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DELFMUT: duplex sequencing-oriented depth estimation model for stable detection of low-frequency mutations.

Authors :
Wu G
Song M
Wang K
Cui T
Jiao Z
Ji L
Gao X
Wang J
Liu T
Xia X
Fang H
Guan Y
Yi X
Source :
Briefings in bioinformatics [Brief Bioinform] 2023 Sep 20; Vol. 24 (5).
Publication Year :
2023

Abstract

Duplex sequencing technology has been widely used in the detection of low-frequency mutations in circulating tumor deoxyribonucleic acid (DNA), but how to determine the sequencing depth and other experimental parameters to ensure the stable detection of low-frequency mutations is still an urgent problem to be solved. The mutation detection rules of duplex sequencing constrain not only the number of mutated templates but also the number of mutation-supportive reads corresponding to each forward and reverse strand of the mutated templates. To tackle this problem, we proposed a Depth Estimation model for stable detection of Low-Frequency MUTations in duplex sequencing (DELFMUT), which models the identity correspondence and quantitative relationships between templates and reads using the zero-truncated negative binomial distribution without considering the sequences composed of bases. The results of DELFMUT were verified by real duplex sequencing data. In the case of known mutation frequency and mutation detection rule, DELFMUT can recommend the combinations of DNA input and sequencing depth to guarantee the stable detection of mutations, and it has a great application value in guiding the experimental parameter setting of duplex sequencing technology.<br /> (© The Author(s) 2023. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Details

Language :
English
ISSN :
1477-4054
Volume :
24
Issue :
5
Database :
MEDLINE
Journal :
Briefings in bioinformatics
Publication Type :
Academic Journal
Accession number :
37539831
Full Text :
https://doi.org/10.1093/bib/bbad277