Targeted capture and massively parallel sequencing of 12 human exomes

Abstract

Genome-wide association studies suggest that common genetic variants explain only a small fraction of heritable risk for common diseases, raising the question of whether rare variants account for a significant fraction of unexplained heritability1,2. While DNA sequencing costs have fallen dramatically3, 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 twelve humans. These include eight HapMap individuals representing three populations4, and four unrelated individuals with a rare dominantly inherited disorder, Freeman-Sheldon syndrome (FSS)5. We demonstrate the sensitive and specific identification of rare and common variants in over 300 megabases (Mb) of coding sequence. Using FSS as a proof-of-concept, we show that candidate genes for monogenic 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 nonsynonymous variants by predicted functional impact.

PyClone: statistical inference of clonal population structure in cancer

“…Variants positions in the four cases used were previously identified in Ng et al 19 . We compiled a list of positions with variants in: i) exactly one of the four cases used in the mixture; ii) shared by NA18507 and NA19240; iii) shared by NA18507, NA19240 and NA12878; iv) shared by all four cases.…”

Identification of OSBPL2 as a novel candidate gene for progressive nonsyndromic hearing loss by whole-exome sequencing

“…[4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19] It is estimated that more than 230 novel rare disease genes have been discovered to date using WES. 11 Several new NSHLcausative genes have also recently been revealed via WES, including GPSM2, DNMT1, BDP1, ELMOD3, TNC, GRXCR2, and ADCY1.…”

Advances in genomics for flatfish aquaculture

“…A second critical point in RNA-seq is the depth of coverage. In humans, protein-coding regions (exome) represent approximately 1 % of the human genome corresponding to approximately 30 Mb (Ng et al 2009). For this transcriptome size, it is estimated that less than 10 million reads of 35 nt in length (*109 coverage) would accurately quantify mRNA expression levels for more than 80 % of the genes, 200 million reads would be required to quantify splicing levels for 80 % of genes (*2009 coverage) and approximately 700 million reads would be necessary to obtain accurate quantification for more than 95 % of the expressed transcripts (*8009 coverage) (Blencowe et al 2009;Tarazona et al 2011).…”