Abstract

Remarkable advancement in next generation sequencing technology has made personal genome analysis feasible and affordable. Here we present the whole genome sequence analysis of an individual from the Kashmir region of India who is from the pandit community (IHGP04). The Indian male’s genome was sequenced at 38.6 X coverage with a total of 110 Gb of sequence data generated using the Illumina HiSeq 2000 platform. The variant analysis revealed over 3.6 million single nucleotide variants and 5 46 681 small insertions and deletions including about 2.7 % of novel (unreported) variants. The known variants were analyzed for their health and disease relevance and drug pharmacogenetic profile. The mitochondrial haplogroup (L3e2b1a1) is indicative of maternal ancestors’ arrival to the Indian subcontinent about 70 000 y ago, while the Y-chromosome haplogroup (J) is suggestive of the arrival of paternal ancestors less than 25 000 y ago. The haplogroups also suggest different routes used by the ancestors to arrive on the subcontinent. The analysis and validation of the novel variants and relationship with health and diseases should be the next logical step.