Whole genome variant analysis in three ethnically diverse Indians

India represents an amazing confluence of geographically, linguistically and socially disparate ethnic populations (Indian Genome Variation Consortium, J Genet 87:3–20, 2008). Understanding the genetic diversity of Indian population remains a daunting task. In this paper we present detailed analysis of genomic variations (high-depth coverage (~?30×) using Illumina Hiseq 2000 platform) from three healthy Indian male individuals each belonging to three geographically delineated regions and linguistic phylum viz. high altitude region of Ladakh (Tibeto-Burman linguistic phylum), sub mountainous region of Kumaun (Indo-European linguistic phylum) and sea level region of Telangana (Dravidian linguistic phylum) for probing the extent of genetic diversity in our population. The sequencing analysis provided high quality data (~?95% of the total reads aligned to the human reference genome for each sample) and very good alignment quality (>?80% of the filtered mapped reads had a quality score of 60). A total of 4.3, 3.7 and 4.3 million single nucleotide variations were identified in the genome of high altitude, sub mountainous and sea level respectively by comparing with human reference genome. Approximately 17.3, 18.2, 17.4% of the variants were unique in the three genomes. The study identified many novel variations in the three diverse genomes (132,970 in Ladakh, 112,317 in Kumaun and 128,881 in Telangana individual) and is an important resource for creating a baseline and a comprehensive catalogue of human genomic variation across the Indian as well as the Asian continent.     

The South Asian Genome

The genetic sequence variation of people from the Indian subcontinent who comprise one-quarter of the world''s population, is not well described. We carried out whole genome sequencing of 168 South Asians, along with whole-exome sequencing of 147 South Asians to provide deeper characterisation of coding regions. We identify 12,962,155 autosomal sequence variants, including 2,946,861 new SNPs and 312,738 novel indels. This catalogue of SNPs and indels amongst South Asians provides the first comprehensive map of genetic variation in this major human population, and reveals evidence for selective pressures on genes involved in skin biology, metabolism, infection and immunity. Our results will accelerate the search for the genetic variants underlying susceptibility to disorders such as type-2 diabetes and cardiovascular disease which are highly prevalent amongst South Asians.     

Cassava mosaic geminiviruses: actual knowledge and perspectives

Cassava mosaic disease (CMD) caused by cassava mosaic geminiviruses (CMGs) is one of the most devastating crop diseases and a major constraint for cassava cultivation. CMD has been reported only from the African continent and Indian subcontinent despite the large-scale cultivation of cassava in Latin America and several South-East Asian countries. Seven CMG species have been reported from Africa and two from the Indian subcontinent and, in addition, several strains have been recognized. Recombination and pseudo-recombination between CMGs give rise not only to different strains, but also to members of novel virus species with increased virulence and a new source of biodiversity, causing severe disease epidemics. CMGs are known to trigger gene silencing in plants and, in order to counteract this natural host defence, geminiviruses have evolved suppressor proteins. Temperature and other environmental factors can affect silencing and suppression, and thus modulate the symptoms. In the case of mixed infections of two or more CMGs, there is a possibility for a synergistic interaction as a result of the presence of differential and combinatorial suppressor proteins. In this article, we provide the status of recent research findings with regard to the CMD complex, present the molecular biology knowledge of CMGs with reference to other geminiviruses, and highlight the mechanisms by which CMGs have exploited nature to their advantage.     

Phylogeography and origin of Indian domestic goats

The Indian subcontinent contains 20 well-characterized goat breeds, which vary in their genetic potential for the production of milk, meat, and fibre; disease resistance; heat tolerance; and fecundity. Indian goats make up 20% of the world's goat population, but there has been no extensive study of these economically important animals. Therefore, we have undertaken the present investigation of 363 goats belonging to 10 different breeds from different geographic regions of India using mtDNA sequence data from the HVRI region. We find evidence for population structure and novel lineages in Indian goats and cannot reconcile the genetic diversity found within the major lineage with domestication starting 10,000 years ago from a single mtDNA ancestor. Thus, we propose a more complex origin for domestic goats.     

Distribution of glyoxalase I (GLO) variants in Western Europe and the Indian subcontinent

Summary English, Italian (including Sardinian), and Spanish populations from Europe and Muslim, Hindu, Sikh, Punjabi, and other populations from the Indian subcontinent currently living either in Birmingham or in India were screened for electrophoretically detectable genetic variants of red cell glyoxalase I (GLO), and their frequencies were reported. All the western European populations investigated, including those reported, exhibited an incidence of close to 44% for the GLO ¹ gene. The frequency distribution of the GLO ¹ gene in various populations from the Indian subcontinent, in contrast, was found to range between 0.15 and 0.33. These observations suggest that the European populations in general are genetically more homogeneous than are the populations of the Indian subcontinent.     

A novel multilocus sequence typing scheme identifying genetic diversity amongst Leishmania donovani isolates from a genetically homogeneous population in the Indian subcontinent

In the Indian subcontinent, infection with Leishmania donovani can cause fatal visceral leishmaniasis. Genetic variation in L. donovani is believed to occur rapidly from environmental changes and through selective drug pressures, thereby allowing continued disease occurrence in this region. All previous molecular markers that are commonly in use multilocus microsatellite typing and multilocus sequence typing, were monomorphic in L. donovani originating from the Indian subcontinent (with only a few exceptions) and hence are not suitable for this region. An multilocus sequence typing scheme consisting of a new set of seven housekeeping genes was developed in this study, based on recent findings from whole genome sequencing data. This new scheme was used to assess the genetic diversity amongst 22 autochthonous L. donovani isolates from Bangladesh. Nineteen additional isolates of the L. donovani complex (including sequences of L. donovani reference strain BPK282A1) from other countries were included for comparison. By using restriction fragment length polymorphism of the internal transcribed spacer 1 region (ITS1-RFLP) and ITS1 sequencing, all Bangladeshi isolates were confirmed to be L. donovani. Population genetic analyses of 41 isolates using the seven new MLST loci clearly separated L. donovani from Leishmania infantum. With this multilocus sequence typing scheme, seven genotypes were identified amongst Bangladeshi L. donovani isolates, and these isolates were found to be phylogenetically different compared with those from India, Nepal, Iraq and Africa. This novel multilocus sequence typing approach can detect intra- and inter-species variations within the L. donovani complex, but most importantly these molecular markers can be applied to resolve the phylogenetically very homogeneous L. donovani strains from the Indian subcontinent. Four of these markers were found suitable to differentiate strains originating from Bangladesh, with marker A2P being the most discriminative one.     

Variations in body melanisation,ovariole number and fecundity in highland and lowland populations of Drosophila melanogaster from the Indian subcontinent

We investigated geographical variations in three fitness‐related traits (body melanisation, ovariole number and fecundity) in laboratory‐reared offspring of 10 populations of Drosophila melanogaster. The populations were collected from adjacent lowland and highland localities (～80–100 km apart) in the tropical as well as subtropical regions (11.15–31.06 °N) covering a linear distance about 3 000 kilometers from south to north on the Indian subcontinent. Persistence of within‐as well as between‐population differences at 21 °C suggest that observed variations in fitness‐related traits have a genetic basis. Populations from higher altitudes showed consistently higher trait values (1.4‐fold increase) as compared with their corresponding lowland populations. By contrast, latitudinal variations were about two‐fold higher across the entire continent. Along latitude as well as altitude, population means showed higher correlation values (r > 0.98) between all the three fitness traits. However, on the basis of within‐population analysis (assorted darker and lighter flies), changes in body melanisation were significantly correlated with fecundity but not with ovariole number. Thus, analysis of within‐population trait variability should be preferred as compared with data on population means for adaptive significance of fitness‐related traits. In the present study, the role of climatic selection is evident from regression analysis with changes in annual average temperature of the sites of origin of populations along latitude as well as altitude.     

Lysoplex: An efficient toolkit to detect DNA sequence variations in the autophagy-lysosomal pathway

The autophagy-lysosomal pathway (ALP) regulates cell homeostasis and plays a crucial role in human diseases, such as lysosomal storage disorders (LSDs) and common neurodegenerative diseases. Therefore, the identification of DNA sequence variations in genes involved in this pathway and their association with human diseases would have a significant impact on health. To this aim, we developed Lysoplex, a targeted next-generation sequencing (NGS) approach, which allowed us to obtain a uniform and accurate coding sequence coverage of a comprehensive set of 891 genes involved in lysosomal, endocytic, and autophagic pathways. Lysoplex was successfully validated on 14 different types of LSDs and then used to analyze 48 mutation-unknown patients with a clinical phenotype of neuronal ceroid lipofuscinosis (NCL), a genetically heterogeneous subtype of LSD. Lysoplex allowed us to identify pathogenic mutations in 67% of patients, most of whom had been unsuccessfully analyzed by several sequencing approaches. In addition, in 3 patients, we found potential disease-causing variants in novel NCL candidate genes. We then compared the variant detection power of Lysoplex with data derived from public whole exome sequencing (WES) efforts. On average, a 50% higher number of validated amino acid changes and truncating variations per gene were identified. Overall, we identified 61 truncating sequence variations and 488 missense variations with a high probability to cause loss of function in a total of 316 genes. Interestingly, some loss-of-function variations of genes involved in the ALP pathway were found in homozygosity in the normal population, suggesting that their role is not essential. Thus, Lysoplex provided a comprehensive catalog of sequence variants in ALP genes and allows the assessment of their relevance in cell biology as well as their contribution to human disease.     

The first draft of the pigeonpea genome sequence

Pigeonpea (Cajanus cajan) is an important grain legume of the Indian subcontinent, South-East Asia and East Africa. More than eighty five percent of the world pigeonpea is produced and consumed in India where it is a key crop for food and nutritional security of the people. Here we present the first draft of the genome sequence of a popular pigeonpea variety ??Asha??. The genome was assembled using long sequence reads of 454 GS-FLX sequencing chemistry with mean read lengths of >550?bp and >10-fold genome coverage, resulting in 510,809,477?bp of high quality sequence. Total 47,004 protein coding genes and 12,511 transposable elements related genes were predicted. We identified 1,213 disease resistance/defense response genes and 152 abiotic stress tolerance genes in the pigeonpea genome that make it a hardy crop. In comparison to soybean, pigeonpea has relatively fewer number of genes for lipid biosynthesis and larger number of genes for cellulose synthesis. The sequence contigs were arranged in to 59,681 scaffolds, which were anchored to eleven chromosomes of pigeonpea with 347 genic-SNP markers of an intra-species reference genetic map. Eleven pigeonpea chromosomes showed low but significant synteny with the twenty chromosomes of soybean. The genome sequence was used to identify large number of hypervariable ??Arhar?? simple sequence repeat (HASSR) markers, 437 of which were experimentally validated for PCR amplification and high rate of polymorphism among pigeonpea varieties. These markers will be useful for fingerprinting and diversity analysis of pigeonpea germplasm and molecular breeding applications. This is the first plant genome sequence completed entirely through a network of Indian institutions led by the Indian Council of Agricultural Research and provides a valuable resource for the pigeonpea variety improvement.     

Developing imidazole analogues as potential inhibitor for Leishmania donovani trypanothione reductase: virtual screening,molecular docking,dynamics and ADMET approach

Visceral leishmaniasis (VL) affects Indian subcontinent, African and South American continent, and it covers 70 countries worldwide. Visceral form of leishmaniasis is caused by Leishmania donovani in Indian subcontinent which is lethal if left untreated. Extensive resistance to antileishmanial drugs such as sodium stibogluconate, pentamidine and miltefosine and their decreased efficacy has been reported in the endemic region. Amphotericin B drug has shown good antileishmanial activity with significant toxicity, but its cost of treatment has limited the outreach of this treatment to affected people living in endemic zone. So, there is an urgent need to identify new antileishmanial drugs with excellent activity and minimal toxicity issues. Trypanothione reductase, a component of antioxidant system, is necessary for parasite growth and survival to raise infection. To develop potential inhibitor, we docked nine hundred and eighty-four 5-nitroimidazole analogues along with clomipramine which is a well-known inhibitor for TR. Total one hundred and forty-seven 5-nitroimidazole analogues with better docking score than clomipramine were chosen for ADMET and QikProp studies. Among these imidazole analogues, total twenty-four imidazole analogues and clomipramine were chosen on the basis of their ADMET, QikProp, and prime MM-GBSA study. Later on, two analogues with best MM-GBSA dG bind were undergone molecular dynamic simulation to ensure protein–ligand interactions. Using above approach, we confirm that ethyl 2-acetyl-5-[4-butyl-2-(3-hydroxypentyl)-5-nitro-1H-imidazol-1-yl]pent-2-enoate can be a drug candidate against L. donovani for the treatment of VL in the Indian subcontinent.     

Phenotypic variability of thoracic pigmentation in Indian populations of Drosophila melanogaster

Fourteen natural populations of Drosophila melanogaster collected along diverse latitudinal and altitudinal ranges, were analysed for thoracic trident pigmentation at two different breeding temperatures (17 and 25°C) for both sexes. Statistical analyses showed significant intra- as well as interpopulational genetic variations. Clinal patterns for thoracic trident pigmentation along latitude as well as altitude are significantly correlated with thermal amplitude ( T _cv). Crosses between dark (Shimla) and light (Kalka) variants of trident pigmentation produced intermediate phenotypes, and a clear maternal effect was observed in the reciprocal F ₁ crosses. Data suggest that the temperature differences have resulted in phenotypic plasticity of thoracic pigmentation across the Indian subcontinent.     

Sequencing and analysis of a South Asian-Indian personal genome

ABSTRACT: BACKGROUND: With over 1.3 billion people, India is estimated to contain three times more genetic diversity than does Europe. Next-generation sequencing technologies have facilitated the understanding of diversity by enabling whole genome sequencing at greater speed and lower cost. While genomes from people of European and Asian descent have been sequenced, only recently has a single male genome from the Indian subcontinent been published at sufficient depth and coverage. In this study we have sequenced and analyzed the genome of a South Asian Indian female (SAIF) from the Indian state of Kerala. RESULTS: We identified over 3.4 million SNPs in this genome including over 89,873 private variations. Comparison of the SAIF genome with several published personal genomes revealed that this individual shared ~50% of the SNPs with each of these genomes. Analysis of the SAIF mitochondrial genome showed that it is closely related to the U1 haplogroup which has been previously observed in Kerala. We assessed the SAIF genome for SNPs with health and disease consequences and found that the individual was at a higher risk for multiple sclerosis and a few other diseases. In analyzing SNPs that modulate drug response we found a variation that predicts a favorable response to metformin, a drug used to treat diabetes. SNPs predictive of adverse reaction to warfarin indicated that the SAIF individual is not at risk for bleeding if treated with typical doses of warfarin. In addition, we report the presence of several additional SNPs of medical relevance. CONCLUSIONS: This is the first study to report the complete whole genome sequence of a female from the state of Kerala in India. The availability of this complete genome and variant will further aid studies aimed at understanding genetic diversity, identifying clinically relevant changes and accessing disease burden in the Indian population.     

Genetic relationships between Indians and their neighboring populations

Using gene frequency data for 18 protein and blood group loci, we studied the genetic relationships of four Indian subcontinent populations (peoples from Punjab, Gujarati, Andhra Pradesh, and Bangladesh) with their neighboring populations (Iranians, Afghans, Sinhalese in Sri Lanka, Nepalese, Bhutanese, Malays, Bataks in northern Sumatra, and Chinese). The results obtained indicate that the four Indian subcontinent populations and the Sinhalese are genetically closer to Iranians and Afghans (Caucasoid) than to the other neighboring Mongoloid populations. Genetic distance analysis shows a clear-cut dichotomy between the Caucasoid and Mongoloid populations.     

Genetic variants of cytoplasmic malate dehydrogenase (MDH:EC:1.1.1.37) in populations in England and the Indian subcontinent

Summary A new variant malate dehydrogenase is described, designated S-MDH^Ind to indicate its discovery in the Indian subcontinent pending full comparison with all other variants. It occurred during a survey of the incidence of variant S-MDH phenotypes in 4149 subjects in north-east England and 1494 subjects from several populations in the Indian region. The variants previously thought to be restricted to the New Guinea region and to African populations occurred in three English subjects in northeast England. The incidence of variant S-MDH phenotypes in other populations is summarised.     

National survey of notifications of tuberculosis in England and Wales in 1983. Medical Research Council Tuberculosis and Chest Diseases Unit.

In a survey of all notifications of tuberculosis in England and Wales for the first six months of 1983 56% of the 3002 newly notified patients who had not been treated before were of white and 37% were of Indian subcontinent (Indian, Pakistani, or Bangladeshi) ethnic origin, findings similar to those of a survey in 1978-9. In the four and a quarter years between the surveys the number of patients notified had declined by 26%, the decline being 28% among those of white and 23% among those of Indian subcontinent ethnic origin. The white patients were on average older than the patients of Indian subcontinent ethnic origin, and a higher proportion of them had respiratory disease (82% compared with 66%). The pulmonary lesions were on average larger and more often bacteriologically positive in the white patients. There were considerable differences between the ethnic groups in the estimated yearly rates of notifications per 100 000 population in England in 1983. The highest rates occurred in the Indian (178) and the Pakistani and Bangladeshi (169) populations and were roughly 25 times the rate in the white population (6 X 9). In the Indian subcontinent ethnic groups the highest rates occurred among those who had arrived in the United Kingdom within the previous five years.     

Types of the cerebral arterial circle (circle of Willis) in a Sri Lankan Population

Background  

The variations of the circle of Willis (CW) are clinically important as patients with effective collateral circulations have a lower risk of transient ischemic attack and stroke than those with ineffective collaterals. The aim of the present cadaveric study was to investigate the anatomical variations of the CW and to compare the frequency of prevalence of the different variations with previous autopsy studies as variations in the anatomy of the CW as a whole have not been studied in the Indian subcontinent.     

Sequence variations of mitochondrial DNA D-loop region are associated with familial nasopharyngeal carcinoma

Mitochondrial DNA (mtDNA) D-loop has been identified as a frequent hot spot of mutations in various tumors. The aim here was to investigate the sequence variations of mitochondrial D-loop region in familial nasopharyngeal carcinoma (FNPC) and their possible associations with cancer risk. 29 subjects from 4 Chinese NPC families and 20 sporadic NPC as well as 122 cases of normal control were recruited. mtDNA extracted from peripheral blood was examined by PCR-based assay for D-loop sequence variations, followed by sequencing analysis. Compared with normal control, four high variations and 6 unrepoted novel polymorphisms were found. Particularly, the np16362 and 16519T to C variants show significantly higher (100%, 81.8%) and lower (0, 22.7%) frequencies in FNPC and unaffected pedigree members, respectively. The occurrence of mitochondrial microsatellite instability (mtMSI) at D310 in experimental groups was statistically significantly higher than in normal control (53.3%). Likewise, in Base Variation Rate consistent with the result, there was a statistically significant difference compared with NC (6.05%). Our results indicated that mtDNA exhibited a high rate of sequence variants in patients with NPC and pedigree members and the mtDNA np16362, np16519 variants and mtMSI at D310 are associated with an increased risk of familial nasopharyngeal carcinoma in pedigree members from families with NPC, which might be involved in the NPC carcinogenesis.     

Cost-Effectiveness Analysis of Combination Therapies for Visceral Leishmaniasis in the Indian Subcontinent

Background

Visceral leishmaniasis is a systemic parasitic disease that is fatal unless treated. We assessed the cost and cost-effectiveness of alternative strategies for the treatment of visceral leishmaniasis in the Indian subcontinent. In particular we examined whether combination therapies are a cost-effective alternative compared to monotherapies.

Methods and Findings

We assessed the cost-effectiveness of all possible mono- and combination therapies for the treatment of visceral leishmaniasis in the Indian subcontinent (India, Nepal and Bangladesh) from a societal perspective using a decision analytical model based on a decision tree. Primary data collected in each country was combined with data from the literature and an expert poll (Delphi method). The cost per patient treated and average and incremental cost-effectiveness ratios expressed as cost per death averted were calculated. Extensive sensitivity analysis was done to evaluate the robustness of our estimations and conclusions. With a cost of US$92 per death averted, the combination miltefosine-paromomycin was the most cost-effective treatment strategy. The next best alternative was a combination of liposomal amphotericin B with paromomycin with an incremental cost-effectiveness of $652 per death averted. All other strategies were dominated with the exception of a single dose of 10mg per kg of liposomal amphotericin B. While strategies based on liposomal amphotericin B (AmBisome) were found to be the most effective, its current drug cost of US$20 per vial resulted in a higher average cost-effectiveness. Sensitivity analysis showed the conclusion to be robust to variations in the input parameters over their plausible range.

Conclusions

Combination treatments are a cost-effective alternative to current monotherapy for VL. Given their expected impact on the emergence of drug resistance, a switch to combination therapy should be considered once final results from clinical trials are available.     

Natural product based leads to fight against leishmaniasis

The growing incidence of parasitic resistance against generic pentavalent antimonials, specifically for visceral disease in Indian subcontinent, is a serious issue in Leishmania control. Notwithstanding the two treatment alternatives, that is amphotericin B and miltefosine are being effectively used but their high cost and therapeutic complications limit their use in endemic areas. In the absence of a vaccine candidate, identification, and characterization of novel drugs and targets is a major requirement of leishmanial research. This review describes current drug regimens, putative drug targets, numerous natural products that have shown promising antileishmanial activity alongwith some key issues and strategies for future research to control leishmaniasis worldwide.