Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays
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AbstractComprehensive 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.
All Author(s) ListMak ACY, Lai YYY, Lam ET, Kwok TP, Leung AKY, Poon A, Mostovoy Y, Hastie AR, Stedman W, Anantharaman T, Andrews W, Zhou X, Pang AWC, Dai H, Chu C, Lin C, Wu JJK, Li CML, Li JW, Yim AKY, Chan S, Sibert J, Dzakula Z, Cao H, Yiu SM, Chan TF, Yip KY, Xiao M, Kwok PY
Journal nameGenetics
Year2016
Month1
Day1
Volume Number202
Issue Number1
PublisherGENETICS SOCIETY AMERICA
Pages351 - +
ISSN0016-6731
eISSN1943-2631
LanguagesEnglish-United Kingdom
Keywordsbiotechnology; genome mapping; structural variation detection
Web of Science Subject CategoriesGenetics & Heredity

Last updated on 2020-09-08 at 06:36