title: Performance comparison of exome DNA sequencing technologies.
abstract: Whole exome sequencing by high-throughput sequencing of target-enriched genomic DNA (exome-seq) has become common in basic and translational research as a means of interrogating the interpretable part of the human genome at relatively low cost. We present a comparison of three major commercial exome sequencing platforms from Agilent, Illumina and Nimblegen applied to the same human blood sample. Our results suggest that the Nimblegen platform, which is the only one to use high-density overlapping baits, covers fewer genomic regions than the other platforms but requires the least amount of sequencing to sensitively detect small variants. Agilent and Illumina are able to detect a greater total number of variants with additional sequencing. Illumina captures untranslated regions, which are not targeted by the Nimblegen and Agilent platforms. We also compare exome sequencing and whole genome sequencing (WGS) of the same sample, demonstrating that exome sequencing can detect additional small variants missed by WGS.
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Clark
authors.forename: Rui
authors.initials: R
authors.lastname: Chen
authors.forename: Hugo Y K
authors.initials: HY
authors.lastname: Lam
authors.forename: Konrad J
authors.initials: KJ
authors.lastname: Karczewski
authors.forename: Rong
authors.initials: R
authors.lastname: Chen
authors.forename: Ghia
authors.initials: G
authors.lastname: Euskirchen
authors.forename: Atul J
authors.initials: AJ
authors.lastname: Butte
authors.forename: Michael
authors.initials: M
authors.lastname: Snyder
mesh_terms: D001482:Base Composition / Q000235:genetics; D001483:Base Sequence; D059472:Exome / Q000235:genetics*; D015894:Genome, Human / Q000235:genetics; D006801:Humans; D016366:Open Reading Frames / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods* / Q000592:standards*; D017384:Sequence Deletion / Q000235:genetics
chemical_list: D012333:RNA, Messenger