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1.
Article in English | MEDLINE | ID: mdl-29868214

ABSTRACT

The Kalyani cohort created in 2010 by the National Institute of Biomedical Genomics, West Bengal, India, is designed to serve as a platform for conducting prospective basic and translational studies on epidemiology and genomics of health and disease-related parameters, particularly of non-communicable diseases (NCDs). The overall goal is to assess behavioural, biological, genetic, social and environmental factors and obtain necessary evidence for effective health improvement. Collected baseline data comprise 15727 individuals, >14 years of age from seven municipal wards in the Kalyani and Gayeshpur regions. Data are being collected on demographics, current health status, medical history and health-related behaviours. Blood samples were also collected from a subset of individuals (n = 5132) and analysed for estimation of known markers of NCDs. DNA has been extracted from blood samples and stored for future use. Important baseline findings include a high prevalence of diabetes, dyslipidemias and hypothyroidism. Prevalence estimates for these disorders obtained from self-reported data are significantly lower, indicating that participants are unaware of their health problems. The identification of 'at risk' individuals will allow formation of sub-cohorts for further investigations of epidemiological and genetic risk factors for NCDs. Access to the resource, including data and blood samples, created by this study will be provided to other researchers.

2.
3.
Ann Hum Genet ; 72(Pt 1): 82-9, 2008 Jan.
Article in English | MEDLINE | ID: mdl-17627800

ABSTRACT

Isolated population groups are useful in conducting association studies of complex diseases to avoid various pitfalls, including those arising from population stratification. Since DNA resequencing is expensive, it is recommended that genotyping be carried out at tagSNP (tSNP) loci. For this, tSNPs identified in one isolated population need to be used in another. Unless tSNPs are highly portable across populations this strategy may result in loss of information in association studies. We examined the issue of tSNP portability by sampling individuals from 10 isolated ethnic groups from India. We generated DNA resequencing data pertaining to 3 genomic regions and identified tSNPs in each population. We defined an index of tSNP portability and showed that portability is low across isolated Indian ethnic groups. The extent of portability did not significantly correlate with genetic similarity among the populations studied here. We also analyzed our data with sequence data from individuals of African and European descent. Our results indicated that it may be necessary to carry out resequencing in a small number of individuals to discover SNPs and identify tSNPs in the specific isolated population in which a disease association study is to be conducted.


Subject(s)
Polymorphism, Single Nucleotide/genetics , Population Groups , Black People , Chromosomes, Human, Y , DNA/genetics , DNA/isolation & purification , Ethnicity , Female , Genetic Markers , Geography , Haplotypes , Humans , India , Linkage Disequilibrium , Male , Sequence Analysis, DNA , White People
4.
Diabet Med ; 24(4): 398-402, 2007 Apr.
Article in English | MEDLINE | ID: mdl-17335469

ABSTRACT

AIMS: The aim of the study was to investigate the association of serum adiponectin levels with the Pro12Ala polymorphism of the peroxisome proliferator activated receptor-gamma (PPARG) gene in Asian Indians. METHODS: We selected 400 diabetic subjects, 200 with the Pro12Pro genotype (100 male and 100 female) and 200 with the Pro12Ala genotype (100 male and 100 female) and 400 age- and sex-matched normal glucose tolerance subjects with similar genotype profiles from the Chennai Urban Rural Epidemiology Study. Fasting serum adiponection levels were measured using radioimmunoassay. The Pro12Ala polymorphism was genotyped by PCR-restriction fragment length polymorphism using BstUI. RESULTS: All clinical and biochemical parameters were similar in the subjects with the Pro12Pro and Pro12Ala genotypes. There was no significant difference in serum adiponectin values between subjects with the Pro12Pro and Pro12Ala genotypes (males 5.4 vs. 5.8 microg/ml, P = 0.546; females 6.9 vs. 7.2 microg/ml, P = 0.748). Adiponectin values did not differ among these two genotypes even when categorized based on their diabetes status (normal glucose tolerance Pro12Pro 7.9 vs. Pro12Ala 7.7 microg/ml, P = 0.994; diabetes Pro12Pro 4.7 vs. Pro12Ala 5.4 microg/ml, P = 0.622). CONCLUSION: The Pro12Ala polymorphism of the PPARG gene is not associated with serum adiponectin levels in Asian Indians.


Subject(s)
Adiponectin/blood , Diabetes Mellitus/genetics , PPAR gamma/genetics , Polymorphism, Genetic/genetics , Proline/genetics , Adult , Alanine/genetics , Asian People , Diabetes Mellitus/ethnology , Epidemiologic Studies , Female , Genotype , Glucose Tolerance Test , Humans , India/epidemiology , Male , Middle Aged
5.
Eye (Lond) ; 21(3): 395-401, 2007 Mar.
Article in English | MEDLINE | ID: mdl-16440015

ABSTRACT

PURPOSE: The main objective of this study was to evaluate if the -429T/C, -374T/A and 63 bp deletion polymorphisms in the RAGE gene are associated with diabetic retinopathy (DR) among Type 2 diabetic subjects in a clinic-based population from South India. METHODS: We screened 149 normal glucose tolerant subjects (NGT), 189 Type 2 diabetes subjects without retinopathy (DM) and 190 subjects with DR for these polymorphisms using the PCR-RFLP method. DR was diagnosed by grading color fundus photography. Logistic regression models were used to evaluate the association of individual polymorphisms with DR. Expectation-maximization algorithms were implemented in haplotype tests of association to examine the combined effects of -429T/C and -374T/A polymorphisms on DR. RESULTS: The allelic frequencies of -429T are 0.83 in NGT, 0.84 in DM and 0.85 in DR subjects, and that of -374T are 0.93 in NGT, 0.92 in DM and 0.88 in DR subjects. The -374 polymorphism was found to be associated with non-proliferative retinopathy when this subgroup was compared to the DM group (OR=1.814, 95% CI=1.005-3.273). However, this association was not obvious when both the subphenotypes of DR (the nonproliferative and proliferative DR groups) were studied jointly. We found no evidence for associations between the -429T/C polymorphism and the DR phenotype. Finally, extension to a 2-SNP haplotype did not reveal any significant statistical difference between the groups (P=0.668). CONCLUSION: In this study, we found a modest association with the -374T/A polymorphism in the nonproliferative DR subgroup.


Subject(s)
Diabetes Mellitus, Type 2/genetics , Diabetic Retinopathy/genetics , Polymorphism, Genetic/genetics , Receptors, Immunologic/genetics , Diabetes Mellitus, Type 2/blood , Diabetes Mellitus, Type 2/epidemiology , Diabetic Retinopathy/blood , Diabetic Retinopathy/epidemiology , Female , Gene Deletion , Gene Frequency/genetics , Haplotypes , Humans , India/epidemiology , Male , Middle Aged , Phenotype , Polymorphism, Single Nucleotide/genetics , Promoter Regions, Genetic/genetics , Receptor for Advanced Glycation End Products
6.
Int J Obes (Lond) ; 31(1): 97-102, 2007 Jan.
Article in English | MEDLINE | ID: mdl-16652127

ABSTRACT

OBJECTIVE: To investigate the association of insulin receptor substrate-2 (IRS-2) G1057D polymorphism with type 2 diabetes and obesity in Asian Indians. METHODS: The study comprised of 1193 normal glucose tolerant (NGT) subjects and 1018 subjects with type 2 diabetes, aged >/=20 years with an average body mass index of 23.7+/-4.6 and 25.3+/-4.2 kg/m(2), respectively. The subjects were unrelated and randomly selected from the Chennai Urban Rural Epidemiology Study (CURES), a population-based study in Chennai in southern India. The G1057D polymorphism of the IRS-2 gene was genotyped using PCR-RFLP assay. RESULTS: The genotype frequency of the IRS-2 G1057D polymorphism was significantly different between the NGT and type 2 diabetic groups (P=0.0007) in the total study subjects and among the obese subjects (P=0.00007). Logistic regression analysis showed that the DD genotype showed an increased susceptibility to diabetes with an odds ratio (adjusted for age and sex) of 2.19 (95% CI: 1.34-3.57, P=0.002) when compared to the GG+GD genotype, among the obese subjects, but not in non obese subjects. In order to explore possible interaction with obesity, logistic regression analysis was performed and the coefficient corresponding to the interaction parameter (genotype x obesity) was significant (P=0.0001). CONCLUSION: In Asian Indians, the DD genotype increases susceptibility to type 2 diabetes by interacting with obesity.


Subject(s)
Diabetes Mellitus, Type 2/genetics , Intracellular Signaling Peptides and Proteins/genetics , Obesity/genetics , Phosphoproteins/genetics , Polymorphism, Genetic/genetics , Diabetes Mellitus, Type 2/epidemiology , Diabetes Mellitus, Type 2/metabolism , Female , Gene Frequency/genetics , Genetic Predisposition to Disease/genetics , Genotype , Humans , India/epidemiology , Insulin/genetics , Insulin Receptor Substrate Proteins , Male , Middle Aged , Obesity/epidemiology , Obesity/metabolism , Risk Factors , Rural Health , Signal Transduction/genetics
7.
Ann Hum Genet ; 70(Pt 5): 623-30, 2006 Sep.
Article in English | MEDLINE | ID: mdl-16907708

ABSTRACT

Oculocutaneous albinism (OCA) is a heterogeneous group of autosomal recessive disorders characterized by an abnormally low amount of melanin in the eyes, skin and hair, and associated with common developmental abnormalities of the eye. Defects in the tyrosinase gene (TYR) cause a common type of OCA, known as oculocutaneous albinism type 1 (OCA1). The molecular basis of OCA has been studied extensively in different population groups, but very little information is available on Indian patients. Our investigation covering thirteen ethnic groups of India, some representing >20 million people, revealed that among 25 OCA families 12 were affected with OCA1, and that these cases were primarily due to founder mutations in TYR. We detected nine mutations and eight SNPs in TYR, of which six mutations (five point mutations & one gross deletion) were novel. In contrast to most reports describing compound heterozygotes, the presence of homozygotes in 10 out of the 12 pedigrees underscores the lack of intermixing between these ethnic groups in India. Haplotype analysis suggested a few founder chromosomes causing the disease in the majority of the patients. Direct detection of the mutations prevalent in specific ethnic groups could be used for carrier detection and genetic counselling.


Subject(s)
Albinism, Oculocutaneous/genetics , Ethnicity , Founder Effect , Monophenol Monooxygenase/genetics , Albinism, Oculocutaneous/enzymology , Albinism, Oculocutaneous/ethnology , Amino Acid Sequence , Base Sequence , Haplotypes , Humans , India , Molecular Sequence Data , Mutation, Missense
8.
Am J Med Genet B Neuropsychiatr Genet ; 141B(8): 868-73, 2006 Dec 05.
Article in English | MEDLINE | ID: mdl-16941653

ABSTRACT

The genetic basis of bipolar disorder (BPD) and schizophrenia (SCZ) has been established through numerous clinical and molecular studies. Although often considered separate nosological entities, evidence now suggests that the two syndromes may share some genetic liability. Recent studies have used a composite phenotype (psychosis) that includes BPD, SCZ, psychosis not otherwise specified, and schizoaffective disorder, to identify shared susceptibility loci. Several chromosomal regions are reported to be shared between these syndromes (18p, 6q, 10p, 13q, 22q). As a part of our endeavor to scan these regions, we report a positive linkage and association finding at 18p11.2 for psychosis. Two-point linkage analysis performed on a series of 52 multiplex pedigrees with 23 polymorphic markers yielded a LOD score of 2.02 at D18S37. An independent set of 159 parent offspring trios was used to confirm this suggestive finding. The TDT analysis yielded support for association between the marker D18S453 and the disease allele (chi2 = 4.829, P < 0.028). This region has been implicated by several studies on BPD [Sjoholt et al. (2004); Mol Psychiatry 9(6):621-629; Washizuka et al. (2004); Biol Psychiatry 56(7):483-489; Pickard et al. (2005); Psychiatr Genet 15(1):37-44], SCZ [Kikuchi et al. (2003); J Med Dent Sci 50(3):225-229; Babovic-Vuksanovic et al. (2004); Am J Med Genet 124(3):318-322] and also as a shared region between the two diseases [Ishiguro et al. (2001); J Neural Transm 108(7):849-854; Reyes et al. (2002); Mol Psychiatry 7(4):337-339; Craddock et al. (2005); J Med Genet 42(3):193-204]. Our findings provide an independent validation of the above reports, and suggest the presence of susceptibility loci for psychoses in this region.


Subject(s)
Chromosomes, Human, Pair 18/genetics , Genetic Predisposition to Disease , Linkage Disequilibrium/genetics , Polymorphism, Genetic , Psychotic Disorders/genetics , Schizophrenia/genetics , Genotype , Humans , India , Lod Score , Pedigree
9.
Int J Obes (Lond) ; 30(6): 884-91, 2006 Jun.
Article in English | MEDLINE | ID: mdl-16446747

ABSTRACT

OBJECTIVE: To evaluate whether polymorphisms in the peroxisome proliferator-activated receptor-gamma coactivator-1 alpha (PPARGC1A) gene were related to body fat in Asian Indians. METHODS: Three polymorphisms of PPARGC1A gene, the Thr394Thr, Gly482Ser and +A2962G, were genotyped on 82 type 2 diabetic and 82 normal glucose tolerant (NGT) subjects randomly chosen from the Chennai Urban Rural Epidemiology Study using PCR-RFLP, and the nature of the variants were confirmed using direct sequencing. Linkage disequilibrium (LD) was estimated from the estimates of haplotypic frequencies using an expectation-maximization algorithm. Visceral, subcutaneous and total abdominal fat were measured using computed tomography, whereas dual X-ray absorptiometry was used to measure central abdominal and total body fat. RESULTS: None of the three polymorphisms studied were in LD. The genotype (0.59 vs 0.32, P=0.001) and allele (0.30 vs 0.17, P=0.007) frequencies of Thr394Thr polymorphism were significantly higher in type 2 diabetic subjects compared to those in NGT subjects. The odds ratio for diabetes (adjusted for age, sex and body mass index) for the susceptible genotype, XA (GA+AA) of Thr394Thr polymorphism, was 2.53 (95% confidence intervals: 1.30-5.04, P=0.009). Visceral and subcutaneous fat were significantly higher in NGT subjects with XA genotype of the Thr394Thr polymorphism compared to those with GG genotype (visceral fat: XA 148.2+/-46.9 vs GG 106.5+/-51.9 cm(2), P=0.001; subcutaneous fat: XA 271.8+/-167.1 vs GG 181.5+/-78.5 cm(2), P=0.001). Abdominal (XA 4521.9+/-1749.6 vs GG 3445.2+/-1443.4 g, P=0.004), central abdominal (XA 1689.0+/-524.0 vs GG 1228.5+/-438.7 g, P<0.0001) and non-abdominal fat (XA 18763.8+/-8789.4 vs GG 13160.4+/-4255.3 g, P<0.0001) were also significantly higher in the NGT subjects with XA genotype compared to those with GG genotype. The Gly482Ser and +A2962G polymorphisms were not associated with any of the body fat measures. CONCLUSION: Among Asian Indians, the Thr394Thr (G --> A) polymorphism is associated with increased total, visceral and subcutaneous body fat.


Subject(s)
Adipose Tissue/pathology , Asian People/genetics , Diabetes Mellitus, Type 2/genetics , Heat-Shock Proteins/genetics , Polymorphism, Genetic , Transcription Factors/genetics , Absorptiometry, Photon , Adult , Anthropometry/methods , Body Composition/genetics , Case-Control Studies , Diabetes Mellitus, Type 2/pathology , Female , Gene Frequency , Genotype , Glucose Tolerance Test , Humans , Intra-Abdominal Fat/pathology , Male , Middle Aged , Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha , Polymerase Chain Reaction/methods , Polymorphism, Restriction Fragment Length , Subcutaneous Fat/pathology , Tomography, X-Ray Computed
10.
Dis Markers ; 22(5-6): 327-34, 2006.
Article in English | MEDLINE | ID: mdl-17264403

ABSTRACT

Hemophilia B, an X-linked recessive bleeding disorder, is caused by heterogeneous mutations in the factor IX (F9) gene. Hence, carriers of the disease are usually detected by F9 gene linked RFLP analysis. We aimed to test a set of RFLP markers (DdeI, XmnI, MnlI, TaqI & HhaI), used worldwide for carrier detection, to estimate its heterozygosity in different population groups of India, and identify additional single nucleotide polymorphisms (SNPs) if necessary. A total of 8 population groups encompassing different regions of India, consisting of 107 unrelated normal females without any history of hemophilia B in the family and 13 unrelated obligate carriers were recruited in the study. Regions of F9 gene were amplified by PCR from genomic DNA of the donors followed by restriction enzyme digestion and/or sequencing as appropriate. Combined informativeness for the markers varied between 52-86% among normal females belonging to different geographical locations of India. Haplotype analysis revealed that the most prevalent haplotype lacked the restriction sites for all five RFLP markers. Screening regions of F9 gene that harbor 10 SNPs reported in dbSNP yielded only two SNPs, which increased the overall informativeness in each population group and heterozygosity in the obligate carriers for the disease from 38% to 69%. Our data show that heterozygosity of commonly used RFLP markers is remarkably variable across different regions of India. Thus prudent selection of the markers based on specific population groups including usage of additional markers is recommended for efficient carrier detection.


Subject(s)
Genetic Carrier Screening/methods , Hemophilia B/diagnosis , Polymorphism, Restriction Fragment Length , Female , Genetic Markers , Humans , India , Male , Polymorphism, Single Nucleotide , Population Groups/genetics
11.
Diabet Med ; 22(11): 1516-21, 2005 Nov.
Article in English | MEDLINE | ID: mdl-16241916

ABSTRACT

AIMS: The objective of the present investigation was to examine the relationship of three polymorphisms, Thr394Thr, Gly482Ser and +A2962G, of the peroxisome proliferator activated receptor-gamma co-activator-1 alpha (PGC-1alpha) gene with Type 2 diabetes in Asian Indians. METHODS: The study group comprised 515 Type 2 diabetic and 882 normal glucose tolerant subjects chosen from the Chennai Urban Rural Epidemiology Study, an ongoing population-based study in southern India. The three polymorphisms were genotyped using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Haplotype frequencies were estimated using an expectation-maximization (EM) algorithm. Linkage disequilibrium was estimated from the estimates of haplotypic frequencies. RESULTS: The three polymorphisms studied were not in linkage disequilibrium. With respect to the Thr394Thr polymorphism, 20% of the Type 2 diabetic patients (103/515) had the GA genotype compared with 12% of the normal glucose tolerance (NGT) subjects (108/882) (P = 0.0004). The frequency of the A allele was also higher in Type 2 diabetic subjects (0.11) compared with NGT subjects (0.07) (P = 0.002). Regression analysis revealed the odds ratio for Type 2 diabetes for the susceptible genotype (XA) to be 1.683 (95% confidence intervals: 1.264-2.241, P = 0.0004). Age adjusted glycated haemoglobin (P = 0.003), serum cholesterol (P = 0.001) and low-density lipoprotein (LDL) cholesterol (P = 0.001) levels and systolic blood pressure (P = 0.001) were higher in the NGT subjects with the XA genotype compared with GG genotype. There were no differences in genotype or allelic distribution between the Type 2 diabetic and NGT subjects with respect to the Gly482Ser and +A2962G polymorphisms. CONCLUSIONS: The A allele of Thr394Thr (G --> A) polymorphism of the PGC-1 gene is associated with Type 2 diabetes in Asian Indian subjects and the XA genotype confers 1.6 times higher risk for Type 2 diabetes compared with the GG genotype in this population.


Subject(s)
Asian People/genetics , Diabetes Mellitus, Type 2/genetics , Heat-Shock Proteins/genetics , PPAR gamma/genetics , Polymorphism, Genetic/genetics , Polymorphism, Restriction Fragment Length , Transcription Factors/genetics , Adult , Female , Gene Frequency , Humans , India , Male , Middle Aged , Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha
12.
J Indian Med Assoc ; 103(11): 580-4, 2005 Nov.
Article in English | MEDLINE | ID: mdl-16570758

ABSTRACT

The epidemiological profile data were collected for diabetes mellitus from the people living in three habitats (rural, industrial and urban) having considerable difference in their lifestyle and socio-economic status. Every 5th (occasionally 4th or 6th) member from each habitat was sampled; no restriction regarding age was kept during screening; OGTT (oral glucose tolerence test) was performed 2 hours after 75 g glucose, in those whose FBS (fasting blood sugar) was >90 mg/dl. Diagnosis of diabetes mellitus was ascertained, if the FBS was >120 mg/dl and/ or postglucose value was >200mg/dl. The per cent prevalence (among all aged people) of diabetes mellitus in rural, industrial and urban habitats were found to be: 1.66 +/- 0.58 (male 1.99 +/- 0.88, female 1.3 +/- 0.75); 3.00 +/- 0.74 (male 3.17 +/- 1.04, female 2.80 +/- 1.04) and 4.8 +/- 0.98 (male 5.31 +/- 1.43, female 4.27 +/- 1.32) respectively.


Subject(s)
Diabetes Mellitus/epidemiology , Adolescent , Adult , Aged , Aged, 80 and over , Child , Data Collection , Female , Geography , Glucose Tolerance Test , Humans , India/epidemiology , Life Style , Male , Middle Aged , Prevalence , Risk Factors , Rural Health/statistics & numerical data , Social Class , Surveys and Questionnaires , Urban Health/statistics & numerical data
13.
Ann Hum Genet ; 68(Pt 6): 574-87, 2004 Nov.
Article in English | MEDLINE | ID: mdl-15598216

ABSTRACT

We have examined the patterns of DNA sequence variation in and around the genes coding for ICAM1 and TNF, which play functional and correlated roles in inflammatory processes and immune cell responses, in 12 diverse ethnic groups of India. We aimed to (a) quantify the nature and extent of the variation, and (b) analyse the observed patterns of variation in relation to population history and ethnic background. At the ICAM1 and TNF loci, respectively, the total numbers of SNPs that were detected were 28 and 12. Many of these SNPs are not shared across ethnic groups and are unreported in the dbSNP or TSC databases, including two fairly common non-synonymous SNPs at positions 13487 and 13542 in the ICAM1 gene. Conversely, the TNF-376A SNP that is reported to be associated with susceptibility to malaria was not found in our study populations, even though some of the populations inhabit malaria endemic areas. Wide between-population variation in the frequencies of shared SNPs and coefficients of linkage disequilibrium have been observed. These findings have profound implications in case-control association studies.


Subject(s)
Genetic Variation , Intercellular Adhesion Molecule-1/genetics , Research Design , Tumor Necrosis Factor-alpha/genetics , Chromosome Mapping , Gene Frequency , Haplotypes , Humans , India , Linkage Disequilibrium , Polymorphism, Single Nucleotide
14.
Ann Hum Genet ; 68(Pt 2): 128-38, 2004 Mar.
Article in English | MEDLINE | ID: mdl-15008792

ABSTRACT

We describe the genetic structure and affinities of five Dravidian-speaking tribal populations inhabiting the Nilgiri hills of Tamil Nadu, in south India, using 24 autosomal DNA markers. Our goals were: (i). to examine what evolutionary forces have most significantly impacted south Indian tribal genetic variation, and (ii). to test whether the phenotypic similarities of some south Indian tribal groups to Africans represent a signature of close relationship to Africans or are due to convergence. All loci were polymorphic and average heterozygosities were substantial (range: 0.347-0.423). Genetic differentiation was high (Gst= 6.7%) and genetic distances were not significantly correlated with geographic distances. Genetic drift therefore probably played a significant role in shaping the patterns of genetic variation observed in southern Indian tribal populations. Otherwise, analyses of population relationships showed that Indian populations are closely related to one another, regardless of phenotypic characteristics, and do not show particular affinities to Africans. We conclude that the phenotypic similarities of some Indian groups to Africans do not reflect a close relationship between these groups, but are better explained by convergence.


Subject(s)
Ethnicity/genetics , Genetic Variation , Adult , Genetic Drift , Genetic Markers , Haplotypes , Heterozygote , Humans , India , Phenotype , Polymorphism, Genetic
15.
Acta Neurol Scand ; 108(6): 407-14, 2003 Dec.
Article in English | MEDLINE | ID: mdl-14616293

ABSTRACT

OBJECTIVES: MJD1/SCA3 is the most common type of spinocerebellar ataxia (SCA) worldwide. To explain the low prevalence of the disease among SCA patients from eastern India, we analysed CAG repeats and two bi-allelic intragenic markers at SCA3 locus among 412 normal individuals and 10 patients. MATERIALS AND METHODS: For CAG repeat analysis, PCR amplified fragments were run on polyacrylamide gel, transferred to a membrane, probed with (CAG)10 and detected on an autoradiograph. Bi-allelic markers were analysed using allele specific PCR amplification. RESULTS: Large normal alleles (>33 CAG repeats) were 0.015 in pooled populations. All the patients had the common haplotype C-A as observed worldwide. Frequency of C-A haplotype among large normal alleles was 0.75. CONCLUSIONS: Observed low prevalence of SCA3 could be because of the low prevalence of large normal alleles that might act as the reservoir for the expanded alleles. SCA3 mutation in Indian populations had the same origin as found worldwide.


Subject(s)
Genetic Variation , Machado-Joseph Disease/genetics , Nerve Tissue Proteins/genetics , Trinucleotide Repeats , Ataxin-3 , Humans , India , Nuclear Proteins , Polymerase Chain Reaction , Polymorphism, Genetic , Repressor Proteins , Sampling Studies
16.
Hum Biol ; 75(6): 873-87, 2003 Dec.
Article in English | MEDLINE | ID: mdl-15018036

ABSTRACT

India has the unique distinction of having perhaps the largest diversities, both biological and cultural. The Nilgiri Hills of southern India, a home for several tribal pockets representing different genetic isolates, provides a genetic wealth to understand human evolution. We have analyzed eight widely distributed polymorphic insertion/deletion loci (AluAPO, AluACE, AluDI, AluPLAT, AluPV92, AluFXIIIB, CD4 del and mtNUC) in 250 unrelated individuals from five tribal populations (Badaga, Irula, Kota, Kurumba, and Toda). All loci were highly polymorphic except the CD4 del locus, at which the deletion allele was fixed in Kotas and Kurumbas. The levels of average heterozygosities were found to be high in all the populations. In most populations, they were also higher than those predicted by the island model of population structure. The gene diversity (GST = 8.3%) was found to be higher than that in populations of most global regions with the exception of Africa. It is clear from the present study that drift effects could have accentuated the process of genetic differentiation of the tribal populations. The possibility of an early demographic expansion of modern humans within south India also cannot be ruled out.


Subject(s)
Alu Elements/genetics , Ethnicity/genetics , Gene Deletion , Genetics, Population , Polymorphism, Genetic/genetics , Biological Evolution , Gene Frequency/genetics , Genetic Markers , Humans , India
17.
Ann Hum Genet ; 66(Pt 5-6): 431-8, 2002 Nov.
Article in English | MEDLINE | ID: mdl-12485475

ABSTRACT

In this article, we provide an overview of the different statistical procedures that have been developed for linkage mapping of quantitative trait loci. We outline the model assumptions, the data requirements and the underlying tests for linkage for the different methods.


Subject(s)
Chromosome Mapping/statistics & numerical data , Genetic Linkage , Quantitative Trait Loci , Genome, Human , Humans , Likelihood Functions , Models, Genetic , Phenotype , Quantitative Trait, Heritable , Statistics, Nonparametric
18.
Ann Hum Genet ; 66(Pt 5-6): 361-8, 2002 Nov.
Article in English | MEDLINE | ID: mdl-12516613

ABSTRACT

The origins and genomic affinities of various tribal populations of India are of considerable contemporary interest. In this study, we have investigated relationships among five tribal groups inhabiting the north-eastern, eastern and sub-Himalayan regions of India. DNA samples have been analysed in respect of 25 polymorphic loci, based on which genetic affinities have been estimated. The interesting findings of this study are (i) the Tibeto-Burman speaking, morphologically Mongoloid, tribal groups of India are not genetically very homogeneous, and (ii) the Tharu, a group inhabiting the sub-Himalayan region, may indeed have undergone considerable admixture as has been postulated by some anthropologists.


Subject(s)
Ethnicity/genetics , Gene Frequency , Genome, Human , Genotype , Haplotypes , Humans , India
19.
Hum Genet ; 109(3): 339-50, 2001 Sep.
Article in English | MEDLINE | ID: mdl-11702215

ABSTRACT

There are various conflicting hypotheses regarding the origins of the tribal groups of India, who belong to three major language groups--Austro-Asiatic, Dravidian and Tibeto-Burman. To test some of the major hypotheses we designed a genetic study in which we sampled tribal populations belonging to all the three language groups. We used a set of autosomal DNA markers, mtDNA restriction-site polymorphisms (RSPs) and mtDNA hypervariable segment-1 (HVS-1) sequence polymorphisms in this study. Using the unlinked autosomal markers we found that there is a fair correspondence between linguistic and genomic affinities among the Indian tribal groups. We reconstructed mtDNA RSP haplotypes and found that there is extensive haplotype sharing among all tribal populations. However, there is very little sharing of mtDNA HVS-1 sequences across populations, and none across language groups. Haplogroup M is ubiquitous, and the subcluster U2i of haplogroup U occurs in a high frequency. Our analyses of haplogroup and HVS-1 sequence data provides evidence in support of the hypothesis that the Austro-Asiatic speakers are the most ancient inhabitants of India. Our data also support the earlier finding that some of the western Eurasian haplogroups found in India may have been present in India prior to the entry of Aryan speakers. However, we do not find compelling evidence to support the theory that haplogroup M was brought into India on an "out of Africa" wave of migration through a southern exit route from Ethiopia. On the contrary, our data raise the possibility that this haplogroup arose in India and was later carried to East Africa from India.


Subject(s)
Ethnicity/genetics , Genome, Human , Linguistics , DNA, Mitochondrial/genetics , Genetics, Population , Haplotypes , Humans , India , Language , Polymorphism, Genetic
20.
J Gastroenterol Hepatol ; 16(9): 1033-7, 2001 Sep.
Article in English | MEDLINE | ID: mdl-11595069

ABSTRACT

BACKGROUND: Pathogenesis and genetic factors influencing predisposition to antituberculosis drug (ATD)-induced hepatotoxicity are not clear. Polymorphism at the genetic locus of a drug and xenobiotic compound metabolizing enzyme, N-acetyltransferase type 2 (NAT2), is reported to be associated with the excess generation of toxic reactive metabolites. Polymorphisms at the glutathione S-transferase (GST) loci (GSTM1 and GSTT1) are involved in the detoxification of these toxic metabolites in the human body to a lesser extent. We have examined whether polymorphisms at these loci are associated with the risk of ATD-induced hepatotoxicity. METHODS: In this case-control study, 33 pulmonary tuberculosis patients with ATD-induced hepatotoxicity and 33 pulmonary tuberculosis patients receiving ATD drugs without any evidence of hepatotoxicity were considered as cases and controls, respectively. Point mutations at NAT2 and homozygous 'null' mutations at GSTM1 and GSTT1 genes were looked into genomic DNA, isolated from peripheral blood mononuclear cells by using polymerase chain reaction (PCR). RESULTS: The frequency of homozygous 'null' mutation at the GSTM1 gene was significantly higher among cases (n = 17, 52%) than controls (n = 8, 24%) (P < 0.05, relative risk 2.13, 95% CI: 1.25-3.10). Frequencies of mutations at GSTT1 and NAT2 genes did not differ significantly between cases and controls. CONCLUSION: Homozygous 'null' mutation at the GSTM1 gene might predispose an individual to ATD-induced hepatotoxicity.


Subject(s)
Antitubercular Agents/adverse effects , Chemical and Drug Induced Liver Injury/genetics , Glutathione Transferase/genetics , Mutation/genetics , Tuberculosis, Pulmonary/drug therapy , Adolescent , Adult , Aged , Antitubercular Agents/administration & dosage , Arylamine N-Acetyltransferase/genetics , Case-Control Studies , DNA Mutational Analysis , Drug Therapy, Combination , Female , Humans , Inactivation, Metabolic/genetics , Liver Function Tests , Male , Middle Aged , Polymerase Chain Reaction , Polymorphism, Genetic/genetics , Risk Factors , Tuberculosis, Pulmonary/enzymology
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