{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["Illumina HiSeq 2000;"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00001000249"],"sample_count":["1"],"description":["EGA dataset EGAD00001000249"],"repository":["EGA"],"title":["SAIF Alignment File"],"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."],"name_synonyms":["Vasp, VASP, Data Set., DmelCG15112, ENHANCER OF ATNSI ACTIVITY, MENA, NDPP1, l(2)02029, Enb, enb, ENA, Ena, CG15112, ENA/VASP"],"pubmed_abstract_synonyms":["Nucleotide Sequencing, Scx, Product, 4-hydroxy-3-[(1RS)-3-oxo-1-phenylbutyl]-2H-chromen-2-one, warfarina, 4-hydroxy-3-[(1RS)-3-oxo-1-phenylbutyl]coumarin, warfarine, Progress Reports, Cost-Minimization, Dose, Relative, Personal, Doses, Donor Artificial Insemination, Compared, \"Multiple sclerosis\" EXACT [SNOMEDCT_2005_07_31:155023009], analysis, Summary Report, responsivity, CDA2, Asian Indian, dose, Related, Analysis, Contains, Cost Comparison, warfarinum, DOSE, Deep Sequencing, average, treatment, Analyses, Genomes, Progress Report, (+-)-warfarin, Illumina Sequencing, Comparison, Did, Cost Analysis, Cambodian, Diabetes mellitus, Field Reports, 2H-1-Benzopyran-2-one, medicine, (RS)-warfarin, Homo sapiens disease, any therapy, Personal Attribute, Relationship, Hmong Americans, db, Add, Therapeutic Procedure, Disseminated Sclerosis, DM, Dosage, Descend, assessment, Diversities, Hindu, Normalcy, female, Descent, Asian unspecified, OB-RGRP, Do, European, Relative Risks, Next-Generation, Heterologous Insemination, Diverse, Warfant, State, finances, Deviation, VARIATION, maleate, Definite Attribution, Field, salaries, \"insular sclerosis\" EXACT [CSP2005:2042-2324], whole genome, Warf 10, Present, State Ownership, Million, Obr, High Throughput Sequencing, Speed, Multiple, Artificial Insemination, Dose Level, Report, People, 4-hydroxy-3-(3-oxo-1-phenylbutyl)-, White, School-Age Population, financial management, obl, Indian, Previous, Dose per Administration, Cost Analyses, Apo-Warfarin, \"multiple sclerosis\" EXACT [NCI2004_11_17:C3243], bleeding, Subject Characteristics, Sclerosis, Multiple Sclerosis, number, High-Throughput DNA, Analytical, Antp P1, Antp P2, Private, Hemorrhages, Chalk, Normalcies, AID, Aid, Next-Generation Sequencing, Therapeutic Technique, modulate, Caucasian, rac-3-(alpha-phenyl-beta-acetylethyl)-4-hydroxycoumarin, Deep, Core Genome, Japanese, Hu, Asian Indian American, Variant, Diabetes mellitus (disorder), disease or disorder, million, Southern Europe, 3.4, \"Multiple sclerosis\" EXACT [ICD9CM_2006:340], Medical, Higher, 4-hydroxy-3-[(1RS)-3-oxo-1-phenylbutyl]-2H-1-benzopyran-2-one, aid, Normalities, \"Multiple sclerosis (disorder)\" EXACT [SNOMEDCT_2005_07_31:24700007], Insemination, \"Multiple sclerosis NOS (disorder)\" EXACT [SNOMEDCT_2005_07_31:192930001], School-Age Populations, American, In, Complete, Whole Genome, Cost Measures, Accessory Genome, Complete Genome Sequencing, obese-like, Former, Pyrosequencing, Population, Sequencing, CG1028, Asians, drugs, rac-3-(acetonylbenzyl)-4-hydroxycoumarin, HEL-S-284, Whole, Investigative Reports, Vietnamese, Including, Potassium, Heterologous, Pharmaceuticals, fees, Individual Health, Products, SINGLE, female human body, disorders, {Dose}, MS (Multiple Sclerosis), DmAntp, Pangenome, Human Donor, Warfarin, Addition, MS, Have, One Million, chemical analysis, Research Reports, warfarin, condition, Sodium, Donor, background, 1.3, Coumafene, Relevant, Caucasoid, Next Generation Sequencing, Relative Risk, Costs and Cost Analyses, Artificial, School Age Populations., Costs, Definitely Related to Intervention, LEPROT, Single Person, 1000000, Warfarin Potassium, Ant, Treated, Pharmaceutic Preparations, Therapeutic Method, Arp2, Asian American, ARP2, Bleeding, SHARED, Cost-Minimization Analysis, Containing, dose level, Understanding, Disseminated, primary structure of sequence macromolecule, Chinese Americans, male human body, 10^6, High, Mitochondrial Genome, Ns, Pan-genome, Mitochondrial Genomes, DmelCG1028, Reports, High Throughput Nucleotide Sequencing, Solitary, DRO15DC96Z, Cost Measure, Pharmaceutical Products, Alone, High-Throughput Nucleotide, Modb1, ANT-C, Previously, adverse reaction, Meth, determination, treatment_or_therapy, Burden, Massively-Parallel, Antp1, CDISC SDTM Model Version 1.3, Korean American, Measure, Highly, School-Age, Readability, High-Throughput RNA Sequencing, Filipino American, diseases, Pharmaceutical Product, AntP1, diseases and disorders, Aldocumar, (2Z)-but-2-enedioate, Leprb, Summary Reports, male, Definite, DM - Diabetes mellitus, Donor Artificial, human disease, Occidental, Vietnamese American, mitochondrial genome, Observed, Identification, availability, Cost-Minimization Analyses, Association, treatment or therapy, Estimated, Comprise, BG:DS07700.1, Progress, Modulated, High Throughput RNA Sequencing, Had, Ice, Pharmaceutical, Great, Analyzed, ANT-P, Coumadine, Comparisons, Affordabilities, Has, High-Throughput RNA, Therapy, Lower, rac-4-hydroxy-3-(3-oxo-1-phenylbutyl)coumarin, TX, PLATEST, Genome Sequencing, High-Throughput DNA Sequencing, white, results, Aus, Contained, Cambodian Americans, Territory, Brumolin, Ion Torrent Sequencing, Complete Genome, rac-3-(1'-phenyl-2'-acetylethyl)-4-hydroxycoumarin, Investigative Report, School Age, Massively-Parallel Sequencing, Common, Diseases, \"Generalized multiple sclerosis (disorder)\" EXACT [SNOMEDCT_2005_07_31:192928003], NOS, Pharmaceutic, Ion Torrent, LOWER, Adverse Event Definitely Related to Intervention, Adverse Event Related to Intervention, Individual, Kumatox, Customary, Assessed, Does, Japanese American, Crystal, Caucasians, Chinese American, Populations, Mitochondrial, Risk, Relevance, Ratron, Genetic Diversity, Presence, Diabetes NOS, Identified, SDTM Version 1.3, Lowering, disease, rac-3-(alpha-acetonylbenzyl)-4-hydroxycoumarin, Health, mitochondrial DNA, 10E6, Republic of India, Rodafarin, Assess, Platelets, Usual, other disease, High Throughput DNA Sequencing, Hmong American, Hmong, Shared, Asian, DMANTPE1, Cost Comparisons, Compare, presence, Illumina, 4-Hydroxy-3-(3-oxo-1-phenylbutyl)-2H-1-benzopyran-2-one, Northern Europe, DL-3-(alpha-acetonylbenzyl)-4-hydroxycoumarin, Investigative, Cost Minimization Analysis, Relations, Tina, Treat, Vietnamese Americans, Kumadu, Massively Parallel Sequencing, Therapeutic Interventions, Coumadin, TREAT, Drugs, rac-warfarin, study, ANTC, reactivity, antp, Diversity, Ion Proton Sequencing, Glass, Genetic, PRESENT, ANALYSIS, Affordability, Descending, Filipino, Measures, Modulation, financing, Contain, non-neoplastic, funding, generalised multiple sclerosis, Korean, Found, High-Throughput, RNA Sequencing, disorder, Zoocoumarin, HIGM2, dose_level, AntP, Preparation, ANTP, generalized multiple sclerosis, School Age Population, rac-1-(4'-hydroxy-3'-coumarinyl)-1-phenyl-3-butanone, Chinese, Asian Indian Americans, Diabetes, Variation, diabetes, Genetic Variations, Possess, FORMER, Tedicumar, Variations, Males, Asian Indians, drug, Certain, medical condition, Gen-Warfarin, Related Attribution, Korean Americans, diabetes mellitus (disease), Usually, US State, count in organism, Americans, DNA Sequencing, Genetic Diversities, Western Europe, racemic warfarin, sequence, Filipino Americans, l(3)84Ba, Indian American, Asian Americans, any_therapy, Modulating, Lowered, mtDNA, Assessment, Indian Asian, diabetes mellitus, Normality, Cost, Risks, Typical, TRTDOS, Cambodian American, Pricing, Warfarin Sodium, introduction, Acute Fulminating, Drug, Marevan, Japanese Americans, cost, Preparations, therapy, Treating, High-Throughput Sequencing, Only, DL-warfarin, Whites, haemorrhage, Inclusive, Treatment, Single, assay, Additional, response, Summary, Ion Proton, Greater, Females, Field Report, Pharmaceutical Preparation"],"description_synonyms":["BamF, bim, biml, BamC, HCAP, bim-beta6, bam, ham, BOD, alpha, whole genome, CDLS3, BMH, fs(3)neo61, Programs, CG10422, BIM, Bam-C, BAM, Bam, SMC3L1, bim-beta7, bod, DmelCG10422, CSPG6, bimel, Genomes."],"additional_accession":[]},"is_claimable":false,"name":"ena-DATASET-SGL-04-10-2012-02:36:03:619-3 - samples","description":"This is the bam file generated after alignment using BWA program for the SAIF genome","dates":{"updated":"2017-07-26 15:39:24"},"accession":"EGAD00001000249","cross_references":{"TAXONOMY":["9606"],"pubmed":["22938532"],"EGA":["EGAC00001000077","EGAS00001000328"]}}