Evidence map›Paper›PMID 37502962›Full record

ArticlebioRxiv : the preprint server for biology2023

Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment.

Marcos Díaz-Gay, Raviteja Vangara, Mark Barnes, Xi Wang, S M Ashiqul Islam, Ian Vermes, Nithish Bharadhwaj Narasimman, Ting Yang, Zichen Jiang, Sarah Moody and 4 more

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed, 28 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

14 authors at 3 institutions in 3 countries.

Marcos Díaz-GayDepartment of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA.
Raviteja VangaraDepartment of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA.
Mark BarnesDepartment of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA.
Xi WangDepartment of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA.
S M Ashiqul IslamDepartment of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA.
Ian VermesCOSMIC, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK.
Nithish Bharadhwaj NarasimmanDepartment of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA.
Ting YangDepartment of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA.
Zichen JiangDepartment of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA.
Sarah MoodyCancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.
Sergey SenkinGenomic Epidemiology Branch, International Agency for Research on Cancer, 69366 Lyon CEDEX 07, France.
Paul BrennanGenomic Epidemiology Branch, International Agency for Research on Cancer, 69366 Lyon CEDEX 07, France.
Michael R StrattonCancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.
Ludmil B AlexandrovDepartment of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA.
University of California San Diego · USWellcome Sanger Institute · GBCentre international de recherche sur le cancer · FR

Funding

Detecting 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
$3.4M
Mutational Signatures of a Combined Environmental Exposure: Arsenic and Ultraviolet RadiationR01ES030993 · NIEHS · UNIVERSITY OF NEW MEXICO HEALTH SCIS CTR · PI HUDSON, LAURIE G, LIU, KE JIAN · 2020 to 2024
$2.5M
Comprehensive identification of germline-somatic interactionsR01CA269919 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Ludmil B Alexandrov, Hannah Kathryn Carter · 2022 to 2026
$2.2M
NCI NIH HHS R01 CA269919NIEHS NIH HHS R01 ES030993NIEHS NIH HHS R01 ES032547
6 · The paper itself

Abstract

Analysis of mutational signatures is a powerful approach for understanding the mutagenic processes that have shaped the evolution of a cancer genome. Here we present SigProfilerAssignment, a desktop and an online computational framework for assigning all types of mutational signatures to individual samples. SigProfilerAssignment is the first tool that allows both analysis of copy-number signatures and probabilistic assignment of signatures to individual somatic mutations. As its computational engine, the tool uses a custom implementation of the forward stagewise algorithm for sparse regression and nonnegative least squares for numerical optimization. Analysis of 2,700 synthetic cancer genomes with and without noise demonstrates that SigProfilerAssignment outperforms four commonly used approaches for assigning mutational signatures. SigProfilerAssignment is freely available at https://github.com/AlexandrovLab/SigProfilerAssignment with a web implementation at https://cancer.sanger.ac.uk/signatures/assignment/.

Identifiers

PMID37502962
PMCPMC10369904
OpenAlexW4384039592

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.