Mark J P Chaisson
Ashley D Sanders
Xuefang Zhao
Ankit Malhotra, The Jackson LaboratoryFollow
David Porubsky
Tobias Rausch
Eugene J Gardner
Oscar L Rodriguez
Li Guo
Ryan L Collins
Xian Fan
Jia Wen
Robert E Handsaker
Susan Fairley
Zev N Kronenberg
Xiangmeng Kong
Fereydoun Hormozdiari
Dillon Lee
Aaron M Wenger
Alex R Hastie
Danny Antaki
Thomas Anantharaman
Peter A Audano
Harrison Brand
Stuart Cantsilieris
Han Cao
Eliza Cerveira, The Jackson LaboratoryFollow
Chong Chen
Xintong Chen
Chen-Shan Chin
Zechen Chong
Nelson T Chuang
Christine C Lambert
Deanna M Church
Laura Clarke
Andrew Farrell
Joey Flores
Timur Galeev
David U Gorkin
Madhusudan Gujral
Victor Guryev
William Haynes Heaton
Jonas Korlach
Sushant Kumar
Jee Young Kwon
Ernest T Lam
Jong Eun Lee
Joyce Lee
Wan-Ping Lee, The Jackson LaboratoryFollow
Sau Peng Lee
Shantao Li
Patrick Marks
Karine Viaud-Martinez
Sascha Meiers
Katherine M Munson
Fabio C P Navarro
Bradley J Nelson
Conor Nodzak
Amina Noor
Sofia Kyriazopoulou-Panagiotopoulou
Andy W C Pang
Yunjiang Qiu
Gabriel Rosanio
Mallory Ryan, The Jackson LaboratoryFollow
Adrian Stütz
Diana C J Spierings
Alistair Ward
AnneMarie E Welch
Ming Xiao
Wei Xu
Chengsheng Zhang, The Jackson LaboratoryFollow
Qihui Zhu, The Jackson LaboratoryFollow
Xiangqun Zheng-Bradley
Ernesto Lowy
Sergei Yakneen
Steven McCarroll
Goo Jun
Li Ding
Chong Lek Koh
Bing Ren
Paul Flicek
Ken Chen
Mark B Gerstein
Pui-Yan Kwok
Peter M Lansdorp
Gabor T Marth
Jonathan Sebat
Xinghua Shi
Ali Bashir
Kai Ye
Scott E Devine
Michael E Talkowski
Ryan E Mills
Tobias Marschall
Jan O Korbel
Evan E Eichler
Charles Lee, The Jackson LaboratoryFollow

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Nat Commun 2019 Apr 16; 10(1):1784







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, strand-specific sequencing technologies, optical mapping, and variant discovery algorithms to comprehensively analyze three trios to define the full spectrum of human genetic variation in a haplotype-resolved manner. We identify 818,054 indel variants (bp) and 27,622 SVs (≥50 bp) per genome. We also discover 156 inversions per genome and 58 of the inversions intersect with the critical regions of recurrent microdeletion and microduplication syndromes. Taken together, our SV callsets represent a three to sevenfold increase in SV detection compared to most standard high-throughput sequencing studies, including those from the 1000 Genomes Project. The methods and the dataset presented serve as a gold standard for the scientific community allowing us to make recommendations for maximizing structural variation sensitivity for future genome sequencing studies.


Open access under Creative Commons Attribution 4.0 International License