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

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Item Type:Article
Title:Multi-platform discovery of haplotype-resolved structural variation in human genomes
Creators Name:Chaisson, M.J.P. and Sanders, A.D. and Zhao, X. and Malhotra, A. and Porubsky, D. and Rausch, T. and Gardner, E.J. and Rodriguez, O.L. and Guo, L. and Collins, R.L. and Fan, X. and Wen, J. and Handsaker, R.E. and Fairley, S. and Kronenberg, Z.N. and Kong, X. and Hormozdiari, F. and Lee, D. and Wenger, A.M. and Hastie, A.R. and Antaki, D. and Anantharaman, T. and Audano, P.A. and Brand, H. and Cantsilieris, S. and Cao, H. and Cerveira, E. and Chen, C. and Chen, X. and Chin, C.S. and Chong, Z. and Chuang, N.T. and Lambert, C.C. and Church, D.M. and Clarke, L. and Farrell, A. and Flores, J. and Galeev, T. and Gorkin, D.U. and Gujral, M. and Guryev, V. and Heaton, W.H. and Korlach, J. and Kumar, S. and Kwon, J.Y. and Lam, E.T. and Lee, J.E. and Lee, J. and Lee, W.P. and Lee, S.P. and Li, S. and Marks, P. and Viaud-Martinez, K. and Meiers, S. and Munson, K.M. and Navarro, F.C.P. and Nelson, B.J. and Nodzak, C. and Noor, A. and Kyriazopoulou-Panagiotopoulou, S. and Pang, A.W.C. and Qiu, Y. and Rosanio, G. and Ryan, M. and Stütz, A. and Spierings, D.C.J. and Ward, A. and Welch, A.E. and Xiao, M. and Xu, W. and Zhang, C. and Zhu, Q. and Zheng-Bradley, X. and Lowy, E. and Yakneen, S. and McCarroll, S. and Jun, G. and Ding, L. and Koh, C.L. and Ren, B. and Flicek, P. and Chen, K. and Gerstein, M.B. and Kwok, P.Y. and Lansdorp, P.M. and Marth, G.T. and Sebat, J. and Shi, X. and Bashir, A. and Ye, K. and Devine, S.E. and Talkowski, M.E. and Mills, R.E. and Marschall, T. and Korbel, J.O. and Eichler, E.E. and Lee, C.
Abstract: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.
Keywords:Algorithms, Chromosome Mapping, Genomics, Genetic Databases, Genomic Structural Variation, Haplotypes, High-Throughput Nucleotide Sequencing, Human Genome, INDEL Mutation, Whole Genome Sequencing
Source:Nature Communications
Publisher:Nature Publishing Group
Page Range:1784
Date:16 April 2019
Official Publication:https://doi.org/10.1038/s41467-018-08148-z
PubMed:View item in PubMed

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