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Title: Sequencing and analysis of a South Asian-Indian personal genome
Authors: Gupta, Ravi
Ratan, Aakrosh
Rajesh, Changanamkandath
Chen, Rong
Kim, Hie Lim
Burhans, Richard
Miller, Webb
Santhosh, Sam
Seshagiri, Somasekar
Thomas, George
Davuluri, Ramana V.
Butte, Atul J.
Schuster, Stephan C.
Keywords: DRNTU::Science::Biological sciences::Genetics
Issue Date: 2012
Source: Gupta, R., Ratan, A., Rajesh, C., Chen, R., Kim, H. L., Burhans, R., et al. (2012). Sequencing and analysis of a South Asian-Indian personal genome. BMC Genomics, 13(1), 440.
Series/Report no.: BMC genomics
Abstract: 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.
ISSN: 1471-2164
DOI: 10.1186/1471-2164-13-440
Rights: © 2012 Gupta et al. This paper was published in BMC Genomics and is made available as an electronic reprint (preprint) with permission of Gupta et al. The paper can be found at the following official DOI:  One print or electronic copy may be made for personal use only. Systematic or multiple reproduction, distribution to multiple locations via electronic or other means, duplication of any material in this paper for a fee or for commercial purposes, or modification of the content of the paper is prohibited and is subject to penalties under law.
Fulltext Permission: open
Fulltext Availability: With Fulltext
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