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Development of the variant calling algorithm, ADIScan, and its use to estimate discordant sequences between monozygotic twins

Title
Development of the variant calling algorithm, ADIScan, and its use to estimate discordant sequences between monozygotic twins
Authors
Cho, YangraeLee, SunhoHong, Jong HuiKim, Byong JoonHong, Woon-YoungJung, JongcheolLee, Hyang BurmSung, JoohonKim, Han-NaKim, Hyung-LaeJung, Jongsun
Ewha Authors
김형래김한나
SCOPUS Author ID
김형래scopus; 김한나scopus
Issue Date
2018
Journal Title
NUCLEIC ACIDS RESEARCH
ISSN
0305-1048JCR Link

1362-4962JCR Link
Citation
NUCLEIC ACIDS RESEARCH vol. 46, no. 15
Publisher
OXFORD UNIV PRESS
Indexed
SCOPUS; SCI; SCIE WOS
Document Type
Article
Abstract
Calling variants from next-generation sequencing (NGS) data or discovering discordant sequences between two NGS data sets is challenging. We developed a computer algorithm, ADIScan1, to call variants by comparing the fractions of allelic reads in a tester to the universal reference genome. We then created ADIScan2 by modifying the algorithm to directly compare two sets of NGS data and predict discordant sequences between two testers. ADIScan1 detected >99.7% of variants called by GATK with an additional 724 393 SNVs. ADIScan2 identified similar to 500 candidates of discordant sequences in each of two pairs of the monozygotic twins. About 200 of these candidates were included in the similar to 2800 predicted by VarScan2. We verified 66 true discordant sequences among the candidates that ADIScan2 and VarScan2 exclusively predicted. ADIScan2 detected many discordant sequences overlooked by VarScan2 and Mutect, which specialize in detecting low frequency mutations in genetically heterogeneous cancerous tissues. Numbers of verified sequences alone were >5 times more than expected based on recently estimated mutation rates from whole genome sequences. Estimated post-zygotic mutation rates were 1.68 x 10(-7) in this study. ADIScan1 and 2 would complement existing tools in screening causative mutations of diverse genetic diseases and comparing two sets of genome sequences, respectively.
DOI
10.1093/nar/gky445
Appears in Collections:
의과대학 > 의학과 > Journal papers
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