Skip to main content
Open Access Publications from the University of California


UC San Francisco Previously Published Works bannerUCSF

Multi-platform discovery of haplotype-resolved structural variation in human genomes.

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

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 (<50 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.

Many UC-authored scholarly publications are freely available on this site because of the UC's open access policies. Let us know how this access is important for you.

Main Content
Current View