Exome sequencing generates high quality data in non-target regions

BMC Genomics. 2012 May 20;13:194. doi: 10.1186/1471-2164-13-194.

Abstract

Background: Exome sequencing using next-generation sequencing technologies is a cost efficient approach to selectively sequencing coding regions of human genome for detection of disease variants. A significant amount of DNA fragments from the capture process fall outside target regions, and sequence data for positions outside target regions have been mostly ignored after alignment.

Result: We performed whole exome sequencing on 22 subjects using Agilent SureSelect capture reagent and 6 subjects using Illumina TrueSeq capture reagent. We also downloaded sequencing data for 6 subjects from the 1000 Genomes Project Pilot 3 study. Using these data, we examined the quality of SNPs detected outside target regions by computing consistency rate with genotypes obtained from SNP chips or the Hapmap database, transition-transversion (Ti/Tv) ratio, and percentage of SNPs inside dbSNP. For all three platforms, we obtained high-quality SNPs outside target regions, and some far from target regions. In our Agilent SureSelect data, we obtained 84,049 high-quality SNPs outside target regions compared to 65,231 SNPs inside target regions (a 129% increase). For our Illumina TrueSeq data, we obtained 222,171 high-quality SNPs outside target regions compared to 95,818 SNPs inside target regions (a 232% increase). For the data from the 1000 Genomes Project, we obtained 7,139 high-quality SNPs outside target regions compared to 1,548 SNPs inside target regions (a 461% increase).

Conclusions: These results demonstrate that a significant amount of high quality genotypes outside target regions can be obtained from exome sequencing data. These data should not be ignored in genetic epidemiology studies.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Adult
  • Breast Neoplasms / genetics
  • Case-Control Studies
  • Exome / genetics*
  • Female
  • Genome, Human*
  • Genotype
  • HapMap Project
  • Humans
  • Oligonucleotide Array Sequence Analysis
  • Pilot Projects
  • Polymorphism, Single Nucleotide
  • Sequence Analysis, DNA*