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TrackSig: reconstructing evolutionary trajectories of mutations in cancer

https://doi.org/10.1101/260471
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What this work says

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

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Genomic Evolution of Breast Cancer Metastasis and Relapse
inferredcites →https://doi.org/10.1016/j.cell.2012.04.023openalex-snapshot
The Life History of 21 Breast Cancers
inferredcites →https://doi.org/10.1016/j.celrep.2012.12.008openalex-snapshot
Deciphering Signatures of Mutational Processes Operative in Human Cancer
inferredcites →https://doi.org/10.1016/j.cels.2015.08.015openalex-snapshot
Optimizing Cancer Genome Sequencing and Analysis
inferredcites →https://doi.org/10.1016/j.mrfmmm.2004.06.057openalex-snapshot
Mutations induced by ultraviolet light
inferredcites →https://doi.org/10.1038/nature12477openalex-snapshot
Signatures of mutational processes in human cancer
inferredcites →https://doi.org/10.1038/nature17676openalex-snapshot
Landscape of somatic mutations in 560 breast cancer whole-genome sequences
inferredcites →https://doi.org/10.1038/ncomms12605openalex-snapshot
Mutational signatures of ionizing radiation in second malignancies
inferredcites →https://doi.org/10.1038/ng.2891openalex-snapshot
Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing
inferredcites →https://doi.org/10.1038/ng.3214openalex-snapshot
A Big Bang model of human colorectal tumor growth
inferredcites →https://doi.org/10.1038/ng.3441openalex-snapshot
Clock-like mutational processes in human somatic cells
inferredcites →https://doi.org/10.1038/ng.3489openalex-snapshot
Identification of neutral tumor evolution across cancer types
inferredcites →https://doi.org/10.1038/ng.3573openalex-snapshot
Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer
inferredcites →https://doi.org/10.1038/ng.3891openalex-snapshot
Between-region genetic divergence reflects the mode and tempo of tumor evolution
inferredcites →https://doi.org/10.1038/nm.3886openalex-snapshot
Subclonal diversification of primary breast cancer revealed by multiregion sequencing
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/s41467-020-14351-8openalex-snapshot
Inferring structural variant cancer cell fraction
inferredcites →https://doi.org/10.1038/s41588-018-0128-6openalex-snapshot
Quantification of subclonal selection in cancer from bulk sequencing data
inferredcites →https://doi.org/10.1038/s41588-018-0258-xopenalex-snapshot
Neutral tumor evolution?
inferredcites →https://doi.org/10.1038/s41592-018-0108-xopenalex-snapshot
Detecting repeated cancer evolution from multi-region tumor sequencing data
inferredcites →https://doi.org/10.1038/sj.onc.1205803openalex-snapshot
Tobacco smoke carcinogens, DNA damage and p53 mutations in smoking-associated cancers
inferredcites →https://doi.org/10.1056/nejmoa1113205openalex-snapshot
Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing
inferredcites →https://doi.org/10.1056/nejmoa1616288openalex-snapshot
Tracking the Evolution of Non–Small-Cell Lung Cancer
inferredcites →https://doi.org/10.1073/pnas.1519556112openalex-snapshot
Extremely high genetic diversity in a single tumor points to prevalence of non-Darwinian cell evolution
inferredcites →https://doi.org/10.1073/pnas.1522203113openalex-snapshot
Assessing intratumor heterogeneity and tracking longitudinal and spatial clonal evolutionary history by next-generation sequencing
inferredcites →https://doi.org/10.1080/01621459.2012.737745openalex-snapshot
Optimal Detection of Changepoints With a Linear Computational Cost
inferredcites →https://doi.org/10.1093/carcin/22.3.367openalex-snapshot
Patterns of p53 G->T transversions in lung cancers reflect the primary mutagenic signature of DNA-damage by tobacco smoke
inferredcites →https://doi.org/10.1098/rsif.2017.0967openalex-snapshot
Passenger mutations can accelerate tumour suppressor gene inactivation in cancer evolution
inferredcites →https://doi.org/10.1101/161562openalex-snapshot
The evolutionary history of 2,658 cancers
inferredcites →https://doi.org/10.1101/322859openalex-snapshot
The Repertoire of Mutational Signatures in Human 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.1253462openalex-snapshot
Spatial and temporal diversity in genomic instability processes defines lung cancer evolution
inferredcites →https://doi.org/10.1126/science.1256930openalex-snapshot
Intratumor heterogeneity in localized lung adenocarcinomas delineated by multiregion sequencing
inferredcites →https://doi.org/10.1126/science.959840openalex-snapshot
The Clonal Evolution of Tumor Cell Populations
inferredcites →https://doi.org/10.1126/science.aag0299openalex-snapshot
Mutational signatures associated with tobacco smoking in human cancer
inferredcites →https://doi.org/10.1145/2133806.2133826openalex-snapshot
Probabilistic topic models
inferredcites →https://doi.org/10.1158/0008-5472.can-15-3476openalex-snapshot
Multiregion Whole-Exome Sequencing Uncovers the Genetic Evolution and Mutational Heterogeneity of Early-Stage Metastatic Melanoma
inferredcites →https://doi.org/10.1162/jmlr.2003.3.4-5.993openalex-snapshot
10.1162/jmlr.2003.3.4-5.993
inferredcites →https://doi.org/10.1186/gb-2013-14-4-r39openalex-snapshot
EMu: probabilistic inference of mutational processes and their localization in the cancer genome
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/10.1371/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.pgen.1005657openalex-snapshot
A Simple Model-Based Approach to Inferring and Visualizing Cancer Mutation Signatures
inferredcites →https://doi.org/10.7554/elife.24284openalex-snapshot
Rapid evolution of the human mutation spectrum

What points at this work

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/10.1093/nargab/lqaa004openalex-snapshot
BATCAVE: calling somatic mutations with a tumor- and site-specific prior
inferred← citeshttps://doi.org/10.1186/s12859-025-06055-xopenalex-snapshot
A Dirichlet-multinomial mixed model for determining differential abundance of mutational signatures
inferred← citeshttps://doi.org/10.1186/s13059-018-1476-3openalex-snapshot
Timing somatic events in the evolution of cancer
inferred← citeshttps://doi.org/10.70675/302fb443z8270z4f6ezbbf7z20e95637a756openalex-snapshot
Statistical methods for deciphering intra-tumor hereterogeneity : challenges and opportunities for cancer clinical management
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