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  1. Article ; Online: Genome maps across 26 human populations reveal population-specific patterns of structural variation.

    Levy-Sakin, Michal / Pastor, Steven / Mostovoy, Yulia / Li, Le / Leung, Alden K Y / McCaffrey, Jennifer / Young, Eleanor / Lam, Ernest T / Hastie, Alex R / Wong, Karen H Y / Chung, Claire Y L / Ma, Walfred / Sibert, Justin / Rajagopalan, Ramakrishnan / Jin, Nana / Chow, Eugene Y C / Chu, Catherine / Poon, Annie / Lin, Chin /
    Naguib, Ahmed / Wang, Wei-Ping / Cao, Han / Chan, Ting-Fung / Yip, Kevin Y / Xiao, Ming / Kwok, Pui-Yan

    Nature communications

    2019  Volume 10, Issue 1, Page(s) 1025

    Abstract: Large structural variants (SVs) in the human genome are difficult to detect and study by conventional sequencing technologies. With long-range genome analysis platforms, such as optical mapping, one can identify large SVs (>2 kb) across the genome in one ...

    Abstract Large structural variants (SVs) in the human genome are difficult to detect and study by conventional sequencing technologies. With long-range genome analysis platforms, such as optical mapping, one can identify large SVs (>2 kb) across the genome in one experiment. Analyzing optical genome maps of 154 individuals from the 26 populations sequenced in the 1000 Genomes Project, we find that phylogenetic population patterns of large SVs are similar to those of single nucleotide variations in 86% of the human genome, while ~2% of the genome has high structural complexity. We are able to characterize SVs in many intractable regions of the genome, including segmental duplications and subtelomeric, pericentromeric, and acrocentric areas. In addition, we discover ~60 Mb of non-redundant genome content missing in the reference genome sequence assembly. Our results highlight the need for a comprehensive set of alternate haplotypes from different populations to represent SV patterns in the genome.
    MeSH term(s) Algorithms ; Base Sequence ; Chromosome Mapping/methods ; Chromosomes, Human, Y ; Computational Biology ; Female ; Gene Dosage ; Genetic Linkage ; Genome, Human ; Genomic Structural Variation ; Genomics ; Humans ; Male ; Mutation ; Phylogeny ; Segmental Duplications, Genomic/genetics ; Sequence Analysis, DNA
    Language English
    Publishing date 2019-03-04
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-019-08992-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays.

    Mak, Angel C Y / Lai, Yvonne Y Y / Lam, Ernest T / Kwok, Tsz-Piu / Leung, Alden K Y / Poon, Annie / Mostovoy, Yulia / Hastie, Alex R / Stedman, William / Anantharaman, Thomas / Andrews, Warren / Zhou, Xiang / Pang, Andy W C / Dai, Heng / Chu, Catherine / Lin, Chin / Wu, Jacob J K / Li, Catherine M L / Li, Jing-Woei /
    Yim, Aldrin K Y / Chan, Saki / Sibert, Justin / Džakula, Željko / Cao, Han / Yiu, Siu-Ming / Chan, Ting-Fung / Yip, Kevin Y / Xiao, Ming / Kwok, Pui-Yan

    Genetics

    2016  Volume 202, Issue 1, Page(s) 351–362

    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 ... ...

    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.
    MeSH term(s) Cell Line ; Chromosome Mapping ; Genome, Human ; Genomic Structural Variation ; Humans ; Microarray Analysis/methods
    Language English
    Publishing date 2016-01
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2167-2
    ISSN 1943-2631 ; 0016-6731
    ISSN (online) 1943-2631
    ISSN 0016-6731
    DOI 10.1534/genetics.115.183483
    Database MEDical Literature Analysis and Retrieval System OnLINE

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