Southern Indian Population Research Articles

Gender-specific association of TSNAX/DISC1 locus for schizophrenia and bipolar affective disorder in South Indian population

Genetic association studies have implicated the TSNAX/DISC1 (disrupted in schizophrenia 1) in schizophrenia (SCZ), bipolar affective disorder (BPAD) and major depression. This study was performed to assess the possible involvement of TSNAX/DISC1 locus in the aetiology of BPAD and SCZ in the Southern Indian population. We genotyped seven single nucleotide polymorphism (SNPs) from TSNAX/DISC1 region in 1252 individuals (419 BPAD patients, 408 SCZ patients and 425 controls). Binary logistic regression revealed a nominal association for rs821616 in DISC1 for BPAD and also combined cases of BPAD or SCZ, but after correcting for multiple testing, these results were non-significant. However, significant association was observed with BPAD, as well as combined cases of BPAD or SCZ, within the female subjects for the rs766288 after applying false discovery rate corrections at the 0.05 level. Two-locus analysis showed C-C (rs766288-rs2812393) as a risk combination in BPAD, and G-T (rs2812393-rs821616) as a protective combination in SCZ and combined cases of BPAD or SCZ. Female-specific associations were observed for rs766288-rs2812393, rs766288-rs821616 and rs8212393-rs821616 in two-locus analysis. Our results provide further evidence for sex-dependent effects of the TSNAX/DISC1 locus in the aetiology of SCZ and BPAD.

Palatal rugae in population differentiation between South and North Indians: A discriminant function analysis

Aim:The present study is aimed at delineation of different types of rugae in two different populations and developing a discriminant function for the same.Materials and Methods:A total of 940 subjects were included in the present study. The sample consisted of 466 subjects from South Indian population and 474 from North Indian population in the age group of 18-23 years. Neo colloid Easy flow(™) alginate impressions of maxillary arch were made and casts were immediately poured with Type IV dental stone. A sharp graphite pencil was used to delineate the rugae and patterns were recorded according to the classification given by Kapali et al. The association between different population and different sexes was analyzed with chi-square test and a stepwise discriminant function analysis was also performed to develop a discriminant formula.Results:Wavy, curved and straight rugae were the most common forms in both groups. Chi-square analysis for association between rugae shape and population groups showed significant differences among all the rugae patterns at the P < 5%. Chi-square analysis for assessing sex differences in the rugae shapes showed significant difference in straight, unification and circular type. Five rugae shapes – curved, wavy, nonspecific, unification and circular – were selected for discriminant function.Conclusion:The discriminant function equation obtained from the different rugae shapes in the present study was highly accurate enough to distinguish the Southern and Northern Indian population with the classification accuracy of 87.8%. Thus to identify a specific population, separate discriminant function formulae have to be developed. Hence, the study of palatal rugae is one of the simple and reliable tools for population identification in forensic science.

Dispersal and dispersion of southern elephant seals in the Kerguelen province, Southern Ocean

AbstractSouthern elephant sealsMirounga leoninawithin the Kerguelen province disperse between Marion Island (MI), Iles Crozet (IC) and Iles Kerguelen (IK) despite the high site fidelity characteristic of this species. From 1987–2002, 199 IC individuals, or 11.63% of the tagged population there, were resighted at MI. Resights of IC seals at MI peaked during the juvenile moult and seals aged 0–2 represent 66% of all resights made. Equal numbers of male and female seals (all age classes) were dispersing. Dispersing breeding females (n= 22, on 33 occasions) outnumbered dispersing breeding males (n= 6, on 16 occasions), after initially emigrating from IC to MI as juvenile seals (natal dispersal). Greater male-mediated gene flow was ultimately attained due to the polygynous mating system and some extremely successful males. Of 132 seals fitted with satellite-relay data loggers at MI, six hauled out at IC and three at IK. Two of the seals which migrated to IC were born at MI; all others were unmarked males likely to be native to IC or IK. Dispersal should ideally be considered when assessing vital rates for southern Indian Ocean elephant seal populations.

The pattern of odontogenic tumors in a government teaching hospital in the southern Indian state of Tamil Nadu

This hospital-based study was designed to provide demographic data on odontogenic tumors from the southern Indian population in the state of Tamil Nadu for comparison with pertinent series from other geographic regions. A total of 489 cases of odontogenic tumors registered over a period of 38 years (February 1970-March 2008) in the Department of Oral and Maxillofacial Pathology of Tamil Nadu Government Dental College and Hospital, Chennai, India, were retrieved from the files of histopathology registers and were retrospectively analyzed. Odontogenic tumors in the present study constituted 4.13% of all the 11,843 registered biopsies. The mandible was the most commonly affected anatomic location, with 362 cases (74.02%). Ameloblastoma with a predilection for posterior mandible was the most frequent odontogenic tumor (67.69%), followed by adenomatoid odontogenic tumor (9%), odontoma (7.77%), and calcifying odontogenic cyst (5.52%). The patients were affected over a wide age range of 5-75 years with a mean age of 32.64 years and peak occurrence in the second and third decades of life. Among the 489 cases, only 15 (3.07%) were malignant. The relative frequency of 4.13% of odontogenic tumors observed in this study, which is the largest series from this part of the world. Ameloblastoma formed the single most common tumor of all odontogenic tumors. This study observed both regional and geographic variations in the frequency and distribution of odontogenic tumors.

Subspecific status of the southern Indian population of Nyctemera coleta (Lepidoptera: Arctiidae)

The hitherto critically unexamined southern Indian population of Nyctemera coleta (Stoll, 1781) was discovered to belong to the nominate subspecies.

Frequency of lactose malabsorption among healthy southern and northern Indian populations by genetic analysis and lactose hydrogen breath and tolerance tests

Lactose malabsorption (LM), the inability to break down lactose into glucose and galactose, is due to a deficiency in the small intestinal lactase phlorizin hydrolase enzyme. Ethnic and geographic variations of LM are known. The aim of this study was to compare the frequency of LM in healthy southern and northern Indian populations. A total of 153 healthy volunteers (76 from southern and 77 from northern India) were evaluated for LM by using a lactose tolerance test (LTT), a lactose hydrogen breath test (lactose HBT), and polymerase chain reaction-restriction fragment length polymorphism to identify the lactase gene C/T-13910 polymorphism (confirmed by sequencing). Volunteers from southern and northern India were comparable in age and sex. The LTT result was abnormal in 88.2% of southern Indians and in 66.2% of northern Indians (P = 0.001). The lactose HBT result was abnormal in 78.9% of southern Indians and in 57.1% of northern Indians (P = 0.003). The CC genotype was present in 86.8% and 67.5% (P = 0.002), the CT genotype was present in 13.2% and 26.0% (P = 0.036), and the TT genotype was present in 0% and 6.5% (P = 0.03) of southern and northern Indians, respectively. The frequency of symptoms after the lactose load (47.4% compared with 15.6%; P < 0.001) and peak concentrations of breath hydrogen (88.5 +/- 71.9 compared with 55.4 +/- 61.9 ppm; P = 0.003), both of which might indicate the degree of lactase deficiency, were higher in southern than in northern Indians. The frequency and degree of LM is higher in southern than in northern Indian healthy populations because of genetic differences in these populations.

CTLA-4 A49G gene polymorphism is not associated with vitiligo in South Indian population

Background:Vitiligo or leukoderma is a chronic skin condition that causes loss of pigment due to destruction of melanocytes, resulting in irregular pale patches of skin. Vitiligo is a polygenic disease and is associated with autoimmunity with an unknown etiology.Aims:One of the candidate genes which has a strong association with several autoimmune diseases is CTLA-4 gene located in chromosome 2q33 region. We investigated the possible association between CTLA-4 gene polymorphism in exon 1 (A49G) and vitiligo in patients from South India and compared the distribution of this polymorphism to matched control groups.Patients and Methods:The polymorphism was detected by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) method in 175 patients and 180 normal, age/ethnicity matched individuals. Consistency of genotype frequencies with the Hardy-Weinberg equilibrium was tested using a χ2 test.Results:There was no significant difference between the genotype (P = 0.93) and allele (P = 0.615) frequencies of CTLA-4 A49G polymorphism in patients and normal healthy individuals. However there was significant association of the CTLA-4 genotype (P = 0.02) and allelic frequency (P = 0.008) between the segmental and non-segmental sub groups within vitiligo.Conclusion:Our results indicate that there is no association between CTLA-4 A49G gene polymorphism and vitiligo in southern Indian population.

Thiopurine S-methyltransferase alleles, TPMT*2, *3B and *3C, and genotype frequencies in an Indian population

Thiopurine S-methyltransferase (TPMT) catalyzes the S-methylation of aromatic and heterocyclic sulfhydryl compounds including thiopurine drugs such as 6-mercaptopurine, 6-thioguanine and azathioprine. TPMT activity exhibits genetic variation and shows tri-modal distribution with 89-94% of individuals possessing high activity, 6-11% intermediate activity and approximately 0.3% low activity. Patients with intermediate or deficient TPMT activity exposed to thiopurine drugs show severe hematopoietic toxicity. Three single nucleotide polymorphisms (SNPs) in TPMT (NM_000367.2:c.238G>C, NM_000367.2:c.460G>A and NM_000367.2:c.719A>G) define the most prevalent mutant alleles associated with loss of catalytic activity reported in several populations. The present study investigated, for the first time, the frequency distribution of these three SNPs of TPMT, their alleles and genotypes in a Southern Indian population. Peripheral blood was obtained from 326 individuals of a Southern Indian population, and genomic DNA was isolated from total peripheral white blood cells. The genotypes at the polymorphic loci were determined by allele-specific polymerase chain reaction, restriction fragment length polymorphism and confirmatory DNA sequencing. The estimated genotype frequency for homozygous TPMT(*)1/(*)1 was 97.24%, for heterozygous TPMT(*)1/(*)2 and TPMT(*)1/(*)3B, 0.61% each, and for heterozygous TPMT(*)1/(*)3C, 1.53%. The frequency of heterozygous mutants in the studied Indian population was 2.76%. This study demonstrated significant variations in TPMT gene polymorphisms in an Indian population in relation to other human populations and may help to predict both clinical efficacy and drug toxicity of thiopurine drugs.

PO18-WE-56 Study of psychogenic non epileptic seizures in southern Indian rural population

PO18-WE-56 Study of psychogenic non epileptic seizures in southern Indian rural population

Haplotype diversity of 17 Y-chromosomal STR loci in the Bangladeshi population

Haplotype and allele frequencies of 17 Y-chromosomal STR loci were determined in 216 unrelated Bangladeshi males. AmpFlSTR ® Y-filer™ PCR Amplification kit (Applied Biosystems) was used to type the following Y-STR markers: DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a/b, DYS438, DYS439, DYS437, DYS448, DYS458, DYS456, DYS635, and Y-GATA-H4. A total of 211 haplotypes for the 17 Y-STR markers were detected and, of these, 206 haplotypes were unique. The haplotype diversity was 0.9998, indicating a high potential for differentiating between male individuals in this population. Comparison analysis via Analysis of Molecular Variance (AMOVA) and construction of Neighbor Joining Tree revealed a close association of Bangladeshi population with Indian Gaddi and Southern Indian populations.

Indian task force for celiac disease: Current status

There are limited data on celiac disease (CD) from India. The limited knowledge about CD in India might be attributed to several factors. The first meeting of the Indian Task Force for Celiac Disease was held in the Asian Institute of Gastroenterology, Hyderabad, India in December 2008. The objectives of the meeting were to focus research on prevalence of CD in the wheat-eating Northern vs the rice-eating Southern Indian population, low-budget serological assays to study the underprivileged population, to involve other medical subspecialties in CD, to suggest proper legislation regarding wheat food labeling, and to organize affordable food substitutes for patients with celiac disease.

Genetic Affinities of the Siddis of South India: An Emigrant Population of East Africa

Historical records indicate that the Portuguese brought the African Siddis to Goa, India, as slaves about 500 years ago. Subsequently, the Siddis moved into the interior regions of the state of Karnataka, India, and have remained there ever since. Over time the Siddis have experienced considerable cultural changes because of their proximity to neighboring population groups. To understand the biological consequences of these changes, we studied the Siddis to determine the extent of genetic variation and the contributions from the African, European, and Indian ancestral populations. In the present study we typed the Siddis for 20 polymorphic serological, red cell, and Alu insertion-deletion loci. The overall pattern of phenotype (and genotype) distribution is in accordance with Hardy-Weinberg expectations. Considering the ethnohistorical records and the availability of secondary-source genetic data, we used two data sets in the analysis: one comprising eight serological and red cell enzyme markers with eight population groups and another comprising six Alu insertion-deletion markers with seven tribal groups of South India. The dendrograms generated from these two data sets on the basis of genetic distance analysis between the selected populations of African, European, and Indian descent reveals that the Siddis are closer to the Africans than they are to the South Indian populations. Genetic admixture analysis using a dihybrid model (19 loci) and a trihybrid model (10 loci and 8 loci) shows that the predominant influence comes from the Africans, a lesser contribution from the South Indians, and a slight contribution from the Portuguese. Thus the original composition of the African genes among the Siddis has been diluted to some extent by the contribution from southern Indian population groups. There is no nonrandom association of alleles among a set of 10 genetic marker systems considered in the present study. The demonstration of genetic homogeneity of the Siddis, despite their admixed origin, suggests the utility of this population for genetic and epidemiological studies.

Genetic Affinities of the Siddis of South India: An Emigrant Population of East Africa

Historical records indicate that the Portuguese brought the African Siddis to Goa, India, as slaves about 500 years ago. Subsequently, the Siddis moved into the interior regions of the state of Karnataka, India, and have remained there ever since. Over time the Siddis have experienced considerable cultural changes because of their proximity to neighboring population groups. To understand the biological consequences of these changes, we studied the Siddis to determine the extent of genetic variation and the contributions from the African, European, and Indian ancestral populations. In the present study we typed the Siddis for 20 polymorphic serological, red cell, and Alu insertion-deletion loci. The overall pattern of phenotype (and genotype) distribution is in accordance with Hardy-Weinberg expectations. Considering the ethnohistorical records and the availability of secondary-source genetic data, we used two data sets in the analysis: one comprising eight serological and red cell enzyme markers with eight population groups and another comprising six Alu insertion-deletion markers with seven tribal groups of South India. The dendrograms generated from these two data sets on the basis of genetic distance analysis between the selected populations of African, European, and Indian descent reveals that the Siddis are closer to the Africans than they are to the South Indian populations. Genetic admixture analysis using a dihybrid model (19 loci) and a trihybrid model (10 loci and 8 loci) shows that the predominant influence comes from the Africans, a lesser contribution from the South Indians, and a slight contribution from the Portuguese. Thus the original composition of the African genes among the Siddis has been diluted to some extent by the contribution from southern Indian population groups. There is no nonrandom association of alleles among a set of 10 genetic marker systems considered in the present study. The demonstration of genetic homogeneity of the Siddis, despite their admixed origin, suggests the utility of this population for genetic and epidemiological studies.

Distinct diversity of KIR genes in three southern Indian populations: comparison with world populations revealed a link between KIR gene content and pre-historic human migrations

By interacting with polymorphic HLA class I molecules, the killer cell immunoglobulin-like receptors (KIR) influence the innate and adaptive immune response to infection. The KIR family varies in gene content and sequence polymorphism, thereby, distinguishing individuals and populations. To investigate KIR diversity in the earliest settlers of India, we have characterized the KIR gene content in three Dravidian-speaking populations (Mollukurumba, Kanikar, and Paravar) from the state of Tamil Nadu, southern India. The activating KIR genes and putative group-B KIR haplotypes were frequent in Paravar and Kanikar, a scenario analogous to those seen previously in other populations of Indian origin, indicating that predominance of group-B KIR haplotypes is the characteristic feature of Indian populations. In contrast, the KIR gene profile of Mollukurumba was more related to Caucasian type. It is not clear whether a local-specific selection or a recent admixture from Iran is responsible for such discrete profile in Mollukurumba. Each southern Indian population had distinct KIR genotype profile. Comparative analyses with world populations revealed that group-B KIR haplotypes were frequent in the natives of India, Australia, and America, the populations associated with those involved in extensive prehistoric human migrations. Whether or not natural selection has acted to enrich group-B KIR haplotypes in these migratory descendants is an issue that requires objective testing.

Deletion analysis of spinal muscular atrophy in southern Indian population

Proximal spinal muscular atrophy (SMA) is a genetically heterogeneous disease with paresis and muscle atrophy due to loss of anterior horn cell function. The survival of motor neuron gene (SMN) and neuronal apoptosis inhibitory protein (NAIP) play a primary role. Both the gene homologues exist as inverted duplications on Chromosome 5q. The telomeric/functional (SMN1) and the centromeric (SMN2) copies differ from each other in eight nucleotides. The C-->T transition (at Codon 280) within Exon 7 of SMN2 causes disruption of an exonic splicing enhancer (ESE) and/or creates an exonic splicing silencer (ESS) leading to abnormal splicing and a truncated protein. To determine the molecular genetics of SMN1 and NAIP genes in SMA from southern India. In the present study, 37 patients from the neuromuscular disorders clinic of National Institute of Mental Health and Neurosciences were assayed for the deletions in the SMN1 and NAIP genes using PCR-RFLP methods. Among the SMA Type I patients, 43% showed deletions of SMN1 and NAIP. In patients Type II SMA, 57% showed deletions of the SMN1 exons. Thus, deletions were found to occur in 47.8% of the Type I and II patients. Lower sensitivity of gene deletion study in clinically suspected SMA needs further study as clinical diagnosis of SMA is not gold standard. However, the results do correlate with other studies conducted in India.

Prevalence of Angle-Closure Disease in a Rural Southern Indian Population

To estimate the prevalence of primary angle-closure glaucoma, primary angle closure (PAC), and primary angle-closure suspect (PACS) and its associated risk factors in a rural population in southern India. Three thousand and nine hundred thirty-four (81.95%) of 4800 enumerated subjects aged 40 years or older underwent a complete ophthalmic examination, including compression gonioscopy. Glaucoma was diagnosed using International Society of Geographical and Epidemiological Ophthalmology classification. Data were analyzed for 3924 subjects (81.75%). Primary angle-closure glaucoma was diagnosed in 34 subjects (0.87%; 95% confidence interval [CI], 0.58 to 1.16) (27 women, 7 men). The mean intraocular pressure was 20.71 +/- 9.24 mm Hg. One subject (2.94%) was blind. Twenty-eight subjects (0.71%; 95% CI, 0.45 to 0.98) were diagnosed to have PAC (21 women, 7 men). Eleven subjects (39.3%) had an intraocular pressure greater than 21 mm Hg, 13 subjects (46.43%) had peripheral anterior synechiae, and 4 subjects (14.29%) had both. Two hundred forty-six subjects (6.27%; 95% CI, 5.51 to 7.03) had PACS (168 women, 78 men). Primary angle closure and primary angle-closure glaucoma were more common in women (age-adjusted odds ratio, 3.02; 95% CI, 1.66 to 5.51) with an increasing prevalence with age. Increasing intraocular pressure was associated with the disease (odds ratio, 1.14; 95% CI, 1.09 to 1.19). There was no association with hypertension and hyperopia. Axial length and anterior chamber depth were longer in the normal group than in the 3 groups with angle closure (P<.05). Women had shorter axial lengths than men (P<.001) in the angle closure groups. The overall prevalence of primary angle closures (PAC and primary angle-closure glaucoma) in a rural population of southern India was 1.58%. There was a female preponderance, and the disease tends to be asymptomatic.

Evaluation of non‐specific effects of infant immunizations on early infant mortality in a southern Indian population

The aim of this study was to assess the relationship between receipt of routine childhood immunizations and infant mortality before 6 months of age. This was an observational study of 10,274 infants, in a randomized trial of vitamin A supplementation, who received the study dose and survived to at least 1 week of age. The primary outcome was mortality before 6 months of age, analysed in Cox regression models as a function of vaccine receipt and gender. Receipt of Bacille Calmette Guerin (BCG) or diphtheria, tetanus, polio (DTP) vaccine was associated with significant reductions of one-half to two-thirds of mortality hazards; among girls, those who received both BCG and DTP experienced higher mortality than those who received only one of the two vaccines (hazards ratio 2.4; 95% confidence interval 1.2-5.0). The reduced mortality rate associated with receipt of BCG or DTP may be due to both biological and selection factors; the analyses regarding the combined effect of these vaccines and gender need to be replicated in other settings.

Assessment of genetic diversity inTectona grandisusing amplified fragment length polymorphism markers

There is much concern over teak (Tectona grandis L. f.) genetic resources because of uncontrolled logging during the past centuries. We investigated patterns of genetic variation within and among nine populations of T. grandis from diverse geographical regions in India, Thailand, and Indonesia using amplified fragment length polymorphism (AFLP). An analysis of molecular variance (AMOVA) showed that 57% of total genetic variance occurred within populations, the remaining 43% occurred between populations. Cluster analysis and principal coordinate analysis indicated that Indian populations are clearly separated from those in Thailand and Indonesia. However, the Berbera population from Orissa near the Indian northeastern coast is an exception, as it seems to have associations with both the Indian and the Thai–Indonesian populations. The Thai and Indian populations cannot mutually be separated in this investigation. The comparisons between Indian populations suggest that the northwestern Allapally plains population (Maharastra) is distinct from the two southern Indian populations that were analyzed.

Social organization of the Asian elephant (Elephas maximus) in southern India inferred from microsatellite DNA

Social organization of the Asian elephant (Elephas maximus) is not well understood in the absence of long-term studies of identified individuals. Adult Asian elephant females and their young offspring of both sexes form matriarchal groups, with pubertal males dispersing from natal groups, but whether these social groups represent families and whether males show locational or social dispersal were unknown. Using nuclear microsatellite loci amplified from dung-extracted DNA of free-ranging elephants in a large southern Indian population, we demonstrate that female-led herds comprise closely related individuals that are indeed families, and that males exhibit non-random locational dispersal.

Genetic structure and affinities among tribal populations of southern India: a study of 24 autosomal DNA markers

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.