A high-quality human reference panel reveals the complexity and distribution of genomic structural variants.

Nat Commun
Authors
Abstract

Structural variation (SV) represents a major source of differences between individual human genomes and has been linked to disease phenotypes. However, the majority of studies provide neither a global view of the full spectrum of these variants nor integrate them into reference panels of genetic variation. Here, we analyse whole genome sequencing data of 769 individuals from 250 Dutch families, and provide a haplotype-resolved map of 1.9 million genome variants across 9 different variant classes, including novel forms of complex indels, and retrotransposition-mediated insertions of mobile elements and processed RNAs. A large proportion are previously under reported variants sized between 21 and 100 bp. We detect 4 megabases of novel sequence, encoding 11 new transcripts. Finally, we show 191 known, trait-associated SNPs to be in strong linkage disequilibrium with SVs and demonstrate that our panel facilitates accurate imputation of SVs in unrelated individuals.

Year of Publication
2016
Journal
Nat Commun
Volume
7
Pages
12989
Date Published
2016 Oct 06
ISSN
2041-1723
DOI
10.1038/ncomms12989
PubMed ID
27708267
PubMed Central ID
PMC5059695
Links
Grant list
R01 HG002385 / HG / NHGRI NIH HHS / United States
U41 HG007497 / HG / NHGRI NIH HHS / United States