Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “genotype frequency”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 91 records · Page 5Linked to original sources
PubMed2001

No substantial difference in genotype frequencies of interleukin and myeloperoxidase polymorphisms between malignant lymphoma patients and non-cancer controls.

BACKGROUND AND OBJECTIVES: The functional polymorphisms regulating immunologic responses may influence the proliferation or suppression of malignant lymphoma. We examined the association between malignant lymphoma risk and the polymorphisms of the IL-1 gene family [IL-1B -31 C/T, IL-1A -889 C/T, and IL-1RN 86-bp variable number of terminal repeat (VNTR)] and myeloperoxidase (MPO -463 G/A). DESIGN AND METHODS: The hospital-based case-control study was conducted in Japan. Genotypes were examined in a total of 372 lymphoma cases and 241 non-cancer control subjects. The relative risks were estimated by unconditional logistic regression analysis. RESULTS: The overall allele distribution of these polymorphisms did not differ substantially between patients and controls; the odds ratios were 0.73 (95% confidence interval, 0.48-1.11) for the T allele carriers of IL-1B relative to the non-carriers, 1.01 (0.56-1.82) for the 2-repeat allele (allele 2) carriers of IL-1RN, 0.96 (0.62-1.48) for the T allele carriers of IL-1A, and 1.04 (0.70-1.57) for the A allele carriers of MPO. Subgroup analyses according to histology [diffuse large B-cell lymphoma (DLBL), follicular lymphoma, low-grade lymphoma of mucosa associated lymphoid tissue, and others] failed to illustrate differences except for DLBL which showed a possible association with IL-1A and IL-1B polymorphisms. INTERPRETATION AND CONCLUSIONS: Our data show a limited association between these polymorphisms and malignant lymphoma risk in total. The possible association of the IL-1A and IL-1B polymorphisms with DLB-needs further clarification.

Adolescent↗
PubMed2002

Allele and genotype frequencies of polymorphic DCP1, CETP, ADRB2, and HTR2A in the Egyptian population.

OBJECTIVE: The goal of this study was to determine the frequencies of important allelic variants of two drug targets, dipeptidyl carboxypeptidase ( DCP1) and cholesteryl ester transfer protein ( CETP), and two other drug receptors, beta-2 adrenergic receptor ( ADRB2) and 5-hydroxy tryptamine 2A receptor ( HTR2A), in the Egyptian population and compare them with the frequencies in other ethnic populations. METHODS: A sensitive real-time polymerase chain reaction assay was developed and successfully applied for genotyping of the consensus (wild-type) alleles plus five variants of four genes: DCP1 [the insertion allele ( I) versus the deletion allele ( D)], CETP*TaqI ( B1 versus B2), ADRB2*R16G, ADRB2*Q27E, and HTR2A*102T>C. This study was carried out in 242 unrelated Egyptian subjects and is the first to describe these allelic variants in the Egyptian population. RESULTS: The frequencies of the tested alleles were found as: DCP1 ( I: D, 0.32:0.68), CETPTaqI ( B1: B2, 0.65:0.35), ADRB2*R16G ( Arg16: Gly16, 0.57:0.43), ADRB2*Q27E ( Gln27: Glu27, 0.76:0.24), and HTR2A*102T>C ( T102: C102, 0.53:0.47). The common Arabian ancestors of the Egyptians, Spanish, Saudi, and Emirate had created a common pattern of distribution of some allelic variants ( DCP1 and CETP). However, in the genotyping of ADRB2, the frequency of the polymorphism at codon 16 was found to be similar to the Chinese population, whereas that at codon 27 was similar to African-Americans with significant differences than other Caucasian populations. The frequency of the HTR2A*102T>C variant appeared to be similar to many Caucasian populations and African-Americans. CONCLUSIONS: We have explored the frequencies of important allelic variants DCP1, CETP, ADRB2, and HTR2A among the Egyptian population focusing on the ethnic diversity in the distribution of the tested mutant alleles. Our results may help in better understanding the observed ethnic variation in angiotensin-converting enzyme inhibition and atherosclerosis therapy. It also may contribute to better characterization of interethnic differences in isoprenaline and clozapine response, which will have implications for the cost effective and rational prescribing of these drugs.

Carrier Proteins↗
PubMedDate not supplied

Identification of NQO1 and GSTs genotype frequencies in Bulgarian patients with Balkan endemic nephropathy.

BACKGROUND: Polymorphisms in NAD[P]H:quinone oxidoreductase (NQO1) and glutathione S-transferases (GSTs) have been reported to be associated with an increased risk for environmentally and/or occupationally induced renal and bladder cancers. Genetic factors related to chronic nephropathy and to urinary bladder or renal cancer development in Balkan endemic nephropathy (BEN) is unknown. In order to evaluate their possible role in BEN susceptibility, we determined the frequencies of NQO1 alleles *1, *2 and *3, as well as the GSTT1 and GSTM1 null genotypes in BEN patients and healthy subjects from a non-endemic region of Bulgaria. METHODS: The respective genotypes of 95 unrelated Bulgarian BEN patients and of 112 healthy individuals (control group) were determined by rapid cycle polymerase chain reaction (PCR) and detected with either SYBR green I fluorescent dye or melting curve analysis using allele specific probes. RESULTS: NQO1 genotyping showed a higher NQO1*2 allele frequency (23.68%) in BEN patients compared to controls (18.75%; p=0.219), while NQO1*3 allele frequencies were similar in both groups (2.63% in BEN patients vs. 2.23% in controls; p=0.791). The GSTT1 deficiencywas observed in 20% of BEN patients vs. 16.1% of controls (p=0.613). The GSTM1 null genotype was found in 45.3% of BEN patients vs. 51.8% of controls (p=0.674). There was no influence of NQO1 and GSTs genotypes found on BEN risk. CONCLUSIONS: Our results established that alleles NQO1*2 and NQO1*3, as well as lack of GSTT1 and GSTM1 did not influence the BEN risk. These findings provide novel information on the genetic heterogeneity in the healthy Bulgarian population.

Balkan Nephropathy↗
PubMed2003

Allele and genotype frequency of CYP2C19 in a Tamilian population.

AIMS: To investigate the frequencies of CYP2C19*1, CYP2C19*2 and CYP2C19*3 alleles and CYP2C19 genotypes in a Tamilian population. METHODS: The study was conducted in 112 unrelated healthy human volunteers. DNA was extracted from leucocytes and analyzed by the PCR-RFLP protocol. The PCR product was digested with restriction enzymes (SmaI and BamH1) and then separated electrophoretically using polyacrylamide gel. RESULTS: The frequencies of the CYP2C19*1, *2 and *3 alleles were 0.598 [95% confidence interval (CI) 0.507, 0.689], 0.379 (95% CI, 0.350,0.407) and 0.022 (95% CI -0.005, 0.049), respectively. The distribution of CYP2C19*1/*1,*1/*2, *1/*3, *2/*2 and *2/*3 genotypes were 0.295 (95% CI, 0.210, 0.379), 0.580 (95% CI, 0.488, 0.671), 0.027 (95% CI -0.003, 0.057), 0.080 (95% CI 0.030, 0.130) and 0.018 (95% CI -0.006, 0.042), respectively. CONCLUSIONS: The distribution of CYP2C19*1/*1 in the Tamilian population is lower than that in Caucasians, Africans and the North Indian population. The CYP2C19*1/*2 is significantly higher in Tamilians when compared with other populations. The CYP2C19*1/*3 allele, which was not reported in the North Indian and Caucasian populations has been identified in 2.7% of the Tamilian population.

Adult↗
PubMed2005

Genotype frequencies at codon 129 of the prion protein gene in Brazil: Implications in susceptibility to variant Creutzfeldt-Jakob disease compared to European and Asian populations.

A polymorphism at codon 129 of the prion protein gene has been shown to confer genetic susceptibility to prion diseases, and to influence the epidemic course of variant Creutzfeldt-Jakob disease. We employed a PCR-endonuclease digestion-based assay to investigate this genetic trait in Brazil, and then compared our results to previously published data from several European and Asian countries.

Adolescent↗
PubMed1998

Greek Cypriot allele and genotype frequencies for Amplitype PM-DQA1 and D1S80 loci.

A sample from the Greek Cypriot population was typed at seven forensically important PCR-based loci: LDLR, GYPA, HBGG, D7S8, GC, HLA-DQA1, and D1S80. The results showed that all loci meet Hardy-Weinberg expectations and that there is no evidence for association of alleles between loci. Allelic frequency distributions at all loci, except HLA-DQA1 and two D1S80 alleles, were similar to those of U.S. Caucasians. Greek Cypriot population databases have been created and can be used for forensic analyses to estimate the frequency of a multiple locus DNA profile.

Alleles↗
PubMed1991

Analysis of coyote mitochondrial DNA genotype frequencies: estimation of the effective number of alleles.

A restriction-site survey of 327 coyotes (Canis latrans) from most parts of their North American range reveals 32 mitochondrial DNA (mtDNA) genotypes. The genotypes are not strongly partitioned in space, suggesting that there is high gene flow among coyote subpopulations. Consequently, each new geographic location added to the study has a decreasing probability of containing a mtDNA genotype that had not been previously discovered. This being the case, by using Monte Carlo sampling experiments, we can estimate the total number of genotypes that would be found if all possible localities were surveyed. This estimate of total genotypic variability agrees qualitatively with estimates based on theoretical considerations of the expected number of alleles in a stable population. We also predict effective population sizes from genotype data. The accuracy of these estimates is thought to be dependent on the fact that coyotes are not highly genetically structured, a situation which may apply to highly mobile species.

Alleles↗
PubMed1999

Validation of methods for CYP2C9 genotyping: frequencies of mutant alleles in a Swedish population.

Cytochrome P450 2C9 (CYP2C9) catalysis the metabolism of important drugs such as phenytoin, S-warfarin, tolbutamide, losartan, torasemide, and nonsteroidal anti-inflammatory drugs. A functional polymorphism of the CYP2C9 gene has been described. The variant alleles include CYP2C9*2 having a point mutation in exon 3 causing an Arg144Cys exchange, and CYP2C9*3 with a point mutation in exon 7 resulting in an Ile359Leu exchange. Genotyping of these variant forms was carried out in 430 Swedish healthy volunteers and three different methods were compared. Sequence analysis of the different PCR products revealed that other genes in the CYP2C locus were co-amplified in one of the methods applied, whereas the other two methods were specific for CYP2C9. The frequencies of the CYP2C9*1, CYP2C9*2 and CYP2C9*3 alleles in the population examined were found to be 0.819, 0.107, and 0.074, respectively. The need for careful evaluation of the genotyping procedure by sequence analysis of PCR products is emphasised.

Adult↗
PubMed1999

[Allele and genotype frequency distribution of D19S400 locus in several populations].

Using polymerase chain reaction and PAG electrophoresis, D19S400 Locus was investigated in the populations of Chinese, Germany, Slovakian, and American Black Population. 620 samples collected from the four populations were tested and a total of 11 alleles (*7 to *17) and 47 genotypes were found. The heterozygosity was observed between 0.78 and 0.88, and the discriminating power was between 0.9385 and 0.9664. The distributions of genotypes in the four populations were in accordance with Hardy-Weinberg equilibrium. Significant differences were observed in the distribution of allele frequencies among the three major racial populations (Mongoloid, Caucasian, Negroid). According to the results obtained in this study, D19S400 locus is a robust STR for forensic and genetic purposes.

Alleles↗
PubMed1997

Contribution of factor VII genotype to activated FVII levels. Differences in genotype frequencies between northern and southern European populations.

The relationship between coagulation factor VII (FVII) levels in plasma and FVII genotypes, determined by three polymorphisms (5'F7, IVS7, and 353R/Q), were studied in 500 control subjects enrolled in European multicenter study. The selection of particular FVII genotypes and the analysis of variance clearly indicated the independent contribution of a single 5'F7 insertion (A2) or 353Q (M2) allele to lowering plasma levels of activated FVII (FVIIa) (by a mean 25%). The M2 allele alone was found to make a major contribution to the genetically determined component of the FVIIa levels. Genotypes associated with low FVII levels were significantly rarer in the northern part of Europe (Oslo) than in the southern part (Rome, Murcia). The contribution made by the FVII genotype to the total variance of FVIIa levels was higher (30%) than that made to either FVII activity (25%) or FVII antigen (12%). Subjects with different FVII genotypes showed up to fivefold differences in mean FVIIa values, thus allowing attribution of a substantial part of the considerable interindividual variation to genetic variation, which may be of assistance in the interpretation of FVIIa levels on an individual basis. When FVII levels were adjusted by age and by triglyceride levels, the contribution of FVII genotypes to the FVII phenotypic variance was virtually unchanged. Taken together, these data indicate that in healthy control subjects the FVII genotype is a major predictor of plasma FVIIa levels and would support further study on the role of FVII genetic components in the development of cardiovascular disease.

Adult↗
PubMed2007

Linear relationship between Gaeumannomyces graminis var. tritici (Ggt) genotypic frequencies and disease severity on wheat roots in the field.

In order to investigate potential links existing between Gaeumannomyces graminis var. tritici (Ggt) population structure and disease development during polyetic take-all epidemics in sequences of Ggt host cereals, seven epidemics in fields with different cropping histories were monitored during the seasons 2001/2002 (two fields), 2002/2003 (two fields) and 2003/2004 (three fields). Take-all incidence and severity were measured at stem elongation and Ggt populations were characterized. The 73 isolates collected in the two fields in 2001/2002 were distributed into two multilocus genotypes, G1 and G2 according to amplified fragment length polymorphism analysis. A monolocus molecular marker amplified by F-12 random amplification polymorphism DNA primer sizing between 1.9 and 2.0 kb that gave strictly the same distinction between the two multilocus genotypes was further applied to measure G1/G2 frequencies among Ggt populations in all fields (266 isolates). The ratios of G1 to G2 differed between fields with different cropping histories. A linear relationship between G2 frequency among Ggt populations and disease severity at stem elongation was measured during the three cropping seasons. When take-all decline was observed, G2 frequencies were low in first wheat crops, highest in short-term sequences and intermediate in longer sequences of consecutive crops of Ggt host cereals. This pattern could be the result of population selection by environmental conditions, in particular by microbial antagonism during the parasitic phase of the fungus. In order to better understand take-all epidemic dynamics, the distinction between these two genotypes could be a basis to develop models that link approaches of quantitative epidemiology and advances in population genetics of Ggt.

Ascomycota↗
PubMed1996

Genotype frequencies of the human platelet antigen, Ca/Tu, in Japanese, determined by a PCR-RFLP method.

Recently, the polymorphism of a new human platelet antigen, Ca/Tu, was shown to be derived from a G-A nucleotide substitution at base 1564 of GPIIIa cDNA, which leads to a single amino acid difference, Arg/Gln at amino acid 489 of GPIIIa. We developed a PCR-RFLP method to determine the genotypes of Ca/Tu and their frequencies in a Japanese population. Fifteen Ca/Tua donors comprising 1 Ca/Tu(a/a) homozygous donor and 14 Ca/Tu(a/b) heterozygous donors were found among the 314 random donors analyzed. The frequencies of Ca/Tu genes were 0.025 (Ca/Tua) and 0.975 (Ca/Tu(b)). The present study showed that the frequency of Ca/Tua individuals in the Japanese (15/314) was approximately 7-fold higher than in the Finnish population (1/150) previously reported by Kekomäki et al. Therefore, attention must be given to the involvement of the Ca/Tu alloantigen in neonatal alloimmune thrombocytopenia and the refractoriness of platelet transfusion.

Antigens, Human Platelet↗
PubMed1994

A study on ADH2 and ALDH2 genotyping by PCR-RFLP and SSCP analyses with description of allele and genotype frequencies in Japanese, Finn and Lapp populations.

Genetic polymorphisms of the alcohol dehydrogenase ADH2 and aldehyde dehydrogenase ALDH2 genes were investigated in Japanese, Finn, and Lapp populations by using PCR-RFLP and SSCP analyses. The ALDH2 genotypes were unequivocally determined by a PCR-RFLP assay with a mismatched primer. The determination of the ADH2 genotypes, however, was found to be problematic in PCR with the reported oligonucleotide primer sets because there are high homologies among the ADHl, ADH2, and ADH3 gene sequences. The problem of the heterozygote excess in typing results obtained by using the previously reported PCR-RFLP methods was resolved by nested PCR, in which an internal primer set reamplified the ADH2 sequence selectively from a mixture of the ADH gene sequences amplified in the first PCR amplification of genomic DNA samples as templates. A newly designed primer pair with longer sequences and single 3' end mismatches was later found to achieve a predominant amplification of the ADH2 sequence in a single PCR. RFLP and SSCP analyses of PCR products with the new primer set gave results fully consistent with those by nested PCR. Thus, the ADH2 genotypes defined in this study were free from any typing errors. The ADH2 and ALDH2 allele frequencies observed in this study were found not to be biased significantly from those reported previously from Japanese populations, and these were monomorphic for Lapp and Finn populations.

Alcohol Dehydrogenase↗
PubMed1983

Effect of population associations and reduced penetrance on observed and expected genotype frequencies in a simple genetic model: application to HLA and insulin dependent diabetes mellitus.

The observed and Hardy--Weinberg-expected frequencies for (HLA) marker heterozygotes in a disease population are calculated where it is assumed that the disease is caused by either homozygosity or heterozygosity (with reduced pentrance) for a disease susceptibility allele at a disease locus, that allele being positively associated with both of the relevant alleles at the marker locus (the single susceptibility allele model of Svejgaard & Ryder, 1981). It is shown that the observed frequency is always less than or equal to the H-W expectation, with the (observed/expected) ratio decreasing as the degree of dominance increases.

Alleles↗