title: 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 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.
  
  
  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 variants will further aid studies aimed at understanding genetic diversity, identifying clinically relevant changes and assessing disease burden in the Indian population.
authors.affiliation: SciGenom Labs Pvt Ltd, Kakkanad, Cochin, Kerala, India.
authors.forename: Ravi
authors.initials: R
authors.lastname: Gupta
authors.forename: Aakrosh
authors.initials: A
authors.lastname: Ratan
authors.forename: Changanamkandath
authors.initials: C
authors.lastname: Rajesh
authors.forename: Rong
authors.initials: R
authors.lastname: Chen
authors.forename: Hie Lim
authors.initials: HL
authors.lastname: Kim
authors.forename: Richard
authors.initials: R
authors.lastname: Burhans
authors.forename: Webb
authors.initials: W
authors.lastname: Miller
authors.forename: Sam
authors.initials: S
authors.lastname: Santhosh
authors.forename: Ramana V
authors.initials: RV
authors.lastname: Davuluri
authors.forename: Atul J
authors.initials: AJ
authors.lastname: Butte
authors.forename: Stephan C
authors.initials: SC
authors.lastname: Schuster
authors.forename: Somasekar
authors.initials: S
authors.lastname: Seshagiri
authors.forename: George
authors.initials: G
authors.lastname: Thomas
mesh_terms: D000925:Anticoagulants / Q000009:adverse effects; D044466:Asian People / Q000235:genetics*; D002874:Chromosome Mapping; D056915:DNA Copy Number Variations; D003920:Diabetes Mellitus / Q000235:genetics / Q000517:prevention & control; D005260:Female; D020022:Genetic Predisposition to Disease; D014644:Genetic Variation; D015894:Genome, Human; D054629:Genome, Mitochondrial; D006239:Haplotypes; D006470:Hemorrhage / Q000139:chemically induced / Q000235:genetics / Q000517:prevention & control; D006801:Humans; D007004:Hypoglycemic Agents / Q000627:therapeutic use; D007194:India; D008687:Metformin / Q000627:therapeutic use; D008875:Middle Aged; D009103:Multiple Sclerosis / Q000235:genetics / Q000517:prevention & control; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D014859:Warfarin / Q000009:adverse effects
chemical_list: D000925:Anticoagulants; D007004:Hypoglycemic Agents; D014859:Warfarin; D008687:Metformin