Targeted capture and massively parallel sequencing of 12 human exomes

Abstract

DNA sequencing costs have fallen dramatically in recent years, but they are still too high for whole-genome sequencing to be used routinely to identify rare and novel variants in large cohorts. Here Ng et al. demonstrate that targeted capture and massively parallel sequencing could be a cost-effective, reproducible, and robust strategy for the sensitive and specific identification of variants causing protein-coding changes in individual human genomes. Using this 'second generation' approach to sequencing they determine 307 megabases across the exomes (the protein-coding regions of the genome) of 12 individuals. Freeman–Sheldon syndrome is used as a proof-of-concept to show that candidate genes for monogenic disorders can be identified by exome sequencing of a small number of unrelated, affected individuals. Although DNA sequencing costs have fallen dramatically, they are still too high for whole genome sequencing to be used to routinely identify rare and novel variants in large cohorts. The targeted capture and massively parallel sequencing of the exomes of 12 humans is now reported. Freeman–Sheldon syndrome is used as a proof-of-concept that candidate genes for monogenic disorders can be identified by exome sequencing of a small number of unrelated, affected individuals. 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 heritability1,2. Although DNA sequencing costs have fallen markedly3, 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 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 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.