Combining microarray-based genomic selection (MGS) with the illumina genome analyzer platform to sequence diploid target regions

David T. Okou, Adam Locke, Karyn M. Steinberg, Katie Hagen, Prashanth Athri, Amol C. Shetty, Viren Patel, Michael E. Zwick

Research output: Contribution to journalArticle

15 Scopus citations

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.

Original languageEnglish
Pages (from-to)502-513
Number of pages12
JournalAnnals of Human Genetics
Volume73
Issue number5
DOIs
StatePublished - Aug 18 2009

Keywords

  • Direct selection
  • Human genetics
  • Illumina genome analyzer
  • Microarray-based genomic selection
  • Personal genomes
  • Targeted sequencing

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