ArticlebioRxiv : the preprint server for biology2025
The Impact of Variant Calling on Substitution Mutational Signature Inference.
Zichen Jiang, Jessica N Au, Mariya Kazachkova, Marcos Díaz-Gay, Raviteja Vangara, Ludmil B Alexandrov
Abstract readPreprint
In one paragraphArticle in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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5 · Who and what moneyAuthors and funding
6 authors.
Zichen JiangDepartment of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
Jessica N AuDepartment of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
Mariya KazachkovaDepartment of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
Marcos Díaz-GayDepartment of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
Raviteja VangaraDepartment of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
Ludmil B AlexandrovDepartment of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0003-3596-4515 Funding
Role of hypernutrition and metabolic stress in non-alcoholic steatohepatitis (NASH) driven hepatocellular carcinoma (HCC)P01CA281819 · NCI · SANFORD BURNHAM PREBYS MEDICAL DISCOVERY INSTITUTE · PI Michael Karin · 2024 to 2026
$9.2MPredoctoral and Postdoctoral Training in Cancer Cell BiologyT32CA067754 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI JEAN Y.J. WANG · 1995 to 2026
$6.5MDetecting Mutational Signatures of Environmental Mutagens in Heathy Individuals for Personalized Cancer PreventionR01ES032547 · NIEHS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI ALEXANDROV, LUDMIL B · 2021 to 2025
$3.4MMapping immuno-genomic drivers of the head and neck precancer invasive-disease transitionU01CA290479 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Ludmil B Alexandrov, Jorge Silvio Gutkind · 2023 to 2026
$3.1MComprehensive identification of germline-somatic interactionsR01CA269919 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Ludmil B Alexandrov, Hannah Kathryn Carter · 2022 to 2026
$2.2MUnderstanding the origins of the mutational landscape in cancerR01ES036931 · NIEHS · UNIV OF ARKANSAS FOR MED SCIS · PI Ludmil B Alexandrov, Gunnar Boysen · 2025 to 2026
$1.5MExploring the Impact of Base Deaminase Deregulation on Precancer EvolutionR01CA296974 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Ludmil B Alexandrov, Catriona Helen Macleod Jamieson · 2025 to 2026
$890kNCI NIH HHS P01 CA281819NCI NIH HHS R01 CA269919NCI NIH HHS R01 CA296974NCI NIH HHS T32 CA067754NCI NIH HHS U01 CA290479NIEHS NIH HHS R01 ES032547NIEHS NIH HHS R01 ES036931
6 · The paper itselfAbstract
Identifying mutational signatures is a key component of cancer genomics studies, yet the influence of variant calling strategies on signature extraction has not been systematically evaluated. Here, we analyzed over 8,900 whole exomes from The Cancer Genome Atlas (TCGA) and over 1,800 whole genomes from the Pan-Cancer Analysis of Whole Genomes (PCAWG) consortium to assess how mutation callers shape
Identifiers
PMID41427300
PMCPMC12713130
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