@article{23928f5f7e97474487a4f40c3d129ecb,
title = "Development of the variant calling algorithm, ADIScan, and its use to estimate discordant sequences between monozygotic twins",
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 ∼500 candidates of discordant sequences in each of two pairs of the monozygotic twins. About 200 of these candidates were included in the ∼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 × 10−7 in this study.",
author = "Yangrae Cho and Sunho Lee and Hong, {Jong Hui} and Kim, {Byong Joon} and Hong, {Woon Young} and Jongcheol Jung and Lee, {Hyang Burm} and Joohon Sung and Kim, {Han Na} and Kim, {Hyung Lae} and Jongsun Jung",
note = "Funding Information: Korea Health Industry Development Institute (KHIDI) funded by the Ministry of Health & Welfare, Republic of Korea [HI14C0072 to J.J. and H.L.K.]; Post-Genome Technology Development Program, Developing Korean Reference Genome, funded by the Ministry of Trade, Industry and Energy (MOTIE, Korea) [10050164 to J.S.] (in part); Cheongju-si industry-academia collaboration (to Y.C.); National Institute of Biological Resources (NIBR), funded by the Ministry of Environment (MOE) of the Republic of Korea under the NIBR [2017-02-001 to H.B.L.]; INNOPO-LIS Foundation [A2014DD101]; Institute for Information & Communications Technology Promotion funded by the Ministry of Science, ICT and Future Planning [B0101-15-0104 to J.J.]. Funding for open access charge: NIBR [2017-02-001]. Conflict of interest statement. We do not anticipate direct financial benefits from this publication, though indirect effects may occur due to publicity for Syntekabio, Inc., a public company. Six of the eleven co-authors are employees of Syntekabio, a company that develops systems for genetic analysis. Publisher Copyright: {\textcopyright} The Author(s) 2018.",
year = "2022",
month = feb,
day = "22",
doi = "10.1093/nar/gky445",
language = "English",
volume = "46",
pages = "E92",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "15",
}