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PubMed2002

[Study of genotype frequencies of ANP 664G/A polymorphism in normal subjects and CVD patients, and its association with plasma ANP levels].

Atrial natriuretic peptide (ANP) plays a crucial role in regulating body fluid volume and blood pressure, by promoting natriuresis and vasodilatation and by inhibiting the renin-angiotensin system. Plasma levels of ANP are elevated in heart failure and hypertension, and ANP is thus believed to be involved in the pathogenesis of cardiovascular disorders. Previous case-control studies have shown that a single nucleotide polymorphism in the first exon of ANP gene, 664G/A, is associated with a risk of cerebrovascular disease (CVD) in white populations. Plasma ANP levels, however, were not evaluated in these studies in relation to the 664G/A, although the nucleotide substitution causes an amino-acid change in the propeptide of ANP. In this study, we analyzed the genotype frequencies of the 664G/A in Japanese patients with CVD (n = 199) and age- and gender-matched control subjects(n = 176). Genotypes with the 664A allele in the Japanese control subjects (G/A and A/A 12.5%) were apparently more frequent compared to the published frequency of the white control population (G/A and A/A 6.6%, p = 0.0437). Genotypes with the 664A allele, however, were not significantly different between our CVD patients(15.1%) and controls (12.5% p = 0.4714). In the control group (n = 137), the mean plasma ANP levels were not different between the 664G/G (15.7 +/- 10.7 pg/ml) and 664G/A genotypes (15.6 +/- 6.8 pg/ml, p = 0.9708). These results suggest that there is a racial difference in the allele frequency of 664G/A, and that this polymorphism may not be a major risk factor for CVD in the Japanese, nor is it a major determinant of plasma ANP level.

Atrial Natriuretic Factor↗
PubMed2006

Selection on gamete recognition proteins depends on sex, density, and genotype frequency.

Gamete recognition proteins can evolve at astonishing rates and lie at the heart of reproductive isolation and speciation in diverse taxa. However, the source of selection driving this evolution remains unknown. We report on how the sperm bindin genotype influences reproductive success under natural conditions. An interaction between genotype frequency and spawning density determines how sperm bindin genotype influences reproductive success. Common genotypes are selected under sperm-limited conditions, whereas rare genotypes are selected under conditions of intense sperm competition and sexual conflict. Variation in the evolutionary rates of bindin may reflect historic differences in sperm availability.

Alleles↗
PubMed1999

STR HUMARA locus gene and genotype frequencies in Han and Bei populations in China.

For the purpose of the population genetics study of the HUMARA locus, the allele, and genotype frequencies were determined in two Chinese population samples (Han-101, Bei-113) using PCR, PAGE, and silver staining. Fourteen alleles were found. The size of amplified fragments were 258 bp-315 bp. The observed heterozygosities were 0.83 in the Han population and 0.73 in the Bei population respectively. The expected heterozygosities were 0.91 in the Han population and 0.97 in the Bei population respectively. Both populations meet Hardy-Weinberg expectation, Han population x2 = 17.7206, df = 11, p > 0.05; Bei population x2 = 7.4268, df = 10, p > 0.05. The discrimination power were 0.95 in females and 0.89 in males in the Han population, 0.94 in females and 0.88 in males in the Bei population. Thus, the allelic frequency data can be used in the personal identification and parentage testing in the forensic science practice. The PCR test established in this study is robust and reproducible.

Alleles↗
PubMed2001

Ethnic variation in genotype frequencies of a p53 intron 7 polymorphism.

Using a PCR-restriction enzyme-based method we found large ethnic variations when a C-->T polymorphism in the human p53 gene at position 14181 in intron 7 was studied in Finnish, Polish, Hungarian, Italian, Japanese, Indian and Chinese populations. The largest variations were found between Caucasian and Asian, genotype frequencies varied from C 0.95 and T 0.05 in the Finnish population to C 0.67 and T 0.33 in the Chinese population, the relative risk (RR) for T being 6.5 (95% CI 3.4-12.3, P < 0.001). Variations were also found between Finnish and Italian and between Italian and Chinese (RR for T 2.4, 95% CI 1.2-4.9 and 2.7, 95% CI 1.7-4.2, respectively).

Asian People↗
PubMed2002

Allele and genotype frequencies of polymorphic cytochromes P450 (CYP2C9, CYP2C19, CYP2E1) and dihydropyrimidine dehydrogenase (DPYD) in the Egyptian population.

AIMS: The goal of this study was to determine the frequencies of important allelic variants of CYP2C9, CYP2C19, CYP2E1 and DPYD in the Egyptian population and compare them with the frequencies in other ethnic populations. METHODS: Genotyping of CYP2C9 (*2 and *3), CYP2C19 (*2 and *3), c2 variant of CYP2E1 and DPYD alleles (*2 A-*6 ) was carried out in a total of 247 unrelated Egyptian subjects. An allele-specific fluorogenic 5' nuclease chain reaction assay was applied for detection of CYP2C9 and CYP2C19 variants. Other variants of the CYP2E1 and DPYD genes were determined using polymerase chain reaction (PCR)-restriction fragment length polymorphism and allele-specific PCR based assays. RESULTS: CYP2C9 allele frequencies in 247 Egyptian subjects were 0.820 for CYP2C9*1, 0.120 for CYP2C9*2 and 0.060 for CYP2C9*3. For CYP2C19, the frequencies of the wild type (CYP2C19*1) and the nonfunctional (*2 and *3) alleles were 0.888, 0.110 and 0.002, respectively. CYP2C19*3, which is considered an Asian mutation, was detected in one subject (0.40%) who was heterozygous (*1/*3). Two subjects (0.80%) were homozygous for *2/*2, while no compound heterozygotes (*2/*3) or homozygotes for *3 were detected. For CYP2E1, only four subjects (1.70%) had the rare c2 variant, expressed heterozygously, giving an allele frequency of 0.009. Five variants of DPYD were analysed, with no splice sites (*2 A) or DeltaC1897 (*3) found in this population. The frequencies of other variants were 0.028, 0.115 and 0.090 for *4, *5 and *6, respectively. CONCLUSIONS: Comparing our data with that obtained in several Caucasian, African-American and Asian populations, we found that Egyptians resemble Caucasians with regard to allelic frequencies of the tested variants of CYP2C9, CYP2C19, CYP2E1 and DPYD. Our results may help in better understanding the molecular basis underlying ethnic differences in drug response, and contribute to improved individualization of drug therapy in the Egyptian population.

Aryl Hydrocarbon Hydroxylases↗
PubMed2005

Breeding programmes for TSE resistance in British sheep. I. Assessing the impact on prion protein (PrP) genotype frequencies.

From April 2005, member states of the European Union were required to implement a compulsory breeding programme for resistance to transmissible spongiform encephalopathies (TSEs) in sheep as part of measures to eradicate TSEs from national flocks. In this paper, we assessed the impact of four different breeding strategies on prion protein (PrP) genotype frequencies using a mathematical model which describes in detail gene flow in the British sheep flock. These strategies ranged from the minimum requirements laid down in by EU legislation to compulsory implementation of the current National Scrapie Plan for Great Britain (NSP) ram genotyping scheme. All four strategies were predicted to substantially reduce the frequency of the VRQ allele, which is associated with the highest risk of scrapie, although schemes with more stringent requirements produced a larger reduction. However, there were marked differences in the impact of the strategies on the frequency of other PrP alleles. In particular, restrictions beyond those required by EU legislation were necessary to change the frequency of other PrP alleles substantially. Consequently, a breeding programme which aims to reduce the risk to human health by reducing the frequency of the ARQ allele (associated with the highest risk of BSE in sheep) must place restrictions on ARQ-bearing animals. Similarly, a programme which seeks to increase the frequency of the ARR allele (associated with the lowest risk of TSE) must favour ARR-bearing animals.

Alleles↗
PubMed2004

Regional European differences in allele and genotype frequencies of low density lipoprotein receptor-related protein 1 polymorphism in Alzheimer's disease.

The low density lipoprotein receptor-related protein 1 (LRP1 gene) is a candidate gene for Alzheimer's disease (AD), because it is a ligand for proteins involved in AD pathogenesis, such as apolipoprotein E (APOE), alpha2-macroglobulin (A2M), amyloid precursor protein (APP), and is located on chromosome 12, within a region linked with AD. An association between a silent polymorphism (C/T) in exon 3 and late onset AD has been reported, with an increased frequency of the C allele, although with conflicting results. We examined this polymorphism in a cohort of 166 sporadic AD patients and 225 sex- and age-matched nondemented controls from Southern Italy. No statistically significant differences were found in LRP1 genotype and allele frequencies between the whole AD sample and controls, nor in early- and late-onset subsets of AD patients. No statistically significant differences in frequencies between LRP1 alleles and AD among APOE allele, age, or gender strata were found. Finally, comparing our results with the findings from other European populations, the LRP1 C allele frequency showed a statistically significant decreasing trend from Northern to Southern regions of Europe, with a concomitant increase in LRP1 T allele frequency, but in AD patients only. Finally, in the AD sample, a decreasing geographical trend from North to South of Europe was found for LRP1 CC genotype, and an inverse trend for LRP1 CT genotype frequency. We suggest that these regional variations in LRP1 genotype and allele frequencies in AD could be related to the different patterns of association between this polymorphism and the disease in various European studies.

Aged↗
PubMed2005

Comparing the effects of genetic drift and fluctuating selection on genotype frequency changes in the scarlet tiger moth.

One of the recurring arguments in evolutionary biology is whether evolution occurs principally through natural selection or through neutral processes such as genetic drift. A 60-year-long time series of changes in the genotype frequency of a colour polymorphism of the scarlet tiger moth, Callimorpha dominula, was used to compare the relative effects of genetic drift and variable natural selection. The analysis showed that most of the variation in frequency was the result of genetic drift. In addition, although selection was acting, mean fitness barely increased. This supports the 'Red Queen's hypothesis' that long-term improvements in fitness may not occur, because populations have to keep pace with changes in the environment.

Animals↗
PubMed2003

Higher glutathione transferase GSTM1 0/0 genotype frequency in young thyroid carcinoma patients.

OBJECTIVE: Glutathione S-transferases (GSTs) comprise a large supergene family and detoxify a variety of endogenous and exogenous electrophilic compounds. Since many GSTs are polymorphic, there has been considerable interest in determining whether particular allelic variants are associated with altered risk for various disorders. RESEARCH DESIGN AND METHODS: In this study the association between the variant GSTM1 0/0 genotype and thyroid carcinoma was investigated. A hospital-based, case-controlled study was carried out. Polymorphisms of GSTM1 0/0 (i.e. the null allele of GSTM1) in samples from 32 cases and 44 controls were detected by polymerase chain reaction (PCR) methodology. The proportions of GSTM1 deleted genotype in cases and controls were 59.4% and 54.5%, respectively. RESULTS: There were significant increments of GSTM 0/0 genotype frequency in a group of patients aged under 40 (p = 0.033, odds ratio (OR) = 4.78, 95% confidence interval (CI) = 1.30-7.13) and in former smokers compared with controls (p = 0.039, OR 2.45, 95% CI 0.216-4.72). CONCLUSION: GSTM1 deleted genotype may be a useful genetic biomarker for thyroid carcinoma susceptibility in young subjects. The absence of this enzyme seems to have a role in the development of thyroid carcinoma; however, the mechanism still needs further study.

Adult↗
PubMed1992

Rhesus genotype frequency in Bangladeshi population.

The prevalence of Rhesus genotypes in Bangladesh has been studied and several important findings were observed. This being the initial report, includes a population of 1600 only. By using five Rh antisera (Anti-C, Anti-D, Anti-E, Anti-c and Anti-e) a genotype can be deduced since anti-d is not available. More often only a probable genotype can be suggested after reference to the known chromosome frequencies in the population. By using family studies in conjunction, it may be possible to determine genotype with certainty. The prominent Rhesus genotype was CDe/cDE (R1R2), i.e., 39.75%, Rhesus genotype cde/cde (rr) was found to be only 1.75%. The genotype cdE/cde (r"r) was not detected in the present series of Bangladeshi population. These results have been compared with the English and the Indian Bengalee Hindu Population.

Bangladesh↗
PubMedDate not supplied

CCR5 chemokine receptor genotype frequencies among Puerto Rican HIV-1-seropositive individuals.

Some individuals remain uninfected by human immunodeficiency virus type 1 (HIV-1), despite multiple sexual contacts with subjects with confirmed HIV-1 infection. Several studies have confirmed that individuals who are homozygous for a 32 base pair (bp) deletion mutation in the chemokine receptor gene CCR5, designated as delta 32/ delta 32, are protected against HIV-1 infection. Heterozygotes of the same chemokine receptor deletion mutation are, however, not protected from acquiring HIV-1 infection but seemingly have slower progression to acquired immunodeficiency syndromes (AIDS). Genotype frequencies of the delta 32 CCR5 mutation vary markedly among different ethnic groups; heterozygosity is found in approximately 15% of Caucasians, about 5-7% of Hispanics and African Americans and 1% or less of Asians. The ethnic background of Puerto Ricans is highly complex and usually includes admixture of Caucasian, Caribbean Indian and African traits to a varying extent. This study was conducted to examine the frequencies of the delta 32 CCR5 mutation among Puerto Ricans who are infected with HIV-1. Samples were received from different geographical regions of the island. Of 377 samples tested, 94.2% were wild type (non-deletion mutant) homozygotes, 5.8% were delta 32 CCR5 heterozygotes, and none were delta 32 CCR5 homozygotes. The incidence of CCR5 delta 32/w heterozygous mutation among Puerto Ricans seems to be somewhat lower than what was reported with US Hispanics. Some age and gender associated bias of the mutation frequency were observed with the study population, the reason for which is unclear at present.

Adolescent↗
PubMed2003

HLA class II genotypic frequencies in atopic asthma: association of DRB1*01-DQB1*0501 genotype with Artemisia vulgaris allergic asthma.

Different human leukocyte antigen (HLA) class II alleles have been associated with the development of atopic asthma. To determine whether HLA class II alleles are associated with atopic asthma in a population from southeast Spain (Murcia region), 213 atopic asthmatic patients and 150 controls were selected for HLA typing. Significant association of the DRB1*01 and DQB1*0501 alleles was found in Artemisia vulgaris allergic patients (p(c) = 0.00052 and p(c) = 0.00023, respectively). No significant correlation was found in other atopic patients allergic to pollens (Phleum pratense, Olea europaea, and Salsola kali), house dust mites (Dermatophagoides pteronyssinus, D. farinae), molds (Alternaria alternata, Cladosporium herbarum), or animal danders (dog, cat). The results reveal that the DRB1*01-DQB1*0501 genotype is strongly associated with a positive response to Artemisia vulgaris in the population studied.

Alleles↗
PubMed2003

Racial differences in selected cytokine allelic and genotypic frequencies among healthy, pregnant women in North Carolina.

BACKGROUND: Genetic susceptibility to diseases is likely influenced by common DNA variants in the form of single nucleotide polymorphisms (SNPs). The value of SNPs for linkage and association mapping studies may depend on the distribution of SNP allele frequencies across populations. OBJECTIVES: To establish the SNP allelic frequencies among Caucasian and African American women for tumor necrosis factor (TNF)alpha, transforming growth factor (TGF)beta1, interleukin-10 (IL10), interleukin-6 (IL6), and interferon (IFN)gamma. MATERIALS AND METHODS: DNA was extracted from whole blood from 123 healthy, pregnant women. PCR-based genotyping was performed for the genes encoding TNFalpha (-308G/A), TGFbeta1 (codon 10C/T, codon 25C/G), IL10 (-1082A/G, -819T/C, -592A/C), IL6 (-174C/G) and IFNgamma (874T/A). Allele frequencies were determined by Hardy-Weinberg Equilibrium and Linkage Disequilibrium tests. Differences in the SNP allelic frequencies between Caucasians and African Americans were assessed by the chi(2) of Amitage trend test. RESULTS: SNP allelic and genotypic frequencies for IL6 and IFNgamma, but not for TNFalpha, TGFbeta1, and IL10, differed significantly between the Caucasian and African American women. CONCLUSIONS: Recognition of racial differences in SNP allelic and genotypic frequencies for selected cytokines is important for designing and powering future linkage and association mapping studies investigating the role of cytokines in human disease.

Black or African American↗
PubMed2003

Genotype frequencies and linkage disequilibrium in the CEPH human diversity panel for variants in folate pathway genes MTHFR, MTHFD, MTRR, RFC1, and GCP2.

BACKGROUND: Genetic variation in enzymes involved in vitamin metabolism is a candidate for analysis in studies of how nutritional covariates may impact a disease state. The role of folate pathway genes in birth defects and cardiovascular disease in humans has been widely studied. Since incidence rates for these disorders vary by geographic origins, it is useful to know which variants are the best candidates for studies based on genotype and allele frequency, as well as linkage disequilibrium (LD) in founder populations. METHODS: Six polymorphisms in five folate metabolism-related genes (MTHFR, MTHFD, MTRR, GCP2, and RFC1) were genotyped on a collection of 1064 DNA samples from populations around the world, which were made available by the Centre d'Etude du Polymorphisme Humain (CEPH) consortium for analysis. RESULTS: In this study we report the genotype frequencies for variants in the MTHFR, MTHFD, MTRR, GCP2, and RFC1 genes, and the LD for two variants (C677T and A1298C) in MTHFR. CONCLUSIONS: The rare allele frequency for each of the five genes studied varied widely. LD is strongest in Pakistani and Brazilian populations (D' = 1.0) and weakest in Mexican populations (D' = 0.45). These findings will allow the selection of variants that will provide the most power in studies of folate pathway genes involving different ancestral populations, and contribute to our knowledge of the population distribution of selected nutritional gene variants.

Carrier Proteins↗
PubMed2002

Allele and genotype frequencies of CYP2B6 and CYP3A5 in the Japanese population.

OBJECTIVE: The goal of this study was to determine the frequencies of allelic variants of CYP2B6and CYP3A5 in the Japanese population. METHODS: Genotyping of CYP2B6 (*2, *3, *4, *5, *6, and *7) and CYP3A5 ( *2, *3, *4, *5, and *6) was carried out in 265 unrelated Japanese subjects by polymerase chain reaction (PCR), restriction fragment length polymorphism and allele-specific, real-time PCR assays. RESULTS: Allele frequencies for CYP2B6*2, *3, *4, *5, *6, and *7 in 256 Japanese subjects were 0.047, 0, 0.093, 0.011, 0.164, and 0, respectively. Ethnic variation in allele frequencies relative to that in Caucasian subjects was observed for CYP2B6*4 (0.093 vs 0.040), *5 (0.011 vs 0.109), *6 (0.164 vs 0.256), and *7 (0 vs 0.030). Allele frequencies for CYP3A5*2, *3, *4, *5, and *6 in 265 Japanese subjects were 0, 0.740, 0, 0.004, and 0, respectively. The frequency of the CYP3A5*1 allele is 2.8 times higher in Japanese than in Caucasians. CONCLUSIONS: Our results contribute to a better understanding of the molecular basis of ethnic differences in drug response, which may help to improve individualization of drug therapy and offer a preliminary basis for more rational use of drugs that are substrates for CYP2B6 and CYP3A5 in the Japanese population.

Aryl Hydrocarbon Hydroxylases↗
PubMed2006

Allele and genotype frequencies of metabolic genes in Native Americans from Argentina and Paraguay.

Interethnic differences in the allele frequencies of CYP2D6, NAT2, GSTM1 and GSTT1 deletions have been documented for Caucasians, Asians, and Africans population. On the other hand, data on Amerindians are scanty and limited to a few populations from southern areas of South America. In this report we analyze the frequencies of 11 allele variants of CYP2D6 and 4 allele variants of NAT2 genes, and the frequency of GSTM1 and GSTT1 homozygous deleted genotypes in a sample of 90 donors representing 8 Native American populations from Argentina and Paraguay, identified as Amerindians on the basis of their geographic location, genealogical data, mitochondrial- and Y-chromosome DNA markers. For CYP2D6, 88.6% of the total allele frequency corresponded to *1, *2, *4 and *10 variants. Average frequencies for NAT2 *4, *5, *6 and *7 alleles were 51.2%, 25%, 6.1%, and 20.1%, respectively. GSTM1 deletion ranged from 20% to 66%, while GSTT1 deletion was present in four populations in less than 50%. We assume that CYP2D6 *2, *4, *10, *14; NAT2 *5, *7 alleles and GSTM1 and GSTT1 *0/*0 genotypes are founder variants brought to America by the first Asian settlers.

Alleles↗
PubMed2001

Analysis of Human Platelet Antigen Genotypic Frequencies in Chinese Population by PCR Amplification with Sequence Specific Primers.

In present study, a method for genotyping for human platelet antigen (HPA) systems by means of the polymerase chain reaction amplification with sequence-specific primers (PCR-SSP) technique was developed and employed to determine the human platelet antigen frequencies in the Chinese population. Primers sets were designed to allow PCR amplification for five systems using the same assay conditions. Platelets from 110 random Chinese blood donors were typed for human platelet alloantigens HPA-1 to -5 by the method. The results showed that the HPA genotypic frequencies observed in the 110 donors were 0.91 and 0.09 for HPA-1a and HPA-1b, 0.86 and 0.14 for HPA-2a and HPA-2b, 0.60 and 0.40 for HPA-3a and HPA-3b, 0.92 and 0.08 for HPA-4a and HPA-4b, and 0.85 and 0.15 for HPA-5a and HPA-5b, respectively. In conclusion the method is feasible and practical and may be available to typing for HPA in the clinical laboratories.

Journal Article↗
PubMed1992

HLA-DQA1 allele and genotype frequencies in a northern Italian population.

HLA-DQA1 typing of 227 randomly selected Northern Italian people by the use of polymerase chain reaction are reported. The combined use of commercial Amplitype HLA-DQalpha system and four sequence-specific oligonucleotide probes allows the definition of 8 alleles and 36 genotypes, arranged according to World Health Organisation nomenclature. Seven of these genotypes are not observed among the analyzed samples. Allele frequencies range from 1.5 to 35.7% and genotype observations do not deviate significantly from Hardy-Weinberg equilibrium; observed heterozygosity is 0.8238 with an allelic diversity value of 0.79 and the power of discrimination is 0.925. Our Italian population sample shows differences from other Caucasian samples both for allele and genotype frequencies. This locus typing for the 8 defined alleles provides a rapid and sensitive method in individual identification and paternity investigation.

Alleles↗