Polymorphism of the theta1 and mu1 glutathione s-transferase genes (GSTT1, GSTM1) in patients with atopic bronchial asthma from the West Siberian region

Polymorphism for the GSTT1 and GSTM1 null alleles was analyzed in 69 patients with atopic bronchial asthma (BA) and in 57 healthy individuals from Tomsk. The two samples did not differ in frequencies of genotypes 0/0 and + of either gene or in frequencies of genotype combinations. No association was observed for GST and BA severity. Thus, the GST null alleles proved to be unimportant for BA.     

Polymorphisms of CYP1a1, CYP2e1, GSTM1, GSTT1, and TP53 genes in Amerindians

Polymorphisms at the TP53, cytochrome P‐450 (CYP), and glutathione S‐transferase (GST) genes are related to cancer susceptibility and present high diversity in allele frequencies among ethnic groups. This study concerns the CYP2E1, GSTM1, and GSTT1 polymorphisms in seven Amerindian populations (Xavante, Guarani, Aché, Wai Wai, Zoró, Surui, and Gavião). Polymorphic sites at CYP1A1 and TP53 were also studied in the Aché and Guarani tribes and compared with previous results about these systems already obtained in the other populations. The CYP2E1*5B haplotype showed, respectively, the highest and the lowest frequencies already observed in human groups. High frequencies of CYP1A1*2A and CYP1A1*2C alleles and mostly low values of GSTM1*0/*0 and GSTT1*0/*0 genotypes were observed. These data may be interpreted as being due to genetic drift or selection for these high‐frequency CYP1A1 alleles and against GST null genotypes during America's colonization. Intrapopulation diversity varied from 0.19 (Guarani) to 0.38 (Surui), and 90% of the total diversity was due to the variability within populations. The relationships between these Amerindians and with other ethnic groups were evaluated based on D_A distances and the neighbor‐joining method. Low correlation was observed between genetic relationships and geographic distances or linguistic groups. In the TP53 comparison with other ethnic groups, Amerindians clustered together and then joined Chinese populations. The cluster analysis seems to indicate that the Aché tribe might descend from a Gê group that could have first colonized that Paraguayan region, but had also assimilated some amount of the Guarani gene pool, maybe through intertribal admixture. Am J Phys Anthropol 119:249–256, 2002. © 2002 Wiley‐Liss, Inc.     

Genetic polymorphisms in GSTM1, GSTT1, GSTP1, GSTM3 and the susceptibility to gallbladder cancer in North India

Abstract

The glutathione S-transferase (GSTs) are polymorphic supergene family of detoxification enzymes that are involved in the metabolism of numerous potential carcinogens. Several allelic variants of polymorphic GSTs show impaired enzyme activity and are suspected to increase the susceptibility to various cancers. To find out the association of GST variants with risk of gallbladder cancer, the distribution of polymorphisms in the GST family of genes (GSTT1, GSTM1, GSTP1, and GSTM3) were studied in 106 cancer patients and 201 healthy controls. Genotypes were analysed by polymerase chain reaction (PCR) and PCR-restriction fragment length polymorphism (RFLP). The frequencies of GSTM1 null and GSTM3*BB genotypes did not differ between patients and controls. The overall frequency of GSTT1 null was lower in cases as compared with controls (p=0.003, Odds ratio (OR)?=?0.2, 95% confidence interval (CI), 0.1–0.6). After sex stratification, the GSTT1 null frequency was reduced only in female patients (p=0.008, OR?=?0.2, 95% CI?=?0.1–0.6). However, the GSTP1, ile/val genotype and the val allele were significantly higher in cases than controls (p=0.013, OR?=?1.9, 95% CI?=?1.1–3.1; p=0.027, OR?=?1.5, 95% CI?=?1.0–2.1), respectively. To study gene–gene interactions, a combined risk of gallbladder cancer due to ile/val or val/val were calculated in combination with null alleles of GSTM1 and GSTT1 or the *B allele of GSTM3, but there was no enhancement of risk. Gallstones were present in 57.5% of patients with gallbladder cancer, but there were no significant differences between allelic/genotype frequencies of the studied GST genes polymorphisms between patients with or without gallstones. To best of our knowledge, this is the first paper showing ile/val genotypes and val allele of GSTP1 to be associated with higher risk of gallbladder cancer.     

Genetic Determinants of Predisposition to Bronchial Asthma

The ratio between the normal (+) and null (0) alleles of the genes encoding glutatione S-transferases M1 (GSTM1) and T1 (GSTT1) were studied in normal individuals from northwestern Russia (control group) and in patients with bronchial asthma (BA). The frequency of the GSTM1 0/0 genotype in the population sample was statistically significantly lower (37.8%) than in the BA patients (82.1%; ² = 16.8;P< 0.001; _W² = 15.7; = 0.01). For the GSTT1 gene, similar data were obtained. The frequency of the GSTT1 0/0 genotype in healthy donors was statistically significantly higher (16.3%) than in the BA patients (73.7%; ² = 28.5;P < 0.001; _W² = 23.22; = 0.01). A significant preponderance of the compound homozygotes for the GSTM1 and GSTT1 null alleles among the BA patients was observed. The frequency of the GSTM1 0/0, GSTT10/0 individuals among the patients was 57.9%, while it was only 4.7% among the controls (² = 27.4; P < 0.001).     

Population estimators or progeny tests: what is the best method to assess null allele frequencies at SSR loci?

Nuclear SSRs are notorious for having relatively high frequencies of null alleles, i.e. alleles that fail to amplify and are thus recessive and undetected in heterozygotes. In this paper, we compare two kinds of approaches for estimating null allele frequencies at seven nuclear microsatellite markers in three French Fagus sylvatica populations: (1) maximum likelihood methods that compare observed and expected homozygote frequencies in the population under the assumption of Hardy-Weinberg equilibrium and (2) direct null allele frequency estimates from progeny where parent genotypes are known. We show that null allele frequencies are high in F. sylvatica (7.0% on average with the population method, 5.1% with the progeny method), and that estimates are consistent between the two approaches, especially when the number of sampled maternal half-sib progeny arrays is large. With null allele frequencies ranging between 5% and 8% on average across loci, population genetic parameters such as genetic differentiation (F _ST) may be mostly unbiased. However, using markers with such average prevalence of null alleles (up to 15% for some loci) can be seriously misleading in fine scale population studies and parentage analysis.     

Comparing the van Oosterhout and Chybicki‐Burczyk methods of estimating null allele frequencies for inbred populations

In spite of the usefulness of codominant markers in population genetics, the existence of null alleles raises challenging estimation issues in natural populations that are characterized by positive inbreeding coefficients (F > 0). Disregarding the possibility of F > 0 in a population will generally lead to overestimates of null allele frequencies. Conversely, estimates of inbreeding coefficients (F) may be strongly biased upwards (excess homozygotes), in the presence of nontrivial frequencies of null alleles. An algorithm has been presented for the estimation of null allele frequencies in inbred populations (van Oosterhout method), using external estimates of the F‐statistics. The goal of this study is to introduce a modification of this method and to provide a formal comparison with an alternative likelihood‐based method (Chybicki‐Burczyk). Using simulated data, we illustrate the strengths and limitations of these competing methods. Under most circumstances, the likelihood method is preferable, but for highly inbred organisms, a modified van Oosterhout method offers some advantages.     

Genetic factors in predisposition to bronchial asthma

The ratio between the normal (+) and null (0) alleles of the genes encoding glutatione S-transferases M1 (GSTM1) and T1 (GSTT1) were studied in normal individuals from northwestern Russia (control group) and in patients with bronchial asthma (BA). The frequency of the GSTM1 0/0 genotype in the population sample was statistically significantly lower (37.8%) than in the BA patients (82.1%; chi 2 = 16.8; P < 0.001; w chi 2 = 15.7; alpha = 0.01). For the GSTT1 gene, similar data were obtained. The frequency of the GSTT1 0/0 genotype in healthy donors was statistically significantly higher (16.3%) than in the BA patients (73.7%; chi 2 = 28.5; P < 0.001; w chi 2 = 23.22; alpha = 0.01). A significant preponderance of the compound homozygotes for the GSTM1 and GSTT1 null alleles among the BA patients was observed. The frequency of the GSTM1 0/0, GSTT1 0/0 individuals among the patients was 57.9%, while it was only 4.7% among the controls (chi 2 = 27.4; P < 0.001).     

Assessing the genetic diversity in Argopecten nucleus (Bivalvia: Pectinidae), a functional hermaphrodite species with extremely low population density and self‐fertilization: Effect of null alleles

Argopecten nucleus is a functional hermaphroditic pectinid species that exhibits self‐fertilization, whose natural populations have usually very low densities. In the present study, the genetic diversity of a wild population from Neguanje Bay, Santa Marta (Colombia), was estimated using microsatellite markers, and the effect of the presence of null alleles on this estimation was assessed. A total of 8 microsatellite markers were developed, the first described for this species, and their amplification conditions were standardized. They were used to determine the genotype of 48 wild individuals from Naguanje Bay, and 1,010 individuals derived from the offspring of 38 directed crosses. For each locus, the frequencies of the identified alleles, including null alleles, were estimated using the statistical package Micro‐Checker, and the parental genotypes were confirmed using segregation analysis. Three to 8 alleles per locus with frequencies from 0.001 to 0.632 were detected. The frequencies of null alleles ranged from 0.10 to 0.45, with Ho from 0.0 to 0.79, and He from 0.53 to 0.80. All loci were in H‐W disequilibrium. The null allele frequencies values were high, with lower estimations using segregation analysis than estimated using Micro‐Checker. The present results show high levels of population genetic diversity and indicate that null alleles were not the only cause of deviation from H‐W equilibrium in all loci, suggesting that the wild population under study presents signs of inbreeding and Wahlund effect.     

GST M1-T1 null Allele Frequency Patterns in Geographically Assorted Human Populations: A Phylogenetic Approach

Genetic diversity in drug metabolism and disposition is mainly considered as the outcome of the inter-individual genetic variation in polymorphism of drug-xenobiotic metabolizing enzyme (XME). Among the XMEs, glutathione-S-transferases (GST) gene loci are an important candidate for the investigation of diversity in allele frequency, as the deletion mutations in GST M1 and T1 genotypes are associated with various cancers and genetic disorders of all major Population Affiliations (PAs). Therefore, the present population based phylogenetic study was focused to uncover the frequency distribution pattern in GST M1 and T1 null genotypes among 45 Geographically Assorted Human Populations (GAHPs). The frequency distribution pattern for GST M1 and T1 null alleles have been detected in this study using the data derived from literatures representing 44 populations affiliated to Africa, Asia, Europe, South America and the genome of PA from Gujarat, a region in western India. Allele frequency counting for Gujarat PA and scattered plot analysis for geographical distribution among the PAs were performed in SPSS-21. The GST M1 and GST T1 null allele frequencies patterns of the PAs were computed in Seqboot, Gendist program of Phylip software package (3.69 versions) and Unweighted Pair Group method with Arithmetic Mean in Mega-6 software. Allele frequencies from South African Xhosa tribe, East African Zimbabwe, East African Ethiopia, North African Egypt, Caucasian, South Asian Afghanistan and South Indian Andhra Pradesh have been identified as the probable seven patterns among the 45 GAHPs investigated in this study for GST M1-T1 null genotypes. The patternized null allele frequencies demonstrated in this study for the first time addresses the missing link in GST M1-T1 null allele frequencies among GAHPs.     

Polymorphic microsatellite DNA markers for Banksia attenuata (Proteaceae)

We developed 11 polymorphic microsatellite DNA markers for an Australian native shrub Banksia attenuata. The number of alleles per locus in 50 individuals varied from five to 18, observed and expected heterozygosities ranged from 0.300 to 0.740 and from 0.537 to 0.918, respectively. Six loci showed no significant deviation from Hardy–Weinberg equilibrium (P > 0.05), and null alleles appear to exist at locus BA‐B1. All loci showed independent inheritance.     

Benzo(a)pyrene diolepoxide adducts to albumin in workers exposed to polycyclic aromatic hydrocarbons: association with specific CYP1A1, GSTM1, GSTP1 and EHPX genotypes

We investigated whether the presence of (+)-anti-benzo(a)pyrene diolepoxide adducts to serum albumin (BPDE-SA) among workers exposed to benzo(a)pyrene (BaP) and unexposed reference controls was influenced by genetic polymorphisms of cytochrome P4501A1 (CYP1A1), microsomal epoxide hydrolase (EHPX), glutathione S-transferases M1 (GSTM1) and P1 (GSTP1), all involved in BaP metabolism. Exposed workers had significantly higher levels of adducts (0.124 ± 0.02 fmol BPTmg^?1 SA, mean ± SE) and a higher proportion of detectable adducts (40.3%) than controls (0.051 ± 0.01 fmol BPT mg^?1 SA; 16.1%) (p = 0:014 and p = 0:012). Smoking increased adduct levels only in occupationally exposed workers with the GSTM1 deletion (GSTM1 null) (p = 0:034). Smokers from the exposed group had higher adduct levels when they were CYP1A1 *1/*1 wild-type rather than heterozygous and homozygous for the variant alleles (CYP1A1 *1/*2 plus *2/*2) (p = 0:01). The dependence of BPDE-SA adduct levels and frequency on the CYP1A1 *1/*1 genotype was most pronounced in GSTM1-deficient smokers. Exposed workers with GSTM1 null/GSTP1 variant alleles had fewer detectable adducts than those with the GSTM1 null/GSTP1*A wild-type allele, supporting for the first time the recent in vitro finding that GSTP1 variants may be more effective in the detoxification of BPDE than the wild-type allele. Logistic regression analysis indicated that occupational exposure, wild-type CYP1A1*1/*1 allele and the combination of GSTM1 null genotype+EHPX genotypes associated with predicted low enzyme activity were significant predictors of BPDE-SA adducts. Though our findings should be viewed with caution because of the relatively limited size of the population analysed, the interaction between these polymorphic enzymes and BPDE-SA adducts seems to be specific for high exposure and might have an impact on the quantitative risk estimates for exposure to polycyclic aromatic hydrocarbons.     

Estimation and adjustment of microsatellite null alleles in nonequilibrium populations

Nonamplified (null) alleles are a common feature of microsatellite genotyping and can bias estimates of allele and genotype frequencies, thereby hindering population genetic analyses. The frequency of microsatellite null alleles in diploid populations can be estimated for populations that are in Hardy–Weinberg equilibrium. However, many microsatellite data sets are from nonequilibrium populations, often with known inbreeding coefficients (F) or fixation indices (F_IS or F_ST). Here, we propose a novel null allele estimator that can be used to estimate the null allele frequency and adjust visible allele frequencies in populations for which independent estimates of F, F_IS or F_ST are available. The algorithm is currently available as an Excel macro that can be downloaded at no cost from http://www.microchecker.hull.ac.uk/ and will be incorporated into the software micro ‐checker .     

Association of glutathione S-transferase polymorphisms (GSTM1 and GSTT1) with primary open-angle glaucoma: An evidence-based meta-analysis

Studies investigating the associations between glutathione S-transferase (GST) genetic polymorphisms and primary open-angle glaucoma (POAG) have reported controversial results. Therefore, a meta-analysis was performed to clarify the effects of GSTM1 and GSTT1 polymorphisms on POAG risk. Published literatures from PubMed, EMBASE, ISI Web of Science and CBM databases were retrieved. All studies evaluating the association between GSTM1/GSTT1 polymorphisms and POAG were included. Pooled odds ratio (OR) and 95% confidence interval (CI) were calculated using fixed- or random-effects model. Eleven studies on GSTM1 (1339 cases and 1412 controls) and seven studies on GSTT1 (958 cases, 1003 controls) were included. Overall analysis showed that the association between GSTM1 and GSTT1 null genotype and POAG risk is not statistically significant. Subgroup analyses showed that the null genotype of GSTM1 increased the risk of POAG in Asians. In GSTM1–GSTT1 interaction analysis, individuals with dual null genotype were associated with a significantly increased risk of POAG when compared with the dual present genotype. In conclusion, the present meta-analysis suggested that GSTM1 null genotypes are associated with increased POAG risk in Asian populations but not in Caucasian and mixed populations. Dual null genotype of GSTM1/GSTT1 is associated with increased risk of POAG. Given the limited sample size, the finding on GST polymorphisms needs further investigation.     

Molecular analysis of C1 alleles in Zea mays defines regions involved in the expression of this regulatory gene

The structure and function of several C1 alleles have been investigated molecularly and the importance of C1 promoter sequences for gene expression was studied using transient transformation assays. The C1 mutants analyzed were the overexpressing allele C1-S, the light-inducible allele c1-p, the null recessive allele c1-n, and the Ds element-induced allele c1-m1. Nucleotide sequence analysis of the alleles revealed a number of differences, predominantly located at the 3 end of the gene. The promoter sequences of the C1 alleles investigated so far (including wild-type and the dominant inhibitor C1-I allele) are almost identical except for two short footprint-like sequences (Box I and Box 11) close to the putative CAAT box. Northern blot experiments and transient expression in particle gun experiments indicate that these sequences may be correlated with the different expression patterns of the alleles in the aleurone of maturing and germinating kernels.     

Polymorphism A/G in Position +49 of CTLA4 Exon 1 in Multiple Sclerosis in Russians

The association of multiple sclerosis (MS) with alleles A and G of the cytotoxic T-lymphocyte antigen 4 (CTLA4) gene, a candidate gene for autoimmune disorders, was studied. The allele polymorhism results from single nucleotide substitution (A/G) in position +49 of exon 1 and leads to substitution Thr Ala in the leader peptide. The case–control study involved two groups of ethnic Russians: 168 MS patients and 209 healthy subjects from central Russia. Genotype frequencies were in agreement with the Hardy–Weinberg equilibrium in both groups (P > 0.05). The controls significantly differed in CTLA4 allele and genotype frequencies from Mongoloids but not from other Caucasians. No association was observed between MS and CTLA4. In addition, the combined association with MS was analyzed for both the CTLA4 alleles and allele groups of HLA DRB1. The results showed that the CTLA4 dimorphism does not affect susceptibility to MS in ethnic Russians, be these stratified or not with regard to DRB1 alleles corresponding to serologic specificities DR1 to DR16.     

Efficiency of the inbreeding coefficient f and other estimators in detecting null alleles,as revealed by empirical data of locus oke3 across 65 populations of chum salmon Oncorhynchus keta

A survey of 65 populations of chum salmon Oncorhynchus keta across the species range revealed homozygote excess (947 homozygotes in 2954 fish) at a polymerase chain reaction (PCR)‐based simple sequence repeat (SSR) locus oke3 with multiple alleles, whereas re‐designed PCR primers indicated that 328 of these homozygotes were actually heterozygotes. Statistically significant high positive values of inbreeding coefficients, f, in multiple populations appeared to be a reliable predictor of null alleles. Based on these data, three methods were checked for their ability to estimate null‐allele frequencies.     

Gene frequencies of caprine αs1-casein polymorphism in Spanish goat breeds

Using electrophoretic techniques (PAGE-SDS and IEF), we report allelic frequencies of caprine α_s1-casein (Cn) locus in four Spanish milking breeds: Murciana-Granadina, Malagueña, Payoya and Canaria. The E allele (intermediate content of α_s1-Cn in milk) was predominant in dairy breeds Murciana-Granadina, E:0.59; Malagueña, E:0.65 and Payoya, E:0.76, while alleles A and B (high content of α_s1-Cn) were more frequent in the Canaria dairy breed (A:0.28 and B:0.32). Among the Spanish breeds, Canaria represents a particular case where 60% of the alleles were of the high type (A and B). The ethnical group Canaria Palmera was particularly high in the frequency of alleles A and B (91%) very similar to the Italian Garganica breed (98%). The low frequency of F allele (reduced level of α_s1-Cn) in Spanish breeds (Murciana-Granadina, F:0.08; Malagueña, F:0.04; Payoya, F:0.00 and Canaria, F: and Saanen breeds. It is important to note that in the Payoya breed no low or null alleles (F, D, 0) were detected. It seems unlikely that genetic selection for milk production has had a significant influence in determining the α_s1-Cn allelic distribution in goat populations. The direct relationship existing between these allelic variants and differences in the Cn content and in the physico-chemical properties of milk, can be used as a tool in the improvement of milk processing quality and cheese yields of Spanish milking breeds.     

Expression of Alleles of the Mdh1Locus in Apozygotic Progenies of Sugar Beet Beta vulgarisL.

Expression of Mdh1alleles has been studied in 60 apozygotic (agamospermic) sugar beet progenies. Seed progenies were obtained by uniparental (pollenless) mode of seed reproduction: selfing of pollen-sterile plants isolated with paper bags. The apozygotic seed progenies demonstrate a disomic gamete autosegregation, i.e., the ratio between genotypes in the progenies correspond to the gamete segregation in a duplex heterozygote of an autotetraploid. It was shown that the ratio between theMdh1phenotypes in apozygotic progenies is strongly affected by spontaneous inactivation of one of the alleles. In most progenies, the excess of FF phenotypes and the deficit of SS phenotypes were observed. In our opinion, such deviations in genotype and phenotype frequencies result from conversion of the active Mdh1-Sinto the inactive Mdh1-S ⁰allele (epigenetic gene inactivation). The spontaneous inactivation of one allele results in extremely variable frequencies of heterozygous Mdh1-F/Mdh1-Sgenotypes and phenotypes in the apozygotic seed progenies. The empirical distribution of the frequencies of heterozygous genotypes in the apozygotic seed progenies is given by a negative binomial distribution describing the expected time of occurrence of random events.     

Isolation and characterization of microsatellite loci from the endangered Mediterranean sponge Spongia agaricina (Demospongiae: Dictyoceratida)

The abundance of the bath sponge Spongia agaricina has decreased drastically in recent years and it is now considered an endangered species under Annex 3 of Bern and Barcelona conventions. We describe eight microsatellite markers and present data on their allelic variation and utility as high resolution genetic markers. We analyzed 36 individuals from two populations and found that the number of alleles per locus ranged between 1 and 7. Observed heterozygosity ranged from 0 to 0.72. We found deviations from Hardy–Weinberg expectations for some loci. We exclusively detected null alleles for those loci that deviated from Hardy–Weinberg expectations. Also, distributions of allele frequencies differed significantly between the two populations, making them suitable for population genetic analyses.     

GSTT1 and GSTM1 gene polymorphisms in European and African populations

Glutathione S-transferases (GSTs) are a superfamily of detoxificant enzymes. Pharmacogenomic studies have revealed interethnic differences in GST allelic frequencies. This study is focused on GSTT1 (gene deletion, rs17850155, rs2234953, and rs11550605) and GSTM1 (gene deletion) gene frequency distributions in two population samples of Europe origin (Italy, n = 120; Spain, n = 94) and two population samples of Africa origin (Cameroon, n = 126; Ethiopia, n = 153). Detection of GSTT1 and GSTM1 null genotypes was performed by multiplex PCR analysis, while the other GSTT1 gene polymorphisms were detected using allele specific PCR and sequencing. GSTT1 and GSTM1 null frequencies in the samples analyzed fit with the variability range observed in European and African populations, respectively. The SNP analysis in GSTT1 gene did not highlight any nucleotide substitution in 493 individuals analyzed. The comparisons among GSTM1 and GSTT1 null phenotype frequencies in worldwide populations show different patterns between Asians, Africans, and Europeans. Important insights into the effects of GSTM1 and GSTT1 gene deletions on the pathogenesis of human diseases have been hypothesized. Detailed studies on the geography of GST variants could therefore increase knowledge about the relationship between ethnicity and the prevalence of certain diseases.