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Mitochondria play a critical role in the generation of metabolic energy in the form of ATP. Tissues and organs that are highly dependent on aerobic metabolism are involved in mitochondrial disorders including nonsyndromic hearing loss (NSHL). Seven pathogenic variants leading to NSHL have so far been reported on two mitochondrial genes: MT-RNR1 encoding 12SrRNA and MT-TS1 encoding tRNA for Ser((UCN)) . We screened 729 prelingual NSHL subjects to determine the prevalence of MT-RNR1 variants at position m.961, m.1555A>G and m.1494C>T, and MT-TS1 m.7445A>G, m.7472insC m.7510T>C and m.7511T>C variants. Mitochondrial pathogenic variants were found in eight probands (1.1%). Five of them were found to have the m.1555A>G variant, two others had m.7472insC and one proband had m.7444G>A. The extended relatives of these probands showed variable degrees of hearing loss and age at onset. This study shows that mitochondrial pathogenic alleles contribute to about 1% prelingual hearing loss. This study will henceforth provide the reference for the prevalence of mitochondrial pathogenic alleles in the South Indian population, which to date has not been estimated. The m.1555A>G variant is a primary predisposing genetic factor for the development of hearing loss. Our study strongly suggests that mitochondrial genotyping should be considered for all hearing impaired individuals and particularly in families where transmission is compatible with maternal inheritance, after ruling out the most common variants., (© 2016 John Wiley & Sons Ltd/University College London.)

Mutations in the GJB2 gene encoding the gap junction protein Connexin 26 have been associated with autosomal recessive as well as dominant nonsyndromic hearing loss. Owing to the involvement of connexins in skin homeostasis, GJB2 mutations have also been associated with syndromic forms of hearing loss showing various skin manifestations. We report an assortatively mating hearing impaired family of south Indian origin with three affected members spread over two generations, having p.R75Q mutation in the GJB2 gene in the heterozygous condition. The inheritance pattern was autosomal dominant with mother and son being affected. Dermatological and histopathologic examinations showed absence of palmoplantar keratoderma. To the best of our knowledge, this is the first report from India on p.R75Q mutation in the GJB2 gene with nonsyndromic hearing loss., (© 2014 John Wiley & Sons Ltd/University College London.)

Mutations in the autosomal genes TMPRSS3, TMC1, USHIC, CDH23 and TMIE are known to cause hereditary hearing loss. To study the contribution of these genes to autosomal recessive, non-syndromic hearing loss (ARNSHL) in India, we examined 374 families with the disorder to identify potential mutations. We found four mutations in TMPRSS3, eight in TMC1, ten in USHIC, eight in CDH23 and three in TMIE. Of the 33 potentially pathogenic variants identified in these genes, 23 were new and the remaining have been previously reported. Collectively, mutations in these five genes contribute to about one-tenth of ARNSHL among the families examined. New mutations detected in this study extend the allelic heterogeneity of the genes and provide several additional variants for structure-function correlation studies. These findings have implications for early DNA-based detection of deafness and genetic counseling of affected families in the Indian subcontinent.

With the etiology being unclear till date, a combination of age, genetic and environmental factors are known to play a significant role in the pathogenesis of Parkinson's disease. Mutations in PARK2 gene have been implicated to cause autosomal recessive early onset PD. We analyzed the 12 coding exons of PARK2 gene in 16 early onset PD patients of South Indian ethnicity. PARK2 mutations were present in 68% of the early onset cases. We report the presence of four PARK2 sequence variants c.1239G>C, c.171+25T>C, c.202A>G, c.601G>A, and a novel insertion mutation, c.798_799insA in the exon 7 of PARK2 gene. These results suggest that mutations in PARK2 gene may be a common cause of PD among South Indian early onset patients., (Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.)

Fragile X syndrome is the most frequent hereditary cause of mental retardation after Down syndrome. Expansion of CGG repeats in the 5' UTR of the fragile X mental retardation gene 1 (FMR1) causes gene inactivation in most of the cases. The FMR1 gene is classified into normal 5-44; gray zone 45-54; premutation 55 to <200; and full mutation ≥ 00 repeats. Precise sizing of FMR1 alleles is important to understand their variation, predisposition, and for genetic counseling. Meta-analysis reveals prevalence of premutation carriers as 1 in 259. No such reports are available in India. About 705 women from Tamil Nadu, South India, were screened for the FMR1 allelic variation by using radioactive polymerase chain reaction-polyacrylamide gel electrophoresis (PAGE) analysis. The women who were homozygous by radioactive polymerase chain reaction (rPCR) were reanalyzed by methylation-specific polymerase chain reaction (Ms-PCR) and GeneScan analysis. The techniques were validated and compared to arrive at a correction factor. Among 122 genotypes, 35 repeat variants ranging in size from 16 to 57 were observed. The most common repeat is 30 followed by 29. One in 353 women carried the premutation. No full mutations were observed. Screening populations with low frequency of premutations may not be applicable. Ms-PCR is more suitable for routine screening and clinical testing compared with rPCR-PAGE analysis.

We analysed the genetic structure of ≈ 1000 samples representing 27 ethnic groups settled in Tamil Nadu, south India, derived from two linguistic families (Dravidians and Indo-Europeans) representing four religious groups (Hinduism, Islam, Christianity and Jainism) using 11 mtDNA markers. Out of 27 ethnic groups, four are in situ populations (Anglo-Indian, Labbai Muslim, Nadar Christian and south Indian Jain) and two are migrants (Gypsy and north Indian Jain) from north India to Tamil Nadu, and 21 are native ethnic groups. Six of the markers we used were monomorphic (HaeIII663, HpaI3592, AluI5176, AluI7025, AluI13262, 9-bp deletion) and five markers were polymorphic (DdeI10394, AluI10397, HinfI12308, HincII13259 and HaeIII16517). Haplogroup frequencies, genetic affinities and admixture analysis are based on the genotype data of polymorphic markers observed in these populations. Haplogroup frequencies indicate that various ethnic groups entered Tamil Nadu during different time periods. Genetic affinities and admixture estimates revealed that the ethnic groups possessing advanced knowledge of farming cluster in a branch (C), and could be the late arrived settlers as agriculture, was introduced to this region at about 5 to 3 thousand years ago. In situ ethnic groups appear to have arisen at various times as a result of the prevailing dominant socio-cultural forces. Hierarchical Hindu caste system created many ethnic groups in the history of its existence; some of them became isolated for considerable period of time. Over all, among Tamil ethnic groups, in spite of caste systems' rigidity, built in flexibility in the system in the form of hypergamy and hypogamy had allowed maternal gene flow between them.

Sensorineural hearing loss affects the quality of life and communication of millions of people, but the underlying molecular mechanisms remain elusive. Here, we identify mutations in Gipc3 underlying progressive sensorineural hearing loss (age-related hearing loss 5, ahl5) and audiogenic seizures (juvenile audiogenic monogenic seizure 1, jams1) in mice and autosomal recessive deafness DFNB15 and DFNB95 in humans. Gipc3 localizes to inner ear sensory hair cells and spiral ganglion. A missense mutation in the PDZ domain has an attenuating effect on mechanotransduction and the acquisition of mature inner hair cell potassium currents. Magnitude and temporal progression of wave I amplitude of afferent neurons correlate with susceptibility and resistance to audiogenic seizures. The Gipc3(343A) allele disrupts the structure of the stereocilia bundle and affects long-term function of auditory hair cells and spiral ganglion neurons. Our study suggests a pivotal role of Gipc3 in acoustic signal acquisition and propagation in cochlear hair cells.

We previously mapped the DFNB17 locus to a 3-4 cM interval on human chromosome 7q31 in a large consanguineous Indian family with congenital profound sensorineural hearing loss. To further refine this interval, 30 new highly polymorphic markers and 8 SNPs were analyzed against the pedigree. Re-analysis in the original DFNB 17 family and additional data from a second unrelated consanguineous family with congenital deafness found to map to the interval, limited the area of shared homozygosity-by-descent (HBD) to approximately 4 megabase (Mb) between markers D7S2453 and D7S525. Nineteen known genes and over 20 other cDNAs have been identified in the refined DFNB 17 interval, including the SLC26A4 gene. We have analyzed 4 other cochlear-expressed genes that map to the DFNB17 interval as candidate genes. Analysis of coding and splice site regions of these cochlear expressed genes did not reveal any disease causing mutations. Further study of other candidate genes is currently underway.

Retinitis pigmentosa (RP) is a group of clinically and genetically heterogeneous disorders characterised by night blindness, constriction of visual field, and dystrophic changes of the retina. Previous genetic studies have shown extensive allelic and non-allelic genetic heterogeneity of RP. Here we describe an Indian family with multiple consanguineous marriages and a total of four patients with autosomal recessive (AR) RP. The homozygosity mapping strategy was successfully used and indicated close linkage between the disease locus and D2S380, D2S441, D2S291, and D2S1394 with maximum lod scores between 1.51-3.07 at theta=0.00. The analysis of multiply informative meioses maps the locus (RP28) for ARRP in this family between D1S1337 and D2S286 on 2p11-p15. The involvement of visinin (VSNL1), a promising candidate gene assigned to chromosome 2p by previous studies, has been excluded by the absence of linkage.

Background: It has been hypothesized that the yearly menarche rhythm could be caused by the seasonal variation of photoperiod and temperature or by the annual distribution of the scholar vacation and study periods., Aim: To test the hypothesis that the distribution of study vacation periods is a condition that modifies the annual menarche rhythm., Subjects and Methods: Two thousand ninety four school girls from Chile, 2,356 girls from Madras, India, 3,454 girls from Medellin, Colombia and 2,627 girls from Debrecen, Hungary, were studied. They were asked about the month of their menarche. Vacation months were considered those with more than 6 days of leave from school., Results: The seasonal hypothesis was refuted because there were contradictions with the expected antithetical behavior in both hemispheres, there was a significant heterogeneity of the yearly menarche among girls from the same region, the expected cline of the menarche frequency variance from equator to poles was not observed, finding an antithetical cline instead and there was a significant heterogeneity among months of the same season. On the other hand, months with vacation periods coincided significantly with peaks of menarche, while study months had lower proportion of menarche (total binomial probability < 10(-6)). Girls whose month of menarche was the same as their month of birth, did not agree completely with the vacation-study hypothesis as the rest of the sample., Conclusions: Vacation periods influenced menarche rhythm. However, these periods coincide with most cultural events and this strong association needs further study to be considered causal. It is not possible to assume school stress as the main explanatory variable. Ontogenetic factors such as birth imprinting also can influence the menarche rhythm, as shown in girls whose month of menarche coincided with their month of birth.

Autosomal recessive childhood-onset severe retinal dystrophy (arCSRD) designates a heterogeneous group of disorders affecting rod and cone photoreceptors simultaneously. The most severe cases are termed Leber congenital amaurosis (LCA), while the less aggressive forms are usually considered juvenile retinitis pigmentosa. Recently, mutations in the retinal-specific guanylate cyclase gene were found in patients with LCA. Disease genes implicated in other forms of arCSRD are expected to encode proteins present in the neuroretina or in the retinal pigment epithelium (RPE). The RPE, a monolayer of cells separating the vascular-rich choroid and the neuroretina, is in intimate contact with the outer segments of rods and cones via the microvilli surrounding the photoreceptors. The RPE expresses a tissue-specific and evolutionarily highly conserved 61 kD protein (RPE65) present at high levels in vivo. Although the function of RPE65 is not yet known, an important role in the RPE/photoreceptor vitamin-A cycle is suggested by the fact that RPE65 associates both with serum retinol-binding protein and with the RPE-specific 11-cis retinol dehydrogenase, an enzyme active in the synthesis of the visual pigment chromophore 11-cis retinal. Here we report that the analysis of RPE65 in a collection of about 100 unselected retinal-dystrophy patients of different ethnic origin revealed five that are likely to be pathogenic mutations, including a missense mutation (Pro363Thr), two point mutations affecting splicing (912 + 1G-->T and 65 + 5G-->A) and two small re-arrangements (ins144T and 831del8) on a total of nine alleles of five patients with arCSRD. In contrast to other genes whose defects have been implicated in degenerative retinopathies, RPE65 is the first disease gene in this group of inherited disorders that is expressed exclusively in the RPE, and may play a role in vitamin-A metabolism of the retina.

A total of 204 blood samples were collected from healthy, unrelated Adi-Dravidars of Chengalput District, Tamil, India. These samples were screened for ABO and RH blood groups using the respective antisera. CP and ALB serum protein electrophoretic phenotypes were assessed. The chi 2 analysis for Hardy-Weinberg equilibrium revealed that the population fits in panmictic equilibrium. The results were compared with the findings reported for other populations of Southern India.

The relationship between maternal stature, number of conceptions, offspring mortality and number of surviving children was studied in 291 Jalari women. Maternal stature averaged 150.98 cm, maternal age 35 years, number of conceptions 5.1 and number of surviving children 4.2. Adjusting for age and number of conceptions, the relationship between maternal stature and surviving children is significantly negative. Shorter women show significantly higher number of conceptions and surviving children than taller women (P less than 0.05). Intensity of natural selection (I) is computed for height and weight.

Opportunity for selection has been studied against their contrasting socioeconomic and cultural backgrounds in two endogamous populations, namely, Brahmins and Jalaris of Visakhapatnam, India. Total selection was slightly higher among the better off Brahmins than in Jalaris. But a marked qualitative and quantitative variation was found in the contributing components; the fertility differential was circa 60% in Brahmins while the mortality differential was circa 60% in Jalaris according to the Crow Index. The decreased mortality differential in Brahmins suggests that this component was directly affected by the better socio-economic level and reflects on the population's transitional phase. Further, the If value fell to a half in women who completed their fertility by family planning when compared to women who completed their fertility by menopause, thus reducing the variance in fertility component in the family planning group.

Variability in genetic load has been studied against their contrasting socioeconomic and cultural backgrounds in two endogamous populations, namely, the well-off Brahmins and the low income Jalaris of Visakhapatnam, India. The A (genetic and environmental damage) and B (hidden genetic damage) estimates are higher in Jalaris. Decreased A estimates indicate the better medical care in Brahmins; the value of B could be low since many of the deaths in consanguineous families due to infectious diseases are now rarer. The genetic load (B/A ratio) indicates that the average gamete carries 0.057 and 2.123 deleterious genes, respectively, in Brahmins and Jalaris, which, if made homozygous, would kill an individual before reproductive age. The load is 35 times higher in Jalaris; this may be due to their higher inbreeding level. Contrasting socioeconomic differences and meagre medical aid might add another bias towards relatively higher B/A in Jalaris. In general the observed genetic load in both populations are lower than in other studies which may be due to gradual elimination of deleterious genes by continued practice of inbreeding.

Segregation distortion for the Rh system is reported. Mother-infant pairs (1018 pairs) from maternity service divisions of government hospital and 216 complete families with a total of 692 children, of Visakhapatnam (Andhra Pradesh, South India) were typed for the D-d alleles of Rh system. The segregations analysis made by means of the T matrix method of ITO matrices, assuming Hardy-Weinberg equilibrium, reveals that: Rh-positive mothers produce fewer Rh-negative children with significance and Rh-negative mothers produce more Rh-positive children with less significance than expected in both the mother-child and family studies. This results in a reduction in the d allele from mothers to their children. Known Rh antigenic specificities and reproductive compensation do not explain the observed distortion. Other selectively acting forces probably linked to Rh compatibility system seem to be operating to gain d alleles to maintain Rh polymorphism.

Using gene frequency data for the ABO locus so far available, gene differentiation and gene identity between 20 castes and 22 tribes of Andhra Pradesh were determined. The interpopulation gene diversity is 1.4 and 1.6% of total genic variation in castes and tribes, respectively. Difficulties in interpreting genetic diversity using just one genetic system is discussed.

A total 2000 unrelated school children were screened for colorblindness in Vishakhapatnam, India. Whether the protan and deutan defects are the result of mutations at one locus or at two loci has not been completely resolved, although the evidence favors two discrete loci. The investigation was extended to the families of the 40 color vision anomalous children to study the descendance patterns of these two loci. The importance of these observations are discussed.

Blood group (ABO, MN, Rh, CcDEe) polymorphisms are reported here for 4 strictly endogamous subcastes of Andhra Brahmins. The coefficient of gene differentiation calculated from the gene frequencies is 0.87% demonstrating that only a small fraction of the total gene diversity is attributable to the differences between subcastes. In spite of the strict endogamy for the past 10-14 centuries, 99.13% of gene differentiation exists within the subcastes.

Selection in ABO, Rh, and MN blood groups was studied in 216 matings and their children in an endogamous population. Incompatibility status with respect to these three systems was considered simultaneously. There is no effect of incompatibility on number of pregnancies. Analysis of variance between groups confirms that prenatal loss is associated with incompatibility, and it is greater when the matings are incompatible for any two systems. There is no significant intergenerational change in ABO and Rh polymorphisms. Segregation analysis for the ABO system suggests that there is no significant difference in the proportion of A, B, and O children, based on the compatibility of the parents, while analysis for Rh-D system showed a segregation distortion which is not related to the known antigenic specificities (mother-child incompatibility).

The frequency distribution of various consanguineous marriages was studied in the city of Madras, Tamil Nadu, South India. Parallel first cousin marriages (PFC) were found to occur in appreciable frequencies in all caste groups of Hindus. While it has been generally believed that PFC marriages among Hindus are mere exceptions and are usually not tolerated, our data show that they can no longer be treated as exceptions. The high frequency (27 per cent) of PFC marriages in some Hindu communities necessitates in-depth studies to elucidate the forces at work which go against the very fundamentals of Dravidian kinship.

The percentage of low birth weight infants (LBWI) weighing less than 2270 g in Visakhapatnam (Andhra Pradesh) is relatively higher (12.8%) than in other parts of India. The frequency of LBWI is high at birth order 1 and 2. Thereafter the curve does not show any consistency although the mean per cent of LBWI is lesser than in birth order 1 and 2. The minimum frequency is at birth order 3. The maternal classes less than or equal to 20-29 years show a gradual decrease in the frequency of LBWI with increasing age. For mothers of greater than or equal to 30-39 years of age a general U-shaped relation is found. The overall distribution of neonatal deaths is bimodal, with a peak at less than 1350 g and at 1810 g.