Sequencing and analysis of a South Asian-Indian personal genome

BMC Genomics. 2012 Aug 31;13:440. doi: 10.1186/1471-2164-13-440.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anticoagulants / adverse effects
  • Asian Continental Ancestry Group / genetics*
  • Chromosome Mapping*
  • DNA Copy Number Variations
  • Diabetes Mellitus / genetics
  • Diabetes Mellitus / prevention & control
  • Female
  • Genetic Predisposition to Disease
  • Genetic Variation
  • Genome, Human*
  • Genome, Mitochondrial*
  • Haplotypes
  • Hemorrhage / chemically induced
  • Hemorrhage / genetics
  • Hemorrhage / prevention & control
  • Humans
  • Hypoglycemic Agents / therapeutic use
  • India
  • Metformin / therapeutic use
  • Middle Aged
  • Multiple Sclerosis / genetics
  • Multiple Sclerosis / prevention & control
  • Polymorphism, Single Nucleotide*
  • Sequence Analysis, DNA
  • Warfarin / adverse effects

Substances

  • Anticoagulants
  • Hypoglycemic Agents
  • Warfarin
  • Metformin