July 7, 2019  |  

Deep sequencing of 10,000 human genomes.

Authors: Telenti, Amalio and Pierce, Levi C T and Biggs, William H and di Iulio, Julia and Wong, Emily H M and Fabani, Martin M and Kirkness, Ewen F and Moustafa, Ahmed and Shah, Naisha and Xie, Chao and Brewerton, Suzanne C and Bulsara, Nadeem and Garner, Chad and Metzker, Gary and Sandoval, Efren and Perkins, Brad A and Och, Franz J and Turpaz, Yaron and Venter, J Craig

We report on the sequencing of 10,545 human genomes at 30×-40× coverage with an emphasis on quality metrics and novel variant and sequence discovery. We find that 84% of an individual human genome can be sequenced confidently. This high-confidence region includes 91.5% of exon sequence and 95.2% of known pathogenic variant positions. We present the distribution of over 150 million single-nucleotide variants in the coding and noncoding genome. Each newly sequenced genome contributes an average of 8,579 novel variants. In addition, each genome carries on average 0.7 Mb of sequence that is not found in the main build of the hg38 reference genome. The density of this catalog of variation allowed us to construct high-resolution profiles that define genomic sites that are highly intolerant of genetic variation. These results indicate that the data generated by deep genome sequencing is of the quality necessary for clinical use.

Journal: Proceedings of the National Academy of Sciences of the United States of America
DOI: 10.1073/pnas.1613365113
Year: 2016

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