Language
English
Publication Date
12-15-2025
Journal
bioRxiv
DOI
10.64898/2025.12.12.692823
PMID
41446189
PMCID
PMC12724167
PubMedCentral® Posted Date
12-15-2025
PubMedCentral® Full Text Version
Pre-Print
Abstract
Detecting somatic mutations in normal tissues is challenging due to sequencing errors and the low allele fractions of post-zygotic variants. Duplex sequencing greatly reduces errors and can detect mutations at any allele fraction, but systematic, cross-platform comparisons are lacking. We present a comprehensive benchmarking of six duplex sequencing technologies used by the SMaHT Network: CODEC, CompDuplex-seq, HiDEF-seq, NanoSeq, ppmSeq, and VISTA-seq. We evaluated their performance using cord blood DNA, a tumor-normal cell line mixture, and homogenates from six human tissues. Each method shows distinct profiles in genomic footprint, sensitivity, and cost. Despite differences in library construction and sequencing platforms, estimates of mutation rates and mutational signatures are highly concordant. Integration with ultra-deep whole-genome sequencing shows that duplex approaches sensitively capture mutations and signatures beyond embryonic or clonally expanded variants. These results provide a foundation for selecting duplex methods and interpreting their data, enabling scalable single-molecule analyses of somatic mutation landscapes.
Published Open-Access
yes
Recommended Citation
Zhang, Yang; Viswanadham, Vinayak V; Andreopoulos, Michail; et al., "Benchmarking of Duplex Sequencing Approaches To Reveal Somatic Mutation Landscapes" (2025). Faculty, Staff and Students Publications. 8338.
https://digitalcommons.library.tmc.edu/baylor_docs/8338