The role of epistasis in the etiology of Polycystic Ovary Syndrome among Indian women: SNP-SNP and SNP-environment interactions.

Polycystic Ovary Syndrome (PCOS) is the most common endocrinopathy in women of reproductive age. It is a heterogeneous androgen excess disorder determined by the interaction of multiple genetic and environmental factors. Our earlier analysis on a panel of six candidate genes (Androgen receptor CAG repeats, Follistatin, Luteinizing hormone ß subunit, Calpain10, Insulin receptor substrate-1 and PPARγ) based on 250 PCOS cases and 299 controls revealed significant association patterns with PCOS among South-Indian women. We report here for the first time, the SNP-SNP and SNP-environment interactions of these genes in the same cohort. Both multivariate logistic regression as well as epistasis analysis (using Multifactor dimensionality reduction software) yielded significant results (P < 0.05). All CAPN10 SNPs show association (either risk-conferring or protective) in the obese group, highlighting the importance of this gene in the PCOS pathophysiology. LHP7(LHß) and UCSNP44(CAPN10) emerged to be the prominent SNPs in the SNP-SNP interaction analysis. The best SNP-SNP interaction model was obtained between CAPN10 UCSNP-44 and PPARγ His447His, implying a significant metabolic component in the PCOS pathology. Replicating our findings in BMI-specific cohorts in different ethnic populations would be warranted in future to identify the physiological networks in PCOS.

Novel alleles of HLA-DQ and -DR loci show association with recurrent miscarriages among South Indian women.

BACKGROUND In this study, recurrent miscarriages (RMs) are defined as loss of two or more clinically detectable pregnancies before 20 weeks of gestation. HLA has been thought to play a role in RM. However, the results of earlier studies on the role of different human leucocyte antigen (HLA) genes were conflicting and inconclusive. In the present study, we investigate HLA genes (HLA-DRA, HLA-DRB1, HLA-DQA1 and HLA-DQB1) in RM couples with unknown etiology and normal couples. METHODS Blood samples from 143 RM couples and 150 control couples were analyzed, firstly to validate previously reported association studies and secondly to explore whether any novel alleles or haplotypes specific to Indian populations can be observed to be associated with RM. HLA typing was carried out by DNA sequencing. RESULTS Results suggest an association of the DQB1*03:03:02 allele with RM (odd ratio = 2.66; p(c) = 0.02; confidence interval = 1.47-4.84). Haplotypes of the DQA1 and DQB1 risk alleles also showed a significant association with RM, albeit not after Bonferroni correction for multiple comparisons. CONCLUSIONS HLA-DQB1 appears to have a strong involvement in the manifestation of RM in this population from South India. The current genetic analysis of RM and control couples not only highlights the genes exhibiting a strong etiological role but also reflects the protective nature of some HLA genes against RM. Nevertheless, most of these alleles/haplotypes were not those that are implicated in RM in other ethnic backgrounds, and hence require further validation in other populations of India, from different ethnic and/or geographic backgrounds.

Molecular genetic perspectives on the Indian social structure.

For historical reasons, the Indian subcontinent is endowed with enormous ethnic, cultural, and genetic heterogeneity of its people. In the process of understanding the dynamics and sociocultural complexity of Indian society, anthropologists have come up with a number of hypotheses involving certain social/cultural processes that may modulate evolutionary processes. In this article, we outline some of those hypotheses and present molecular genetic evidences, both published and unpublished, to demonstrate the effects of those social/cultural processes.

Global patterns in human mitochondrial DNA and Y-chromosome variation caused by spatial instability of the local cultural processes.

Because of the widespread phenomenon of patrilocality, it is hypothesized that Y-chromosome variants tend to be more localized geographically than those of mitochondrial DNA (mtDNA). Empirical evidence confirmatory to this hypothesis was subsequently provided among certain patrilocal and matrilocal groups of Thailand, which conforms to the isolation by distance mode of gene diffusion. However, we expect intuitively that the patterns of genetic variability may not be consistent with the above hypothesis among populations with different social norms governing the institution of marriage, particularly among those that adhere to strict endogamy rules. We test the universality of this hypothesis by analyzing Y-chromosome and mtDNA data in three different sets of Indian populations that follow endogamy rules to varying degrees. Our analysis of the Indian patrilocal and the matrilocal groups is not confirmatory to the sex-specific variation observed among the tribes of Thailand. Our results indicate spatial instability of the impact of different cultural processes on the genetic variability, resulting in the lack of universality of the hypothesized pattern of greater Y-chromosome variation when compared to that of mtDNA among the patrilocal populations.

Present status of understanding on the genetic etiology of polycystic ovary syndrome.

Polycystic ovary syndrome (PCOS) is the most common endocrinopathy in women of reproductive age with a prevalence of approximately 7-10% worldwide. PCOS reflects multiple potential aetiologies and variable clinical manifestations. This syndrome is characterized by serious health implications such as diabetes, coronary heart diseases and cancer and also leads to infertility. PCOS can be viewed as a heterogeneous androgen excess disorder with varying degrees of reproductive and metabolic abnormalities determined by the interaction of multiple genetic and environmental factors. In this paper, we have attempted a comprehensive review of primarily molecular genetic studies done so far on PCOS. We have also covered the studies focusing on the environmental factors and impact of ethnicity on the presentation of this syndrome. A large number of studies have been attempted to understand the aetiological mechanisms behind PCOS both at the clinical and molecular genetic levels. In the Indian context, majority of the PCOS studies have been confined to the clinical dimensions. However, a concrete genetic mechanism behind the manifestation of PCOS is yet to be ascertained. Understanding of this complex disorder requires comprehensive studies incorporating relatively larger homogenous samples for genetic analysis and taking into account the ethnicity and the environmental conditions of the population/cohort under study. Research focused on these aspects may provide better understanding on the genetic etiology and the interaction between genes and environment, which may help develop new treatment methods and possible prevention of the syndrome.

Utility of anthropometric traits and indices in predicting the risk of coronary artery disease in the adult men of southern Andhra Pradesh.

BACKGROUND/AIM: Optimal cutoff values are influenced by ethnicity, geography, lifestyles, and physical activity, and hence, there is a need for establishing population- and disease-specific cutoff values to screen individuals/populations. Therefore, the present study was carried out to determine the optimal cutoff values of anthropometric variables for coronary artery disease (CAD) for the population of southern Andhra Pradesh. METHODS: One hundred sixty five patients with CAD and 87 controls were recruited, and 52 anthropometric variables were measured for them. RESULTS: Higher means in 22 anthropometric variables covering circumferences, skinfold thickness (sft), and indices were observed in patients than those in controls. Receiver operator curve analysis revealed that 18 variables including circumference, sft, and fat measures with an area under curve ranging from 0.61 to 0.72 were found to have the ability of predicting the risk of CAD. A stepwise discriminant analysis showed 9 variables to correctly classify 87.4% of subjects into CAD and controls. In logistic regression analysis, among these 9 variables, only circumferences of abdomen and foot; sft of supratellar, thigh and calf; and sum of subscapular/suprailiac, waist-hip ratio and lean body mass were associated with CAD and explained 73.4% of its variation. CONCLUSIONS: Eighteen anthropometric variables were found to have the ability of predicting the risk of CAD. Longitudinal studies are needed to confirm the use of anthropometric variables in predicting the risk of CAD.

Genetic affinities among the lower castes and tribal groups of India: inference from Y chromosome and mitochondrial DNA.

BACKGROUND: India is a country with enormous social and cultural diversity due to its positioning on the crossroads of many historic and pre-historic human migrations. The hierarchical caste system in the Hindu society dominates the social structure of the Indian populations. The origin of the caste system in India is a matter of debate with many linguists and anthropologists suggesting that it began with the arrival of Indo-European speakers from Central Asia about 3500 years ago. Previous genetic studies based on Indian populations failed to achieve a consensus in this regard. We analysed the Y-chromosome and mitochondrial DNA of three tribal populations of southern India, compared the results with available data from the Indian subcontinent and tried to reconstruct the evolutionary history of Indian caste and tribal populations. RESULTS: No significant difference was observed in the mitochondrial DNA between Indian tribal and caste populations, except for the presence of a higher frequency of west Eurasian-specific haplogroups in the higher castes, mostly in the north western part of India. On the other hand, the study of the Indian Y lineages revealed distinct distribution patterns among caste and tribal populations. The paternal lineages of Indian lower castes showed significantly closer affinity to the tribal populations than to the upper castes. The frequencies of deep-rooted Y haplogroups such as M89, M52, and M95 were higher in the lower castes and tribes, compared to the upper castes. CONCLUSION: The present study suggests that the vast majority (> 98%) of the Indian maternal gene pool, consisting of Indio-European and Dravidian speakers, is genetically more or less uniform. Invasions after the late Pleistocene settlement might have been mostly male-mediated. However, Y-SNP data provides compelling genetic evidence for a tribal origin of the lower caste populations in the subcontinent. Lower caste groups might have originated with the hierarchical divisions that arose within the tribal groups with the spread of Neolithic agriculturalists, much earlier than the arrival of Aryan speakers. The Indo-Europeans established themselves as upper castes among this already developed caste-like class structure within the tribes.

Status of Austro-Asiatic groups in the peopling of India: An exploratory study based on the available prehistoric, linguistic and biological evidences.

Among the most contentious currently debated issues is about the people who had settled first in the Indian subcontinent. It has been suggested that the communities affiliated to the Austro-Asiatic linguistic family are perhaps the first to settle in India and the palaeoanthropological evidences suggest the earliest settlement probably around 60,000 years BP. Recent speculations, based on both traditional genetic markers and DNA markers, seem to corroborate the aforesaid view. However, these studies are inadequate both in terms of the representation of the constituent groups within this broad linguistic category as well as the number of samples that represent each of them. We strongly feel that, before making any formidable conclusions on the peopling of India and/or the history of settlement, it is necessary to ascertain that the Austro-Asiatic speakers, represented by over 30 different tribal groups, either genetically constitute a homogenous single entity or are a heterogeneous conglomeration, derived from different sources. As a first step towards this we tried to collate and analyse the existing information geographic, ethno-historic, cultural and biological. The results of the analyses of anthropometric and genetic marker data indicate that the Austro-Asiatic groups, particularly the Mundari speakers, with certain exceptions, show greater homogeneity among them when compared to the other linguistic groups, although certain groups show as outliers. However, traditional genetic markers show lower within population heterozygosity compared to Dravidian and other Indian populations. This is contrary to what has been claimed in case of certain DNA markers. Given that relatively greater heterozygosity among the Austro-Asiatic populations has been taken as one of the important evidences supporting greater antiquity of these populations one should await results of detailed DNA studies being currently undertaken by us, involving a number of Austro-Asiatic and other ethnic populations of India to resolve the issue unequivocally.

Fluctuating asymmetry and canalization: An appraisal based on a-b ridge counts among Indian populations with diverse backgrounds.

The relationship between fluctuating asymmetry, measured as the absolute difference between the right and left a-b ridge counts, and total a-b (R + L) ridge count was studied in an assortment of Indian population samples representing a wide spectrum of socioeconomic and occupational backgrounds. They included marine fishermen, inland and estuarine fishermen as well as migrants and their parental counterparts, tribes, and castes of different hierarchy- lower, middle, and upper. The samples together numbered a total of 3,239 subjects, 2,240 males and 999 females. The results failed to support Jantz and Webb's (1980) hypothesis of a quadratic relationship between fluctuating asymmetry of a-b ridge count and its phenotypic value. Only 3 of 22 samples (about 13%) showed a significant fit with a reasonable degree of consistency over a set of independent random subsamples; even initially only 7 of 22 (about 30%) samples showed a significant fit, or nearly so. Supplementary evidence drawn from these populations with reference to the relationship between fluctuating asymmetry and heterozygosity levels and inbreeding coefficients was also consistent with the interference that fluctuating asymmetry of a-b as it is measured and examined at the population level does not reflect canalization. Am. J. Hum. Biol. 11:367-381, 1999. Copyright 1999 Wiley-Liss, Inc.

Dermatoglyphic affinities among the Telugu populations with contrasting ethnohistorical backgrounds.

Using 22 finger dermatoglyphic variables (radial and ulnar ridge counts on each of the 10 fingers, total number of whorls and total number of loops per individual), affinities among the five endogamous populations of Andhra Pradesh with contrasting ethnohistorical backgrounds were examined. The samples constitute rolled fingerprints of 1,334 individuals of all ages, 736 males and 598 females, and were drawn from the three southern districts of Andhra Pradesh. Univariate analysis of variance, cluster analysis of Mahalanobis' D2 -values, and stepwise discriminant analysis were employed to study the extent of population heterogeneity and nature of relationships among them. The observed dermatoglyphic affinities conform to the known ethnohistorical and geographical backgrounds. The smallest set of 9 most discriminating variables gives the best configuration expected under ethnohistorical backgrounds. Addition of more variables, although further augmenting the dispersion among the group centroids, distrots the picture of known ethnohistorical relatiohships. © 1992 Wiley-Liss, Inc.

Quantitative dermatoglyphics and population structure in Northwest India.

The nature and extent of dermatoglyphic variation in northwest India is examined with the help of 28 quantitative variables-20 finger ridge counts and 8 palmar pattern ridge counts-among 12 endogamous populations. These populations represent the entire spectrum of ethnic and socioeconomic variation of the region and are presently distributed in three different states-Rajasthan, Punjab, and Himachal Pradesh. Of a total sample of 1,160 adult males, about 100 from each group were considered. Multiple discriminant analysis and R-matrix analysis were used to derive population relationships and patterns of external gene flow, respectively. Published data on genetic markers were reanalyzed to make the comparative evaluation of the patterns with reference to dermatoglyphs. Both the discriminant analysis and the F(ST) from R-matrix analysis suggest highly significant discrimination among the northwestern groups, whether one uses only 20 finger ridge count variables or all 28 variables, including the 8 palmar pattern ridge counts. The 8 palmar variables add very little to the variation explained by the 20 finger ridge count variables. F(ST) values suggest that the populations of Punjab are most homogeneous and those of Himachal Pradesh most heterogeneous. However, the levels of differentiation are similar for dermatoglyphs and genetic markers. The pattern of external gene flow as inferred through R-matrix analysis is consistent with the breeding and population structure of the groups, although genetic markers portray a relatively more realistic picture. Overall, the patterns of variation observed in dermatoglyphs and genetic markers are consistent with different dimensions of population structure; whereas dermatoglyphs conform more to the geographic pattern and less to ethnic resemblance, the reverse is true in the case of genetic markers. Am. J. Hum. Biol. 12:315-326, 2000. Copyright 2000 Wiley-Liss, Inc.

Genetic affinities between the migrant and parental populations of fishermen, East coast, India.

Genetic affinities between the migrant groups of fishermen from Puri and their parental counterparts in the Southern areas were examined using 11 genetic loci: four blood groups, five red cell enzymes, and two serum proteins. The samples for the parental populations (about 430 subjects) were drawn from 34 villages spread along the 400 km coast in Ganjam district of Orissa and the contiguous Srikakulam, Vishakhapatnam, and East Godavari districts of Andhra Pradesh. Significant departures between the migrant groups and their parental counterparts were observed at some loci, although the configuration of interpopulation distances among the migrants mimicked that of the parental populations. While the observed differences may be due to a founder effect and subsequent random genetic drift in at least two of the three small populations, given high child mortality and the systematic nature of differences observed, the role of selection cannot be totally ruled out. © 1995 Wiley-Liss, Inc.

Polymorphisms in the IRS-1 and PPAR-γ genes and their association with polycystic ovary syndrome among South Indian women.

Polycystic ovary syndrome is known to be characterized by metabolic abnormalities such as hyperinsulinemia, adiposity and dyslipidemia. Both insulin receptor substrate-1 and peroxisome proliferator-activated receptor-γ have emerged as significant candidate genes in the pathogenesis of PCOS. In this study, we report for the first time, the association pattern of these genes with PCOS among South Indian women. Two hundred fifty PCOS cases and 299 controls were sequenced for IRS-1 exon1 and PPAR-γ exon 2 and exon 6 to study the already reported SNPs in other ethnic groups and to identify any novel SNP in these exonic regions specific to the Indian population. We did not find any novel SNP in our population except for those already reported- two IRS-1 polymorphisms (Gly972Arg and G2323A) and two PPAR-γ polymorphisms (Pro12Ala and His447His). While the IRS-1 polymorphic alleles had a similar distribution between cases and controls, the PPAR-γ exon 2 Ala allele and exon 6 His447His T allele were significantly more in the controls than in the cases (p≤0.05). Haplotype association analysis also suggests that both IRS-1 and PPAR-γ haplotypes with mutations depicted reduced frequency of hyperandrogenic and metabolic traits in PCOS compared to the haplotype with only wild type alleles. Our study on Indian women suggests that while IRS-1, contrary to the earlier findings in other ethnic groups, seems to have a probable protective role against development of specific PCOS sub-phenotypes, the evidence for a probable protective role of PPAR-γ is reaffirmed in our study.

Association of CAPN10 SNPs and haplotypes with polycystic ovary syndrome among South Indian Women.

Polycystic Ovary Syndrome (PCOS) is known to be characterized by metabolic disorder in which hyperinsulinemia and peripheral insulin resistance are central features. Given the physiological overlap between PCOS and type-2 diabetes (T2DM), and calpain 10 gene (CAPN10) being a strong candidate for T2DM, a number of studies have analyzed CAPN10 SNPs among PCOS women yielding contradictory results. Our study is first of its kind to investigate the association pattern of CAPN10 polymorphisms (UCSNP-44, 43, 56, 19 and 63) with PCOS among Indian women. 250 PCOS cases and 299 controls from Southern India were recruited for this study. Allele and genotype frequencies of the SNPs were determined and compared between the cases and controls. Results show significant association of UCSNP-44 genotype CC with PCOS (p = 0.007) with highly significant odds ratio when compared to TC (OR = 2.51, p = 0.003, 95% CI = 1.37-4.61) as well as TT (OR = 1.94, p = 0.016, 95% CI = 1.13-3.34). While the haplotype carrying the SNP-44 and SNP-19 variants (21121) exhibited a 2 fold increase in the risk for PCOS (OR = 2.37, p = 0.03), the haplotype containing SNP-56 and SNP-19 variants (11221) seems to have a protective role against PCOS (OR = 0.20, p = 0.004). Our results support the earlier evidence for a possible role of UCSNP-44 of the CAPN10 gene in the manifestation of PCOS.

Role of luteinizing hormone ß-subunit gene variants among South Indian women with polycystic ovary syndrome.

Abnormal luteinizing hormone (LH) secretion and action are known to affect ovarian steroidogenesis and thus playing a crucial role in manifestation of polycystic ovary syndrome (PCOS). This study is first of its kind to study association of LH ß-subunit gene variants with PCOS among South-Indian women. 250 PCOS cases and 299 controls were recruited for the study. All the exons of LH ß gene were screened. Allele and genotype frequencies of the SNPs were compared between the cases and controls. We identified seven SNPs in the LH ß gene; one SNP in exon 3 (rs#1056917) exhibited significant difference in the allele frequency between the PCOS cases and controls (p=0.015). Although, the LH ß variants that are found to be more frequent among PCOS cases are silent in nature and not of any functional significance, they might influence other significant functional polymorphisms in the hypothalamic-pituitary-gonadal axis which needs to be explored.

Role of androgen receptor CAG repeat polymorphism and X-inactivation in the manifestation of recurrent spontaneous abortions in Indian women.

The aim of the present study was to investigate the role of CAG repeat polymorphism and X-chromosome Inactivation (XCI) pattern in Recurrent Spontaneous Abortions among Indian women which has not been hitherto explored. 117 RSA cases and 224 Controls were included in the study. Cases were recruited from two different hospitals--Lakshmi Fertility Clinic, Nellore and Fernandez Maternity Hospital, Hyderabad. Controls were roughly matched for age, ethnicity and socioeconomic status. The CAG repeats of the Androgen Receptor gene were genotyped using a PCR-based assay and were analysed using the GeneMapper software to determine the CAG repeat length. XCI analysis was also carried out to assess the inactivation percentages. RSA cases had a significantly greater frequency of allele sizes in the polymorphic range above 19 repeats (p = 0.006), which is the median value of the controls, and in the biallelic mean range above 21 repeats (p = 0.002). We found no evidence of abnormal incidence of skewed X-inactivation. We conclude that longer CAG repeat lengths are associated with increased odds for RSA with statistical power estimated to be ∼90%.

Mitochondrial DNA variations associated with recurrent pregnancy loss among Indian women.

Several genetic factors have been found to be associated with recurrent pregnancy loss (RPL). However, not many attempts have been made to associate the mitochondrial DNA (mtDNA) variations with RPL. Therefore, we have analyzed the complete mtDNA of 100 women with RPL and 12 aborted fetal tissues. Our analysis revealed a total of 681 variations, most of which were in NADH Dehydrogenase (ND) genes that encode mitochondrial enzyme Complex I. Presence of T4216C variation (ND1 gene) in 9% of the RPL women and several pathogenic, and novel mutations suggest the role of mtDNA variations in RPL.

Androgen receptor CAG repeat polymorphism and epigenetic influence among the south Indian women with Polycystic Ovary Syndrome.

The present study was carried out to assess the role of androgen receptor CAG repeat polymorphism and X chromosome inactivation (XCI) pattern among Indian PCOS women and controls which has not been hitherto explored and also to test the hypothesis that shorter CAG alleles would be preferentially activated in PCOS. CAG repeat polymorphism and X chromosome methylation patterns were compared between PCOS and non-PCOS women. 250 PCOS women and 299 controls were included for this study. Androgen receptor CAG repeat sizes, XCI percentages, and clinical and biochemical parameters were measured. The mean CAG repeat number is similar between the cases (18.74±0.13) and controls (18.73±0.12). The obese PCOS women were significantly more frequent in the <18 and >20 CAG repeat category than the lean PCOS women, yielding a highly significant odds (p=0.001). Among the women with non-random X-inactivation, alleles with <19 repeats were more frequently activated among cases than controls (p=0.33). CAG repeat polymorphism by itself cannot be considered as a useful marker for discriminating PCOS. We observed a trend of preferential activation of the shorter allele among the PCOS cases with non random XCI pattern. In the obese PCOS women, this microsatellite variation may account for the hyperandrogenicity to a larger extent than the lean PCOS women.

Role of progesterone receptor polymorphisms in the recurrent spontaneous abortions: Indian case.

BACKGROUND: We attempt to ascertain if the 3 linked single nucleotide polymorphisms (SNPs) of the Progesterone Receptor (PR) gene (exon 1: G 1031 C; S344T, exon 4: G 1978 T; L660V and exon 5: C 2310 T; H770H) and the PROGINS insertion in the intron G, between exons 7 and 8, are associated with Recurrent Spontaneous Abortion (RSA) in the Indian population. METHODOLOGY/PRINCIPAL FINDINGS: A total of 143 women with RSA and 150 controls were sequenced for all the 8 exons looking for the above 3 linked SNPs of the PR gene earlier implicated in the RSA, as well as for any new SNPs that may be possibly found in the Indian population. PROGINS insertion was screened by electrophoresis. We did not find any new mutations, not observed earlier, in our population. Further, we did not find significant role of the *2 allele (representing the mutant allele at the three SNP loci) or the T2 allele (PROGINS insertion) in the manifestation of RSA. We also did not find an LD pattern between each of the 3 SNPs and the PROGINS insertion. CONCLUSIONS/SIGNIFICANCE: The results suggest that the PR gene mutations may not play any exclusive role in the manifestation of RSA, and instead, given significantly higher frequency of the *2 allele among the normal women, we surmise if it does not really confer a protective role among the Indian populations, albeit further studies are required in the heterogeneous populations of this region before making any conclusive statement.

Austro-Asiatic tribes of Northeast India provide hitherto missing genetic link between South and Southeast Asia.

Northeast India, the only region which currently forms a land bridge between the Indian subcontinent and Southeast Asia, has been proposed as an important corridor for the initial peopling of East Asia. Given that the Austro-Asiatic linguistic family is considered to be the oldest and spoken by certain tribes in India, Northeast India and entire Southeast Asia, we expect that populations of this family from Northeast India should provide the signatures of genetic link between Indian and Southeast Asian populations. In order to test this hypothesis, we analyzed mtDNA and Y-Chromosome SNP and STR data of the eight groups of the Austro-Asiatic Khasi from Northeast India and the neighboring Garo and compared with that of other relevant Asian populations. The results suggest that the Austro-Asiatic Khasi tribes of Northeast India represent a genetic continuity between the populations of South and Southeast Asia, thereby advocating that northeast India could have been a major corridor for the movement of populations from India to East/Southeast Asia.