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Patterns of genic intolerance of rare copy number variation in 59,898 human exomes

2016; Nature Portfolio; Volume: 48; Issue: 10 Linguagem: Inglês

10.1038/ng.3638

1546-1718

Douglas M. Ruderfer, Tymor Hamamsy, Monkol Lek, Konrad J. Karczewski, David Kavanagh, Kaitlin E. Samocha, Mark J. Daly, Daniel G. MacArthur, Menachem Fromer, Shaun Purcell,

Chromosomal and Genetic Variations

Douglas Ruderfer, Shaun Purcell and colleagues characterized the rates and properties of rare genic copy number variants in exome sequencing data from nearly 60,000 individuals in the Exome Aggregation Consortium. These data are available through an integrated database that spans the spectrum of human genetic variation, aiding in the interpretation of personal genomes and population-based disease studies. Copy number variation (CNV) affecting protein-coding genes contributes substantially to human diversity and disease. Here we characterized the rates and properties of rare genic CNVs (<0.5% frequency) in exome sequencing data from nearly 60,000 individuals in the Exome Aggregation Consortium (ExAC) database. On average, individuals possessed 0.81 deleted and 1.75 duplicated genes, and most (70%) carried at least one rare genic CNV. For every gene, we empirically estimated an index of relative intolerance to CNVs that demonstrated moderate correlation with measures of genic constraint based on single-nucleotide variation (SNV) and was independently correlated with measures of evolutionary conservation. For individuals with schizophrenia, genes affected by CNVs were more intolerant than in controls. The ExAC CNV data constitute a critical component of an integrated database spanning the spectrum of human genetic variation, aiding in the interpretation of personal genomes as well as population-based disease studies. These data are freely available for download and visualization online.