{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"contact_person":["Ravi Gupta"],"full_dataset_link":["https://ega-archive.org/dacs/EGAC00001000077"],"host":["EGA"],"description":["EGA DAC EGAC00001000077"],"repository":["EGA"],"email":["ravig@scigenom.com"],"pubmed_abstract":["<h4>Background</h4>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.<h4>Results</h4>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 was 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.<h4>Conclusions</h4>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 variants will further aid studies aimed at understanding genetic diversity, identifying clinically relevant changes and assessing disease burden in the Indian population."],"pubmed_title":["Sequencing and analysis of a South Asian-Indian personal genome."],"pubmed_authors":["Gupta Ravi R, Ratan Aakrosh A, Rajesh Changanamkandath C, Chen Rong R, Kim Hie Lim HL, Burhans Richard R, Miller Webb W, Santhosh Sam S, Davuluri Ramana V RV, Butte Atul J AJ, Schuster Stephan C SC, Seshagiri Somasekar S, Thomas George G"],"pubmed_title_synonyms":["assay, Hindu, whole genome, Indian Asian, Indian, determination, chemical analysis, Asian Indians, Asian Indian, Genomes."],"pubmed_abstract_synonyms":["Modb1, adverse reaction, Meth, Product, 4-hydroxy-3-[(1RS)-3-oxo-1-phenylbutyl]-2H-chromen-2-one, determination, warfarina, 4-hydroxy-3-[(1RS)-3-oxo-1-phenylbutyl]coumarin, warfarine, Korean American, Progress Reports, Measure, Cost-Minimization, Relative, School-Age, Readability, Donor Artificial Insemination, \"Multiple sclerosis\" EXACT [SNOMEDCT_2005_07_31:155023009], Filipino American, diseases, Summary Report, responsivity, CDA2, Pharmaceutical Product, Asian Indian, diseases and disorders, Aldocumar, Analysis, (2Z)-but-2-enedioate, Cost Comparison, Leprb, Summary Reports, warfarinum, male, DM - Diabetes mellitus, Donor Artificial, average, human disease, Occidental, Vietnamese American, mitochondrial genome, Analyses, Genomes, Progress Report, (+-)-warfarin, availability, Cost-Minimization Analyses, Comparison, Estimated, Cost Analysis, Progress, Cambodian, Diabetes mellitus, Field Reports, 2H-1-Benzopyran-2-one, Ice, medicine, Pharmaceutical, (RS)-warfarin, Homo sapiens disease, Coumadine, Comparisons, Affordabilities, Hmong Americans, db, Disseminated Sclerosis, rac-4-hydroxy-3-(3-oxo-1-phenylbutyl)coumarin, PLATEST, DM, Genome Sequencing, white, Diversities, Hindu, Normalcy, female, results, Asian unspecified, OB-RGRP, Cambodian Americans, Brumolin, Complete Genome, rac-3-(1'-phenyl-2'-acetylethyl)-4-hydroxycoumarin, Investigative Report, European, School Age, Relative Risks, Diseases, Heterologous Insemination, \"Generalized multiple sclerosis (disorder)\" EXACT [SNOMEDCT_2005_07_31:192928003], NOS, Warfant, Pharmaceutic, Individual, Kumatox, finances, Japanese American, Crystal, Caucasians, Chinese American, Populations, Mitochondrial, Risk, maleate, Field, salaries, \"insular sclerosis\" EXACT [CSP2005:2042-2324], Ratron, whole genome, Genetic Diversity, Warf 10, Obr, Diabetes NOS, Speed, disease, Multiple, rac-3-(alpha-acetonylbenzyl)-4-hydroxycoumarin, Artificial Insemination, Health, Report, mitochondrial DNA, 4-hydroxy-3-(3-oxo-1-phenylbutyl)-, Republic of India, Rodafarin, White, School-Age Population, financial management, obl, Indian, Platelets, Cost Analyses, Apo-Warfarin, \"multiple sclerosis\" EXACT [NCI2004_11_17:C3243], other disease, bleeding, Hmong American, Hmong, Asian, Sclerosis, Multiple Sclerosis, number, Cost Comparisons, Hemorrhages, Chalk, Normalcies, presence, AID, Aid, 4-Hydroxy-3-(3-oxo-1-phenylbutyl)-2H-1-benzopyran-2-one, Northern Europe, DL-3-(alpha-acetonylbenzyl)-4-hydroxycoumarin, Caucasian, Investigative, Cost Minimization Analysis, rac-3-(alpha-phenyl-beta-acetylethyl)-4-hydroxycoumarin, Core Genome, Japanese, Tina, Asian Indian American, Vietnamese Americans, Diabetes mellitus (disorder), Kumadu, disease or disorder, Southern Europe, \"Multiple sclerosis\" EXACT [ICD9CM_2006:340], Coumadin, 4-hydroxy-3-[(1RS)-3-oxo-1-phenylbutyl]-2H-1-benzopyran-2-one, aid, Normalities, Drugs, rac-warfarin, \"Multiple sclerosis (disorder)\" EXACT [SNOMEDCT_2005_07_31:24700007], Insemination, study, \"Multiple sclerosis NOS (disorder)\" EXACT [SNOMEDCT_2005_07_31:192930001], reactivity, School-Age Populations, American, Complete, Diversity, Whole Genome, Glass, Genetic, Cost Measures, Affordability, Accessory Genome, Complete Genome Sequencing, Filipino, Measures, obese-like, financing, Population, Sequencing, Asians, non-neoplastic, funding, drugs, generalised multiple sclerosis, Korean, rac-3-(acetonylbenzyl)-4-hydroxycoumarin, HEL-S-284, Whole, disorder, Zoocoumarin, HIGM2, Preparation, generalized multiple sclerosis, School Age Population, rac-1-(4'-hydroxy-3'-coumarinyl)-1-phenyl-3-butanone, Investigative Reports, Vietnamese, Chinese, Asian Indian Americans, Diabetes, Variation, diabetes, Potassium, Heterologous, Pharmaceuticals, Genetic Variations, fees, Individual Health, Products, Tedicumar, Variations, female human body, Males, Asian Indians, drug, disorders, medical condition, MS (Multiple Sclerosis), Gen-Warfarin, Pangenome, Korean Americans, diabetes mellitus (disease), Human Donor, Warfarin, count in organism, MS, Americans, chemical analysis, Research Reports, Genetic Diversities, Western Europe, warfarin, racemic warfarin, sequence, condition, Filipino Americans, Sodium, Donor, background, Coumafene, Indian American, Asian Americans, Caucasoid, Relative Risk, Costs and Cost Analyses, Artificial, School Age Populations., Costs, LEPROT, mtDNA, Warfarin Potassium, Indian Asian, Pharmaceutic Preparations, diabetes mellitus, Normality, Arp2, Cost, Asian American, ARP2, Bleeding, Risks, Cost-Minimization Analysis, Cambodian American, Pricing, Understanding, Warfarin Sodium, Disseminated, primary structure of sequence macromolecule, introduction, Chinese Americans, Acute Fulminating, male human body, Drug, Marevan, Japanese Americans, cost, Mitochondrial Genome, Preparations, Pan-genome, Mitochondrial Genomes, DL-warfarin, Reports, Whites, haemorrhage, assay, response, Cost Measure, Pharmaceutical Products, Summary, Females, Field Report, Pharmaceutical Preparation"],"additional_accession":[]},"is_claimable":false,"name":"SGDAC- SciGenom Data Access Committee","description":"Data Access Committee EGAC00001000077","dates":{"output":"2025-1-9"},"accession":"EGAC00001000077","cross_references":{"TAXONOMY":["9606"],"pubmed":["22938532"],"EGA":["EGAS00001000328","EGAD00001000249","EGAD00001000254"]}}