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Analysis of unmapped regions associated with long deletions in Korean whole genome sequences based on short read data

Title
Analysis of unmapped regions associated with long deletions in Korean whole genome sequences based on short read data
Author
고인송
Keywords
deletion; Korean; structural variation; unmapped region; whole genome sequencing
Issue Date
2019-12
Publisher
한국유전체학회
Citation
Genomics & Informatics, v. 17, no. 4, article no. e40
Abstract
While studies aimed at detecting and analyzing indels or single nucleotide polymorphisms within human genomic sequences have been actively conducted, studies on detecting long insertions/deletions are not easy to orchestrate. For the last 10 years, the availability of long read data of human genomes from PacBio or Nanopore platforms has increased, which makes it easier to detect long insertions/deletions. However, because long read data have a critical disadvantage due to their relatively high cost, many next generation sequencing data are produced mainly by short read sequencing machines. Here, we constructed programs to detect so-called unmapped regions (UMRs, where no reads are mapped on the reference genome), scanned 40 Korean genomes to select UMR long deletion candidates, and compared the candidates with the long deletion break points within the genomes available from the 1000 Genomes Project (1KGP). An average of about 36,000 UMRs were found in the 40 Korean genomes tested, 284 UMRs were common across the 40 genomes, and a total of 37,943 UMRs were found. Compared with the 74,045 break points provided by the 1KGP, 30,698 UMRs overlapped. As the number of compared samples increased from 1 to 40, the number of UMRs that overlapped with the break points also increased. This eventually reached a peak of 80.9% of the total UMRs found in this study. As the total number of overlapped UMRs could probably grow to encompass 74,045 break points with the inclusion of more Korean genomes, this approach could be practically useful for studies on long deletions utilizing short read data.
URI
https://genominfo.org/journal/view.php?doi=10.5808/GI.2019.17.4.e40https://repository.hanyang.ac.kr/handle/20.500.11754/158534
ISSN
2234-0742
DOI
10.5808/GI.2019.17.4.e40
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COLLEGE OF MEDICINE[S](의과대학) > MEDICINE(의학과) > Articles
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