Communicated by Richard G. H. Cotton
Systematic analysis and functional annotation of variations in the genome of an Indian individual†
Article first published online: 16 APR 2012
© 2012 Wiley Periodicals, Inc.
Volume 33, Issue 7, pages 1133–1140, July 2012
How to Cite
Patowary, A., Purkanti, R., Singh, M., Chauhan, R. K., Bhartiya, D., Dwivedi, O. P., Chauhan, G., Bharadwaj, D., Sivasubbu, S. and Scaria, V. (2012), Systematic analysis and functional annotation of variations in the genome of an Indian individual. Hum. Mutat., 33: 1133–1140. doi: 10.1002/humu.22091
- Issue published online: 5 JUN 2012
- Article first published online: 16 APR 2012
- Accepted manuscript online: 27 MAR 2012 11:10AM EST
- Manuscript Accepted: 5 MAR 2012
- Manuscript Received: 11 NOV 2011
- Council of Scientific and Industrial Research (CSIR), India (grants NWP0036 and FAC002)
- whole genome sequence;
- disease associations
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 in addition to 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 490,000 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. Hum Mutat 33:1133–1140, 2012. © 2012 Wiley Periodicals, Inc.