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Published, Version of Record (VoR)Open Access (License Unspecified), Open
Journal article
Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays
Genetics (Austin), v 202(1), pp 351-362
Jan 2016
PMID: 26510793
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
Comprehensive whole-genome structural variation detection is challenging with current approaches. With diploid cells as DNA source and the presence of numerous repetitive elements, short-read DNA sequencing cannot be used to detect structural variation efficiently. In this report, we show that genome mapping with long, fluorescently labeled DNA molecules imaged on nanochannel arrays can be used for whole-genome structural variation detection without sequencing. While whole-genome haplotyping is not achieved, local phasing (across >150-kb regions) is routine, as molecules from the parental chromosomes are examined separately. In one experiment, we generated genome maps from a trio from the 1000 Genomes Project, compared the maps against that derived from the reference human genome, and identified structural variations that are >5 kb in size. We find that these individuals have many more structural variants than those published, including some with the potential of disrupting gene function or regulation.
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Details
- Title
- Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays
- Creators
- Angel C Y Mak - University of California, San FranciscoYvonne Y Y Lai - University of California, San FranciscoErnest T Lam - BioNano Genomics (United States)Tsz-Piu Kwok - Chinese University of Hong KongAlden K Y Leung - Chinese University of Hong KongAnnie Poon - University of California, San FranciscoYulia Mostovoy - University of California, San FranciscoAlex R Hastie - BioNano Genomics (United States)William Stedman - BioNano Genomics (United States)Thomas Anantharaman - BioNano Genomics (United States)Warren Andrews - BioNano Genomics (United States)Xiang Zhou - BioNano Genomics (United States)Andy W C Pang - BioNano Genomics (United States)Heng Dai - BioNano Genomics (United States)Catherine Chu - University of California, San FranciscoChin Lin - University of California, San FranciscoJacob J K Wu - University of Hong KongCatherine M L Li - University of Hong KongJing-Woei Li - Chinese University of Hong KongAldrin K Y Yim - Chinese University of Hong KongSaki Chan - BioNano Genomics (United States)Justin Sibert - Drexel UniversityŽeljko Džakula - BioNano Genomics (United States)Han Cao - BioNano Genomics (United States)Siu-Ming Yiu - University of Hong KongTing-Fung Chan - Chinese University of Hong KongKevin Y Yip - Chinese University of Hong KongMing Xiao - Drexel UniversityPui-Yan Kwok - University of California, San Francisco
- Publication Details
- Genetics (Austin), v 202(1), pp 351-362
- Number of pages
- 12
- Grant note
- R01 HG005946 / NHGRI NIH HHS T32 AR007175 / NIAMS NIH HHS
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- School of Biomedical Engineering, Science, and Health Systems
- Web of Science ID
- WOS:000367718100028
- Scopus ID
- 2-s2.0-84953888917
- Other Identifier
- 991019167854804721
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- Collaboration types
- Domestic collaboration
- International collaboration
- Web of Science research areas
- Genetics & Heredity