title: Targeted capture and massively parallel sequencing of 12 human exomes.
abstract: Genome-wide association studies suggest that common genetic variants explain only a modest fraction of heritable risk for common diseases, raising the question of whether rare variants account for a significant fraction of unexplained heritability. Although DNA sequencing costs have fallen markedly, they remain far from what is necessary for rare and novel variants to be routinely identified at a genome-wide scale in large cohorts. We have therefore sought to develop second-generation methods for targeted sequencing of all protein-coding regions ('exomes'), to reduce costs while enriching for discovery of highly penetrant variants. Here we report on the targeted capture and massively parallel sequencing of the exomes of 12 humans. These include eight HapMap individuals representing three populations, and four unrelated individuals with a rare dominantly inherited disorder, Freeman-Sheldon syndrome (FSS). We demonstrate the sensitive and specific identification of rare and common variants in over 300 megabases of coding sequence. Using FSS as a proof-of-concept, we show that candidate genes for Mendelian disorders can be identified by exome sequencing of a small number of unrelated, affected individuals. This strategy may be extendable to diseases with more complex genetics through larger sample sizes and appropriate weighting of non-synonymous variants by predicted functional impact.
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA. sarahng@u.washington.edu
authors.forename: Sarah B
authors.initials: SB
authors.lastname: Ng
authors.forename: Emily H
authors.initials: EH
authors.lastname: Turner
authors.forename: Peggy D
authors.initials: PD
authors.lastname: Robertson
authors.forename: Steven D
authors.initials: SD
authors.lastname: Flygare
authors.forename: Abigail W
authors.initials: AW
authors.lastname: Bigham
authors.forename: Choli
authors.initials: C
authors.lastname: Lee
authors.forename: Tristan
authors.initials: T
authors.lastname: Shaffer
authors.forename: Michelle
authors.initials: M
authors.lastname: Wong
authors.forename: Arindam
authors.initials: A
authors.lastname: Bhattacharjee
authors.forename: Evan E
authors.initials: EE
authors.lastname: Eichler
authors.forename: Michael
authors.initials: M
authors.lastname: Bamshad
authors.forename: Deborah A
authors.initials: DA
authors.lastname: Nickerson
authors.forename: Jay
authors.initials: J
authors.lastname: Shendure
mesh_terms: D005091:Exons / Q000235:genetics*; D005787:Gene Frequency / Q000235:genetics; D015723:Gene Library; D005799:Genes, Dominant / Q000235:genetics; D020022:Genetic Predisposition to Disease / Q000235:genetics*; D005820:Genetic Testing / Q000379:methods*; D014644:Genetic Variation / Q000235:genetics*; D015894:Genome, Human / Q000235:genetics*; D006239:Haplotypes / Q000235:genetics; D006801:Humans; D054643:INDEL Mutation / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D022821:RNA Splice Sites / Q000235:genetics; D018401:Sample Size; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods*; D013577:Syndrome
chemical_list: D022821:RNA Splice Sites
references.citation: Nat Methods. 2007 Nov;4(11):891-2
references.pmid: 17971778
references.citation: Science. 2009 Apr 10;324(5924):217
references.pmid: 19264984
references.citation: Genome Res. 2008 Dec;18(12):2016-23
references.pmid: 18836033
references.citation: Nat Methods. 2009 May;6(5):315-6
references.pmid: 19349981
references.citation: Science. 2006 Oct 13;314(5797):268-74
references.pmid: 16959974
references.citation: PLoS Genet. 2008 May 30;4(5):e1000083
references.pmid: 18516229
references.citation: Nat Genet. 2006 May;38(5):561-5
references.pmid: 16642020
references.citation: Nature. 2008 Nov 6;456(7218):60-5
references.pmid: 18987735
references.citation: Am J Hum Genet. 2009 Feb;84(2):224-34
references.pmid: 19200524
references.citation: Genome Res. 2008 Nov;18(11):1851-8
references.pmid: 18714091
references.citation: Nat Rev Genet. 2009 Apr;10(4):241-51
references.pmid: 19293820
references.citation: Nat Genet. 2008 Jun;40(6):722-9
references.pmid: 18438408
references.citation: Hum Mol Genet. 2001 Mar 15;10(6):591-7
references.pmid: 11230178
references.citation: Nature. 2008 Apr 17;452(7189):872-6
references.pmid: 18421352
references.citation: Nat Genet. 2007 Dec;39(12):1522-7
references.pmid: 17982454
references.citation: Nat Genet. 2005 Feb;37(2):161-5
references.pmid: 15654334
references.citation: Nat Methods. 2007 Nov;4(11):903-5
references.pmid: 17934467
references.citation: Nat Biotechnol. 2008 Oct;26(10):1135-45
references.pmid: 18846087
references.citation: Nature. 2005 Oct 27;437(7063):1299-320
references.pmid: 16255080
references.citation: PLoS Biol. 2007 Sep 4;5(10):e254
references.pmid: 17803354
references.citation: Nat Biotechnol. 2008 Mar;26(3):256
references.pmid: 18327223
references.citation: Nature. 2008 May 1;453(7191):56-64
references.pmid: 18451855
references.citation: Proc Natl Acad Sci U S A. 2009 Mar 10;106(10):3871-6
references.pmid: 19202052
references.citation: Am J Hum Genet. 1999 Jan;64(1):18-23
references.pmid: 9915938
references.citation: Genome Res. 1998 Mar;8(3):186-94
references.pmid: 9521922
references.citation: Nature. 2008 Nov 6;456(7218):53-9
references.pmid: 18987734
references.citation: Science. 2004 Aug 6;305(5685):869-72
references.pmid: 15297675
references.citation: Nature. 2008 Nov 6;456(7218):66-72
references.pmid: 18987736
references.citation: PLoS Genet. 2008 Aug 15;4(8):e1000160
references.pmid: 18704161