Polymorphism of trinucleotide repeats at loci FRAXA and FRAXE in the population of Tomsk

Polymorphism of CGG and GCC trinucleotide repeats, whose expansions at the FRAXA and FRAXE loci have been identified as causative mutations in two forms of mental retardation, was studied in Slavic population of Tomsk. At the FRAXA locus a total of 31 allelic variants ranging from 8 to 56 copies of CGG repeat with two modal classes of 28-29 and 18-20 repeat units (with the frequencies of 24.6 and 11.5% respectively) were revealed. Compared to other populations, this locus was characterized by unusually high frequency of intermediate alleles with the sizes of more than 40 CGG repeat units (12.4%). Since intermediate repeats of the FRAXA locus were more prone to instability than normal alleles, it was suggested that Slavic population of Siberia had higher risk of the development of FMR1 dynamic mutations, giving rise to the Martin-Bell syndrome. The FRAXE allele frequency distribution was demonstrated to be normal with 18 allelic variants ranging from 9 to 27 GCC repeat units. In the population of Tomsk this locus had higher than in other populations frequency (26.7%) of short (less than 15 repeat units in size) alleles. In addition, in the Tomsk population both loci were characterized by high level of heterozygosity and low frequencies of modal allele classes. These results can be explained by the high level of outbreeding typical of the population of Siberia.     

Polymorphism of Trinucleotide Repeats at Loci FRAXA and FRAXE in the Population of Tomsk

Polymorphism of CGG and GCC trinucleotide repeats, whose expansions at the FRAXA and FRAXE loci have been identified as causative mutations in two forms of mental retardation, was studied in Slavic population of Tomsk. At the FRAXA locus a total of 31 allelic variants ranging from 8 to 56 copies of CGG repeat with two modal classes of 28–29 and 18–20 repeat units (with the frequencies of 24.6 and 11.5% respectively) were revealed. Compared to other populations, this locus was characterized by unusually high frequency of intermediate alleles with the sizes of more than 40 CGG repeat units (12.4%). Since intermediate repeats of the FRAXAlocus were more prone to instability than normal alleles, it was suggested that Slavic population of Siberia had higher risk of the development of FMR1 dynamic mutations, giving rise to the Martin–Bell syndrome. The FRAXE allele frequency distribution was demonstrated to be normal with 18 allelic variants ranging from 9 to 27 GCC repeat units. In the population of Tomsk this locus had higher than in other populations frequency (26.7%) of short (less than 15 repeat units in size) alleles. In addition, in the Tomsk population both loci were characterized by high level of heterozygosity and low frequencies of modal allele classes. These results can be explained by the high level of outbreeding typical of the population of Siberia.     

Population and family studies of CAG repeats in the IT-15 gene

A simple and effective method for typing of CAG repeats in the IT-15 gene has been suggested. This method was applied for examination of the CAG allele distribution in Huntington's disease (HD) patients in five different populations from the Commonwealth of Independent States. A total of 21 normal alleles with the sizes ranging from 9 to 32 triplet repeat units were revealed. Moreover, alleles with the size ranging from 16 to 20 repeats predominated constituting from 54.4 to 74.6% of all alleles in different populations. The number of repeats in one allele in HD patients exceeded 38 units (43 triplets on average). In two families an increase in the CAG repeat units number in the mutant allele upon its paternal transmission was recorded.     

Population and Family Studies of the CAG Repeats in the IT-15Gene

A simple and effective method for typing of CAG repeats in the IT-15gene has been suggested. This method was applied for examination of the CAG allele distribution in Huntington's disease (HD) patients in five different populations from the Commonwealth of Independent States. A total of 21 normal alleles with the sizes ranging from 9 to 32 triplet repeats units were revealed. Moreover, alleles with the sizes ranging from 16 to 20 repeats predominated constituting from 54.4 to 74.6% of all alleles in different populations. The number of repeats in one allele in HD patients exceeded 38 units (43 triplets on average). In two families an increase in the CAG repeat units number in the mutant allele upon its paternal transmission was recorded.     

Rate and directionality of mutations and effects of allele size constraints at anonymous, gene-associated, and disease-causing trinucleotide loci.

We studied the patterns of within- and between-population variation at 29 trinucleotide loci in a random sample of 200 healthy individuals from four diverse populations: Germans, Nigerians, Chinese, and New Guinea highlanders. The loci were grouped as disease-causing (seven loci with CAG repeats), gene-associated (seven loci with CAG/CCG repeats and eight loci with AAT repeats), or anonymous (seven loci with AAT repeats). We used heterozygosity and variance of allele size (expressed in units of repeat counts) as measures of within-population variability and GST (based on heterozygosity as well as on allele size variance) as the measure of genetic differentiation between populations. Our observations are: (1) locus type is the major significant factor for differences in within-population genetic variability; (2) the disease-causing CAG repeats (in the nondisease range of repeat counts) have the highest within-population variation, followed by the AAT-repeat anonymous loci, the AAT-repeat gene-associated loci, and the CAG/CTG-repeat gene-associated loci; (3) an imbalance index beta, the ratio of the estimates of the product of effective population size and mutation rate based on allele size variance and heterozygosity, is the largest for disease-causing loci, followed by AAT- and CAG/CCG-repeat gene-associated loci and AAT-repeat anonymous loci; (4) mean allele size correlates positively with allele size variance for AAT- and CAG/CCG-repeat gene-associated loci and negatively for anonymous loci; and (5) GST is highest for the disease-causing loci. These observations are explained by specific differences of rates and patterns of mutations in these four groups of trinucleotide loci, taking into consideration the effects of the past demographic history of the modern human population.     

Patterns of instability of expanded CAG repeats at the ERDA1 locus in general populations.

A highly polymorphic CAG repeat locus, ERDA1, was recently described on human chromosome 17q21.3, with alleles as large as 50-90 repeats and without any disease association in the general population. We have studied allelic distribution at this locus in five human populations and have characterized the mutational patterns by direct observation of 731 meioses. The data show that large alleles (>/=40 CAG repeats) are generally most common in Asian populations, less common in populations of European ancestry, and least common among Africans. We have observed a high intergenerational instability (46. 3%+/-5.1%) of the large alleles. Although the mutation rate is not dependent on parental sex, paternal transmissions have predominantly resulted in contractions, whereas maternal transmissions have yielded expansions. Within this class of large alleles, the mutation rate increases concomitantly with increasing allele size, but the magnitude of repeat size change does not depend on the size of the progenitor allele. Sequencing of specific alleles reveals that the intermediate-sized alleles (30-40 repeats) have CAT/CAC interruptions within the CAG-repeat array. These results indicate that expansion and instability of trinucleotide repeats are not exclusively disease-associated phenomena. The implications of the existence of massively expanded alleles in the general populations are not yet understood.     

Low variability of the POLG (CAG)n repeat in north Eurasian populations

We investigated the frequency of different repeat-length alleles of the trinucleotide CAG microsatellite repeat in the coding sequence of the nuclear gene for the catalytic subunit of mitochondrial DNA polymerase gamma (POLG) in 12 ethnic groups from northern Eurasia. The population sample consisted of 1,330 individuals from 3 large geographic areas: Europe, Southwest Asia, and Siberia/East Asia. We found that the 10-repeat allele of the POLG gene is the most frequent in all analyzed populations, with a frequency of 88-96%. The heterozygosity level ranges from 22% in Europe to 13.6% in Southwest Asia with the lowest value of 7.4% in Siberia/East Asia. The present study provides evidence of clinal distribution of POLG gene heterozygosity in North Eurasian populations. In general, we found an extremely low variability of the trinucleotide CAG microsatellite repeat, suggesting that purifying selection acts against deleterious alleles, although low mutability of the repeated region cannot be ruled out.     

Molecular analysis of autosomal dominant hereditary ataxias in the Indian population: high frequency of SCA2 and evidence for a common founder mutation

Expansion of CTG/CAG trinucleotide repeats has been shown to cause a number of autosomal dominant cerebellar ataxias (ADCA) such as SCA1, SCA2, SCA3/ MJD, SCA6, SCA7, SCA8 and DRPLA. There is a wide variation in the clinical phenotype and prevalence of these ataxias in different populations. An analysis of ataxias in 42 Indian families indicates that SCA2 is the most frequent amongst all the ADCAs we have studied. In the SCA2 families, together with an intergenerational increase in repeat size, a horizontal increase with the birth order of the offspring was also observed, indicating an important role for parental age in repeat instability. This was strengthened by the detection of a pair of dizygotic twins with expanded alleles showing the same repeat number. Haplotype analysis indicates the presence of a common founder chromosome for the expanded allele in the Indian population. Polymorphism of CAG repeats in 135 normal individuals at the SCA loci studied showed similarity to the Caucasian population but was significantly different from the Japanese population.     

Relationship of (CAG)nC configuration to repeat instability of the Machado-Joseph disease gene

The mutation responsible for Machado-Joseph disease (MJD) has been identified as an expansion of a CAG trinucleotide repeat in a novel gene on chromosome 14q32.1. The CAG repeat tract is followed by C or G, and alleles are thereby divided into two types on the basis of molecular configuration, (CAG)nC and (CAG)nG. We have studied the relationship between the repeat length and the configuration in 38 patients from 28 Japanese families with MJD, and 31 unrelated normal Japanese subjects. The CAG repeat length in 100 normal alleles ranged from 13 to 37 repeats, while 38 MJD patients had one expanded allele with 64 to 84 repeats. Surprisingly, the expanded alleles had exclusively the (CAG)nC configuration, while both (CAG)nC and (CAG)nG were seen in normal alleles from MJD and control subjects. Furthermore, in normal alleles, the CAG repeat tract was significantly longer in (CAG)nC than in (CAG)nG. These findings suggest that the (CAG)nC configuration is related to repeat instability of the MJD gene. Received: 23 April 1996 / Revised: 24 June 1996     

Ethnic and Geographical Aspects of the Prevalence of the Polymorphic Variants of Genes Associated with Tuberculosis

Specificity of the structure of gene pools of different ethno-territorial groups of the human population can underlie the epidemiological features of the spread of tuberculosis (TB) and the structure of the genetic component of the susceptibility to the disease. The variability of 62 genetic variants potentially associated with the risk of the development of TB in the Russian population of the city of Tomsk has been studied and the differentiation of various ethno-territorial groups of the world by these markers has been assessed. The studied sample comprised 445 Russian residents of the city of Tomsk without bronchopulmonary pathology. For comparison, the data on the variability of the genetic markers of interest in 26 populations from the 1000 Genomes Project was involved. In the Tomsk population, only the ancestral allele was found for seven of the 58 SNPs studied; the allele frequencies for 36 markers were within the limits of the values seen in other European populations; for 12 SNPs, the observed frequencies were closer to populations with a significant Mongoloid component. By the total of the SNPs, the Tomsk population, despite the geographical distance from the rest of the European populations, did not differ from them (in genetic distances and G_st statistics), although it had some features of the gene pool. Intergroup differentiation of the world populations by these SNPs reflects mainly interracial differences. The greatest differences in the genetic structure between the studied populations were seen for the markers localized in intergenic regions. Statistically significant differences were found when comparing the levels of the average expected heterozygosity between groups of “L4 carrier populations” of mycobacteria and “non-L4” populations, which indicates the impact of the prevalence of different pathogenic lineages of M. tuberculosis on the formation of population specificity of the allelic frequencies.     

Distribution of CAG repeat size in the dentatorubral and pallidoluysian atrophy (DRPLA) gene in a normal population in Taiwan

Dentatorubral and pallidoluysian atrophy (DRPLA) is an autosomal dominant neurodegenerative disorder with expansion of trinucleotide CAG repeats in the coding region of the gene. Expansion of the repeat tract beyond the normal range produces gene products with extended polyglutamine tracts. In this study, we analyzed the distribution of the CAG repeats in the DRPLA alleles in a normal Taiwanese population. We observed 15 different alleles and found that the range of the CAG repeat number was from 7-21. The most frequent allele contained 15 CAG repeats that represented 20% of the total analyzed alleles, followed by the 17 repeats (15.8%). The heterozygosity rate of this locus was 88%. Twelve parents-to-children transmissions of the DRPLA alleles in a Machado-Joseph disease family appeared to be normal without any alteration of the CAG repeat numbers. Phenotypes of DRPLA overlapped those of autosomal dominant cerebellar ataxia (ADCA). In order to identify DRPLA patients in Taiwan, we screened six autosomal dominant cerebellar ataxia patients without expansion in known spinocerebellar ataxia genes. All six patients had the repeat numbers within the normal range; thus, the possibility of DRPLA could be excluded.     

Extent of linkage disequilibrium between the androgen receptor gene CAG and GGC repeats in human populations: implications for prostate cancer risk

While studies have implicated alleles at the CAG and GGC trinucleotide repeats of the androgen receptor gene with high-grade, aggressive prostate cancer disease, little is known about the normal range of variation for these two loci, which are separated by about 1.1 kb. More importantly, few data exist on the extent of linkage disequilibrium (LD) between the two loci in different human populations. Here we present data on CAG and GGC allelic variation and LD in six diverse populations. Alleles at the CAG and GGC repeat loci of the androgen receptor were typed in over 1000 chromosomes from Africa, Asia, and North America. Levels of linkage disequilibrium between the two loci were compared between populations. Haplotype variation and diversity were estimated for each population. Our results reveal that populations of African descent possess significantly shorter alleles for the two loci than non-African populations (P<0.0001). Allelic diversity for both markers was higher among African Americans than any other population, including indigenous Africans from Sierra Leone and Nigeria. Analysis of molecular variance revealed that approx. 20% of CAG and GGC repeat variance could be attributed to differences between the populations. All non-African populations possessed the same common haplotype while the three populations of African descent possessed three divergent common haplotypes. Significant LD was observed in our sample of healthy African Americans. The LD observed in the African American population may be due to several reasons; recent migration of African Americans from diverse rural communities following urbanization, recurrent gene flow from diverse West African populations, and admixture with European Americans. This study represents the largest genotyping effort to be performed on the two androgen receptor trinucleotide repeat loci in diverse human populations.     

No CAG repeat expansion of polymerase gamma is associated with male infertility in Tamil Nadu,South India

Mitochondria contains a single deoxyribonucleic acid (DNA) polymerase, polymerase gamma (POLG) mapped to long arm of chromosome 15 (15q25), responsible for replication and repair of mitochondrial DNA. Exon 1 of the human POLG contains CAG trinucleotide repeat, which codes for polyglutamate. Ten copies of CAG repeat were found to be uniformly high (0.88) in different ethnic groups and considered as the common allele, whereas the mutant alleles (not -10/not -10 CAG repeats) were found to be associated with oligospermia/oligoasthenospermia in male infertility. Recent data suggested the implication of POLG CAG repeat expansion in infertility, but are debated. The aim of our study was to explore whether the not -10/not -10 variant is associated with spermatogenic failure. As few study on Indian population have been conducted so far to support this view, we investigated the distribution of the POLG CAG repeats in 61 infertile men and 60 normozoospermic control Indian men of Tamil Nadu, from the same ethnic background. This analysis interestingly revealed that the homozygous wild type genotype (10/-10) was common in infertile men (77% - 47/61) and in normozoospermic control men (71.7% - 43/60). Our study failed to confirm any influence of the POLG gene polymorphism on the efficiency of the spermatogenesis.     

SCA8 repeat expansion: large CTA/CTG repeat alleles are more common in ataxic patients,including those with SCA6

We analyzed the SCA8 CTA/CTG repeat in a large group of Japanese subjects. The frequency of large alleles (85-399 CTA/CTG repeats) was 1.9% in spinocerebellar ataxia (SCA), 0.4% in Parkinson disease, 0.3% in Alzheimer disease, and 0% in a healthy control group; the frequency was significantly higher in the group with SCA than in the control group. Homozygotes for large alleles were observed only in the group with SCA. In five patients with SCA from two families, a large SCA8 CTA/CTG repeat and a large SCA6 CAG repeat coexisted. Age at onset was correlated with SCA8 repeats rather than SCA6 repeats in these five patients. In one of these families, at least one patient showed only a large SCA8 CTA/CTG repeat allele, with no large SCA6 CAG repeat allele. We speculate that the presence of a large SCA8 CTA/CTG repeat allele influences the function of channels such as alpha(1A)-voltage-dependent calcium channel through changing or aberrant splicing, resulting in the development of cerebellar ataxia, especially in homozygous patients.     

Analysis of polymorphic loci of Huntington genes in peoples from the Volga-Ural region

Eleven populations of the Volga-Ural region were analyzed with respect to three intragenic polymorphisms of the Huntington disease gene (IT15), including highly polymorphic (CAG)n and moderately polymorphic (CCG)n of exon 1 and neutral del2642 of exon 58. In the case of (CAG)n, 101 genotypes were observed, with genotype number varying from 15 in Southeastern Bashkirs to 34 in Mari. Allele diversity RS ranged from 9.70 in Southeastern Bashkirs to 18.00 in Chuvash, averaging 13.79 +/- 2.12. The (CAG)n allele frequency distribution was unimodal and had a maximum at (CAG)17. In the case of (CCG)n, six alleles with 6-10 or 12 repeats were observed. RS was 4.13 +/- 0.44, ranging from 3.73 in Udmurts to 4.99 in Tatars. In the case of del2642, allele del- was detected at a frequency 0.830 in Mari to 0.932 in Udmurts. Of all Volga-Ural ethnic populations, Finno-Ugric ones proved to be most heterogeneous with respect to the three polymorphisms, whereas Turkic populations and, in particular, Bashkirs were homogeneous. Micro-differentiation of the Volga-Ural populations corresponded to the European type.     

Alcohol dehydrogenases ADH1B and ADH7 gene polymorphism in Russian population from the Siberian region

The Allele and genotype didtributions of the two alcohol dehydrogenase genes ADH1B (polymorphism A/G in exon 3, detected with restrictase MslI) and ADH7 (polymorphism G/C in intron 5, detected with restrictase StyI) was studied in three Russian populations from the Siberian region. The absence of interpopulation and intersexual differences in the allele frequency was determined. The allele ADH1B*G (+MslI, A2) was found in low frequency (3.6-7.5%), the mutant allele ADH7 (-StyI, B2) frequency in total population (n = 339) was 46.02%. The genotype distributions of the ADH1B and ADH7 in these populations were agreed with the Hardy-Weinberg equilibrium and linkage equilibrium. Increased frequency of ADH7 B2 allele was revealed in elder group (after 40 years) in the total sample and in the Tomsk city inhabitants (n = 113) on 11% (P = 0.001) and 9% (P = 0.017) accordingly. ADH7 and ADH1B genes polymorpisms did not show association with antioxidant activity, which was determined from the blood plasma ability to reduce the yield of products interacting with thiobarbituric acid in the lecitin-Fe2+ ions model system. The statistically significant decrease of serum very low density lipoproteins (LPVLD) level (on 9.95%, P = 0.045) and close to statistically significant decrease systolic pressure (on 6.80%, P = 0.068) and serum triglycerides level (on 6.16 of %, P = 0.058) were revealed among the A2 allele ADH1B gene carriers in Tomsk population.     

Length Variation of Cag/Caa Trinucleotide Repeats in Natural Populations of Drosophila Melanogaster and Its Relation to the Recombination Rate

Eleven genes distributed along the Drosophila melanogaster chromosome 2 and showing exonic tandem repeats of glutamine codons (CAG or CAA) were surveyed for length variation in a sample of four European and African populations. Only one gene was monomorphic. Eight genes were polymorphic in all populations, with a total number of alleles varying between five and 12 for 120 chromosomes. The average heterozygozity per locus and population was 0.41. Selective neutrality in length variation could not be rejected under the assumptions of the infinite allele model. Significant population subdivision was found though no geographical pattern emerged, all populations being equally different. Significant linkage disequilibrium was found in four out of seven cases where the genetic distance between loci was <1 cM and was negligible when the distance was larger. There is evidence that these associations were established after the populations separated. An unexpected result was that variation at each locus was independent of the coefficient of exchange, although the latter ranged from zero to the relatively high value of 6.7%. This would indicate that background selection and selective hitchhiking, which are thought to affect levels of nucleotide substitution polymorphism, have no effect on trinucleotide repeat variation.     

Analysis of the IT15 gene in Huntington's disease families

Direct molecular genetic testing carried out in 59 Huntington's disease patients belonging to 46 families from Bashkortostan revealed the (CAG)n repeat expansion in exon 1 of the IT15 gene in 57 of them. By use of this analysis the disease status was not confirmed in two patients with atypical form of the disease and negative family history. The (CAG)n repeat expansion was identified in 27 out of 127 asymptomatic at-risk individuals. Analysis of the mutant (CAG)n allele inheritance demonstrated extremely high instability and high mutation rate predominantly leading to the appearance of the alleles with increasing number of (CAG)n repeats in subsequent generations. The instability was mostly observed in cases of paternal transmission. Almost complete linkage disequilibrium between the (CCG)7 mutant alleles and the del2642 deletion was demonstrated. Three major haplotypes revealed, (CCG)7/del-, (CCG)7/del+, and (CCG)10/del-, implied the existence of at least three sources of the origin of Huntington's disease in Bashkortostan. The identified haplotype frequency distribution patterns displayed similarities with those in European populations. The contribution of a number of genetic factors to the age of onset of Huntington's disease was analyzed.