Systematic analysis and functional annotation of variations in the genome of an Indian individual
Ashok Patowary1, Ramya Purkanti1,2, Meghna Singh1, Rajendra Kumar Chauhan1, Deeksha Bhartiya2, Om Prakash Dwivedi1, Ganesh Chauhan1, Dwaipayan Bharadwaj1, Sridhar Sivasubbu1,$, Vinod Scaria2,$
1Genomics and Molecular Medicine,
2G.N. Ramachandran Knowledge Center for Genome Informatics,
CSIR Institute of Genomics and Integrative Biology,
$Address for correspondence:
Whole genome sequencing of personal genomes has revealed a large repertoire of genomic variations and has provided a rich template for identification of common and rare variants in genomes and understanding the genetic basis of diseases. The widespread application of personal genome sequencing in clinical settings for predictive and preventive medicine has been limited due to the lack of comprehensive computational analysis pipelines. We have used next-generation sequencing technology to sequence the whole genome of a self-declared healthy male of Indian origin. We have generated around 28X of the reference human genome with over 99% coverage. Analysis revealed over 3 million single nucleotide variations and about 480 thousand small insertion-deletion events including several novel variants. Using this dataset as a template, we designed a comprehensive computational analysis pipeline for the systematic analysis and annotation of functionally relevant variants in the genome. This study follows a systematic and intuitive data analysis workflow to annotate genome variations and its potential functional effects. Moreover, we integrate predictive analysis of pharmacogenomic traits with emphasis on drugs for which pharmacogenomic testing has been recommended. This study thus provides the template for genome-scale analysis of personal genomes for personalized medicine.
Keywords: Whole genome sequence, pharmacogenomics, variation, disease associations.