripheral blood. RESULTS: A statistically significant increase in the proportion of homozygous slow acetylators with 2 mutated alleles (84.1%) was found among patients with RA in comparison with healthy subjects (52.5%; P <.0001). The risk of development of RA was almost 5-fold greater in slow acetylators than in fast acetylators (odds ratio, 4.79; 95% confidence interval, 2.28-10.21). There was no correlation between NAT2 polymorphism and presence of rheumatoid factor, extra-articular manifestations, and age at first occurrence of disease symptoms. CONCLUSIONS: NAT2 slow acetylation genotype may be a risk factor of individual susceptibility to RA.

Acetylation↗
PubMed1999

PrP genotype frequencies of the most dominant sheep breed in a country free from scrapie.

Polymorphisms within the prion protein (PrP) gene are associated with scrapie susceptibility. We analysed the PrP genes of 140 Romney Marsh sheep, the dominant breed in New Zealand, a country free from scrapie. We found PrP alleles that are associated with a high susceptibility to scrapie. Sheep with these PrP genotypes would probably succumb to scrapie when born and raised in a scrapie endemic environment. These findings correspond to those obtained in minor breeds from New Zealand. We conclude that scrapie development not only depends on host genetic factors but also requires exogenous factors. Our findings demonstrate the effectiveness of the measures taken by New Zealand to maintain free from scrapie.

Alleles↗
PubMed2004

Power for genetic association studies with random allele frequencies and genotype distributions.

One of the first and most important steps in planning a genetic association study is the accurate estimation of the statistical power under a proposed study design and sample size. In association studies for candidate genes or in fine-mapping applications, allele and genotype frequencies are often assumed to be known when, in fact, they are unknown (i.e., random variables from some distribution). For example, if we consider a diallelic marker with allele frequencies of 0.5 and 0.5 and Hardy-Weinberg proportions, the three genotype frequencies are often assumed to be 0.25, 0.50, and 0.25, and the statistical power is calculated. Unfortunately, ignoring this source of variation can inflate the estimated power of the study. In the present article, we propose averaging the estimates of power over the distribution of the genotype frequencies to calculate the true estimate of power for a fixed allele frequency. For the usual situation, in which allele frequencies in a population are not known, we propose placing a prior distribution on the allele frequency, taking advantage of any available genotype information. This Bayesian approach provides a more accurate estimate of power. We present examples for quantitative and qualitative traits in cohort studies of unrelated individuals and results from an extensive series of examples that show that ignoring the uncertainty in allele frequencies can inflate the estimated power of the study. We also present the results from case-control studies and show that standard methods may also overestimate power. As discussed in this article, the approach of fixing allele frequencies even if they are not known is the common approach to power calculations. We show that ignoring the sources of variation in allele frequencies tends to result in overestimates of power and, consequently, in studies that are underpowered. Software in C is available at http://www.ambrosius.net/Power/.

Alleles↗
PubMed2002

Genotype frequencies of the +874T-->A single nucleotide polymorphism in the first intron of the interferon-gamma gene in a sample of Sicilian patients affected by tuberculosis.

In the light of the key role played by interferon (IFN)-gamma in the control of tuberculosis, in the present paper we have evaluated the distribution of the functional +874T --> A IFN-gamma single nucleotide polymorphism (SNP) in Sicilian patients affected by tuberculosis. Our aim was to determine whether there is an association between the TT genotype, which has been suggested to be linked to an increased production of IFN-gamma, and resistance to chronic tuberculosis. DNA samples were obtained from 45 patients and 97 healthy controls. Polymorphism at +874 was identified using amplification refractory mutational system methodology. The +874T SNP was less frequent in patients than in controls (0.42 vs. 0.50) but the difference was not significant. The +874TT genotype, which has been suggested to be associated with high IFN-gamma production, was significantly decreased in the patients. Thus, resistance to chronic lung tuberculosis might be associated with a genetically determined high IFN-gamma production capacity. In conclusion, the present data add another piece of evidence to the complex puzzle of genetic and environmental factors involved in control of infectious diseases. Studies on cytokine gene polymorphisms may elucidate the complex network of trans-interactive genes influencing the type and strength of responses to environmental stressors and may help to identify the genetic factors that affect survival in humans.

Adult↗