期刊
GENETICS
卷 202, 期 1, 页码 351-+出版社
GENETICS SOCIETY AMERICA
DOI: 10.1534/genetics.115.183483
关键词
biotechnology; genome mapping; structural variation detection
资金
- National Institutes of Health (NIH) [R01 HG005946, T32 AR007175]
- NATIONAL HUMAN GENOME RESEARCH INSTITUTE [R01HG005946] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE OF ARTHRITIS AND MUSCULOSKELETAL AND SKIN DISEASES [T32AR007175] Funding Source: NIH RePORTER
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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