AI Article Synopsis
- Current methods for detecting structural variations in genomes are limited, especially with short-read DNA sequencing used on diploid cells, due to challenges like repetitive elements.
- The study demonstrates that using long, fluorescently labeled DNA molecules on nanochannel arrays allows for effective whole-genome structural variation detection without sequencing, achieving routine local phasing over large regions.
- In experiments with samples from the 1000 Genomes Project, the researchers identified more structural variants than previously recorded, some of which could impact gene function or regulation significantly.
Article 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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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4701098 | PMC |
| http://dx.doi.org/10.1534/genetics.115.183483 | DOI Listing |
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