Multi-platform discovery of haplotype-resolved structural variation in human genomes
Ashley D. Sanders,
Eugene J Gardner,
Ryan L. Collins,
Robert E Handsaker,
Zev N. Kronenberg,
Aaron M. Wenger,
Nelson T. Chuang,
Christine C. Lambert,
Deanna M Church,
William Haynes Heaton,
Jee Young Kwon,
Jong Eun Lee,
Sau Peng Lee,
Katherine M. Munson,
Bradley J Nelson,
Diana C.J. Spierings,
AnneMarie E. Welch,
Chong Lek Koh,
Peter M. Lansdorp,
Scott E. Devine,
Ryan E. Mills,
Evan E. Eichler,
Posted 23 Sep 2017
bioRxiv DOI: 10.1101/193144 (published DOI: 10.1038/s41467-018-08148-z)
Posted 23 Sep 2017
The incomplete identification of structural variants (SVs) from whole-genome sequencing data limits studies of human genetic diversity and disease association. Here, we apply a suite of long-read, short-read, and strand-specific sequencing technologies, optical mapping, and variant discovery algorithms to comprehensively analyze three human parent-child trios to define the full spectrum of human genetic variation in a haplotype-resolved manner. We identify 818,054 indel variants (<50 bp) and 27,622 SVs (≥50 bp) per human genome. We also discover 156 inversions per genome - most of which previously escaped detection. Fifty-eight of the inversions we discovered intersect with the critical regions of recurrent microdeletion and microduplication syndromes. Taken together, our SV callsets represent a sevenfold increase in SV detection compared to most standard high-throughput sequencing studies, including those from the 1000 Genomes Project. The method and the dataset serve as a gold standard for the scientific community and we make specific recommendations for maximizing structural variation sensitivity for future large-scale genome sequencing studies.
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