Publication Type : Journal Article
Publisher : Annals of Human Genetics
Source : Annals of Human Genetics, John Wiley & Sons, Volume 73, Number 5, p.502–513 (2009)
Url : http://onlinelibrary.wiley.com/doi/10.1111/j.1469-1809.2009.00530.x/pdf
Keywords : direct selection, human genetics, illumina genome analyzer, microarray-based genomic selection, Personal genomes, targeted sequencing
Campus : Amritapuri, Bengaluru
School : School of Engineering
Center : Biotechnology
Department : Computer Science
Year : 2009
Abstract : Novel methods of targeted sequencing of unique regions from complex eukaryotic genomes have generated a great deal of excitement, but critical demonstrations of these methods efficacy with respect to diploid genotype calling and experimental variation are lacking. To address this issue, we optimized microarray-based genomic selection (MGS) for use with the Illumina Genome Analyzer (IGA). A set of 202 fragments (304 kb total) contained within a 1.7 Mb genomic region on human chromosome X were MGS/IGA sequenced in ten female HapMap samples generating a total of 2.4 GB of DNA sequence. At a minimum coverage threshold of 5X, 93.9% of all bases and 94.9% of segregating sites were called, while 57.7% of bases (57.4% of segregating sites) were called at a 50X threshold. Data accuracy at known segregating sites was 98.9% at 5X coverage, rising to 99.6% at 50X coverage. Accuracy at homozygous sites was 98.7% at 5X sequence coverage and 99.5% at 50X coverage. Although accuracy at heterozygous sites was modestly lower, it was still over 92% at 5X coverage and increased to nearly 97% at 50X coverage. These data provide the first demonstration that MGS/IGA sequencing can generate the very high quality sequence data necessary for human genetics research.
Cite this Research Publication : D. T. Okou, Locke, A. E., Steinberg, K. M., Hagen, K., Dr. Prashanth Athri, Shetty, A. C., Patel, V., and Zwick, M. E., “Combining Microarray-based Genomic Selection (MGS) with the Illumina Genome Analyzer Platform to Sequence Diploid Target Regions”, Annals of Human Genetics, vol. 73, pp. 502–513, 2009.