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CloneSig can jointly infer intra-tumor heterogeneity and mutational signature activity in bulk tumor sequencing data

https://doi.org/10.1101/825778
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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cgpPindel: Identifying Somatically Acquired Insertion and Deletion Events from Paired End Sequencing
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cgpCaVEManWrapper: Simple Execution of CaVEMan in Order to Detect Somatic Single Nucleotide Variants in NGS Data
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Oncotator: Cancer Variant Annotation Tool
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Comprehensive Genetic Landscape of Uveal Melanoma by Whole-Genome Sequencing
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Inferring mutational timing and reconstructing tumour evolutionary histories
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Genomic Evolution of Breast Cancer Metastasis and Relapse
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Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma
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Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas
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The Life History of 21 Breast Cancers
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Universal Patterns of Selection in Cancer and Somatic Tissues
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The Evolutionary Landscape of Localized Prostate Cancers Drives Clinical Aggression
inferredcites →https://doi.org/10.1016/j.cell.2018.03.043openalex-snapshot
Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal
inferredcites →https://doi.org/10.1016/j.celrep.2018.03.076openalex-snapshot
Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas
inferredcites →https://doi.org/10.1016/j.ygyno.2018.10.032openalex-snapshot
Analysis of mutational signatures in primary and metastatic endometrial cancer reveals distinct patterns of DNA repair defects and shifts during tumor progression
inferredcites →https://doi.org/10.1038/nature12477openalex-snapshot
Signatures of mutational processes in human cancer
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Landscape of somatic mutations in 560 breast cancer whole-genome sequences
inferredcites →https://doi.org/10.1038/nbt.2203openalex-snapshot
Absolute quantification of somatic DNA alterations in human cancer
inferredcites →https://doi.org/10.1038/nbt.2514openalex-snapshot
Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples
inferredcites →https://doi.org/10.1038/ncomms9971openalex-snapshot
Systematic pan-cancer analysis of tumour purity
inferredcites →https://doi.org/10.1038/ng.3036openalex-snapshot
Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications
inferredcites →https://doi.org/10.1038/ng.3214openalex-snapshot
A Big Bang model of human colorectal tumor growth
inferredcites →https://doi.org/10.1038/nm.4292openalex-snapshot
HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures
inferredcites →https://doi.org/10.1038/nmeth.2883openalex-snapshot
PyClone: statistical inference of clonal population structure in cancer
inferredcites →https://doi.org/10.1038/s41467-017-00921-wopenalex-snapshot
Pan-cancer analysis of bi-allelic alterations in homologous recombination DNA repair genes
inferredcites →https://doi.org/10.1038/s41467-017-01358-xopenalex-snapshot
Mutational signatures reveal the dynamic interplay of risk factors and cellular processes during liver tumorigenesis
inferredcites →https://doi.org/10.1038/s41467-020-14352-7openalex-snapshot
Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig
inferredcites →https://doi.org/10.1038/s41467-020-15912-7openalex-snapshot
Mutational signatures are jointly shaped by DNA damage and repair
inferredcites →https://doi.org/10.1038/s41586-018-0024-3openalex-snapshot
Intra-tumour diversification in colorectal cancer at the single-cell level
inferredcites →https://doi.org/10.1038/s41586-019-1056-zopenalex-snapshot
Genomic characterization of metastatic breast cancers
inferredcites →https://doi.org/10.1038/s41586-019-1907-7openalex-snapshot
The evolutionary history of 2,658 cancers
inferredcites →https://doi.org/10.1038/s41586-020-1943-3openalex-snapshot
The repertoire of mutational signatures in human cancer
inferredcites →https://doi.org/10.1038/s41586-020-1969-6openalex-snapshot
Pan-cancer analysis of whole genomes
inferredcites →https://doi.org/10.1038/s41587-019-0364-zopenalex-snapshot
A community effort to create standards for evaluating tumor subclonal reconstruction
inferredcites →https://doi.org/10.1038/s41588-018-0179-8openalex-snapshot
Copy number signatures and mutational processes in ovarian carcinoma
inferredcites →https://doi.org/10.1038/s41598-018-25544-zopenalex-snapshot
Genomic features of renal cell carcinoma with venous tumor thrombus
inferredcites →https://doi.org/10.1038/s42003-020-01119-5openalex-snapshot
Mutational signature SBS8 predominantly arises due to late replication errors in cancer
inferredcites →https://doi.org/10.1093/bib/bbx082openalex-snapshot
Computational approaches for discovery of mutational signatures in cancer
inferredcites →https://doi.org/10.1093/bioinformatics/btp394openalex-snapshot
Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads
inferredcites →https://doi.org/10.1093/bioinformatics/bts378openalex-snapshot
DELLY: structural variant discovery by integrated paired-end and split-read analysis
inferredcites →https://doi.org/10.1093/bioinformatics/bty388openalex-snapshot
Palimpsest: an R package for studying mutational and structural variant signatures along clonal evolution in cancer
inferredcites →https://doi.org/10.1093/bioinformatics/btz340openalex-snapshot
Modeling clinical and molecular covariates of mutational process activity in cancer
inferredcites →https://doi.org/10.1093/nar/gkw1121openalex-snapshot
COSMIC: somatic cancer genetics at high-resolution
inferredcites →https://doi.org/10.1101/312041openalex-snapshot
Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes
inferredcites →https://doi.org/10.1101/322859openalex-snapshot
The Repertoire of Mutational Signatures in Human Cancer
inferredcites →https://doi.org/10.1101/484402openalex-snapshot
Ccube: A fast and robust method for estimating cancer cell fractions
inferredcites →https://doi.org/10.1101/508127openalex-snapshot
Comprehensive analysis of tumour initiation, spatial and temporal progression under multiple lines of treatment
inferredcites →https://doi.org/10.1101/cshperspect.a026625openalex-snapshot
Principles of Reconstructing the Subclonal Architecture of Cancers
inferredcites →https://doi.org/10.1101/gr.141382.112openalex-snapshot
Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability
inferredcites →https://doi.org/10.1111/cas.13582openalex-snapshot
Molecular genomic landscapes of hepatobiliary cancer
inferredcites →https://doi.org/10.1111/j.2517-6161.1977.tb01600.xopenalex-snapshot
Maximum Likelihood from Incomplete Data Via the EM Algorithm
inferredcites →https://doi.org/10.1126/science.959840openalex-snapshot
The Clonal Evolution of Tumor Cell Populations
inferredcites →https://doi.org/10.1126/science.aba8347openalex-snapshot
Extensive heterogeneity in somatic mutation and selection in the human bladder
inferredcites →https://doi.org/10.1126/scisignal.2004088openalex-snapshot
Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal
inferredcites →https://doi.org/10.1142/9789811215636_0022openalex-snapshot
TrackSigFreq: subclonal reconstructions based on mutation signatures and allele frequencies
inferredcites →https://doi.org/10.1182/blood-2017-11-817601openalex-snapshot
Genetic landscape of hepatitis B virus–associated diffuse large B-cell lymphoma
inferredcites →https://doi.org/10.1186/s13059-015-0602-8openalex-snapshot
PhyloWGS: Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors
inferredcites →https://doi.org/10.1186/s13059-016-0893-4openalex-snapshot
deconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution
inferredcites →https://doi.org/10.1186/s13073-019-0632-zopenalex-snapshot
Translating insights into tumor evolution to clinical practice: promises and challenges
inferredcites →https://doi.org/10.12688/f1000research.14148.1openalex-snapshot
segment_liftover : a Python tool to convert segments between genome assemblies
inferredcites →https://doi.org/10.1371/journal.pcbi.1003665openalex-snapshot
SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution
inferredcites →https://doi.org/10.1371/journal.pone.0221235openalex-snapshot
Computational tools to detect signatures of mutational processes in DNA from tumours: A review and empirical comparison of performance
inferredcites →https://doi.org/10.1371/journal.pone.0224143openalex-snapshot
Assessing reliability of intra-tumor heterogeneity estimates from single sample whole exome sequencing data
inferredcites →https://doi.org/10.17632/by4gbgr9gdopenalex-snapshot
PCAWG Intra-Tumor Heterogeneity Simulations
inferredcites →https://doi.org/10.18632/oncotarget.24797openalex-snapshot
Fanconi anemia and homologous recombination gene variants are associated with functional DNA repair defects in vitro and poor outcome in patients with advanced head and neck squamous cell carcinoma
inferredcites →https://doi.org/10.2139/ssrn.3155634openalex-snapshot
Reliability of Whole-Exome Sequencing for Assessing Intratumor Genetic Heterogeneity
inferredcites →https://doi.org/10.3390/ijms21239025openalex-snapshot
E2F1 Promotes Progression of Bladder Cancer by Modulating RAD54L Involved in Homologous Recombination Repair
inferredcites →https://doi.org/10.5281/zenodo.5021290openalex-snapshot
judithabk6/Clonesig_analysis:
inferredcites →https://doi.org/10.5281/zenodo.5021300openalex-snapshot
judithabk6/clonesig:
inferredcites →https://doi.org/10.7303/syn2813581openalex-snapshot
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Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1093/bioinformatics/btaa672openalex-snapshot
A statistical approach for tracking clonal dynamics in cancer using longitudinal next-generation sequencing data
inferred← citeshttps://doi.org/10.1146/annurev-biodatasci-122320-120920openalex-snapshot
Mutational Signatures: From Methods to Mechanisms
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.