articleCell GenomicsSep 23, 2022GOLD OA

Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor

SMS. M. Ashiqul IslamMDMarcos Díaz‐GayYWYang WuMBMark BarnesRVRaviteja Vangara

University of California San Diego · La Jolla Bioengineering Institute · +16 more institutions

PubMed
Indexed incrossrefdoajpubmed

Abstract

Extraction of mutational signatures, and benchmark it against another 13 bioinformatics tools by using 34 scenarios encompassing 2,500 simulated signatures found in 60,000 synthetic genomes and 20,000 synthetic exomes. For simulations with 5% noise, reflecting high-quality datasets, SigProfilerExtractor outperforms other approaches by elucidating between 20% and 50% more true-positive signatures while yielding 5-fold less false-positive signatures. Applying SigProfilerExtractor to 4,643 whole-genome- and 19,184 whole-exome-sequenced cancers reveals four novel signatures. Two of the signatures are confirmed in independent cohorts, and one of these signatures is associated with tobacco smoking. In summary, this…

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Topics & keywords

Topics
Keywords
  • Computational biology
  • Signature (topology)
  • Biology
  • Genetics
  • Mathematics
UN Sustainable Development Goals
  • Good health and well-being
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