Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays
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 genom...
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| Format: | Online |
| Language: | English |
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Genetics Society of America
2016
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4701098/ |
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pubmed-4701098 |
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oai_dc |
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pubmed-47010982016-01-06 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 Investigations 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. Genetics Society of America 2016-01 2015-10-28 /pmc/articles/PMC4701098/ /pubmed/26510793 http://dx.doi.org/10.1534/genetics.115.183483 Text en Copyright © 2016 by the Genetics Society of America Available freely online through the author-supported open access option. |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
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 |
| spellingShingle |
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 Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays |
| author_facet |
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 |
| author_sort |
Mak, Angel C. Y. |
| title |
Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays |
| title_short |
Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays |
| title_full |
Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays |
| title_fullStr |
Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays |
| title_full_unstemmed |
Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays |
| title_sort |
genome-wide structural variation detection by genome mapping on nanochannel arrays |
| description |
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. |
| publisher |
Genetics Society of America |
| publishDate |
2016 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4701098/ |
| _version_ |
1613519923090292736 |