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Quantifying the Influence of Mutation Detection on Tumour Subclonal Reconstruction

https://doi.org/10.1101/418780
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What this work says

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

inferredcites →https://doi.org/10.1016/j.ccr.2013.01.002openalex-snapshot
Integrative Genomic Analyses Reveal an Androgen-Driven Somatic Alteration Landscape in Early-Onset Prostate Cancer
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.cell.2013.03.021openalex-snapshot
Punctuated Evolution of Prostate Cancer Genomes
inferredcites →https://doi.org/10.1016/j.cell.2015.10.025openalex-snapshot
The Molecular Taxonomy of Primary Prostate Cancer
inferredcites →https://doi.org/10.1016/j.cell.2018.02.020openalex-snapshot
Timing the Landmark Events in the Evolution of Clear Cell Renal Cell Cancer: TRACERx Renal
inferredcites →https://doi.org/10.1016/j.cell.2018.03.029openalex-snapshot
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.cell.2018.03.057openalex-snapshot
Tracking Cancer Evolution Reveals Constrained Routes to Metastases: TRACERx Renal
inferredcites →https://doi.org/10.1016/j.trecan.2017.06.004openalex-snapshot
Multiregional Tumor Trees Are Not Phylogenies
inferredcites →https://doi.org/10.1038/nature09744openalex-snapshot
The genomic complexity of primary human prostate cancer
inferredcites →https://doi.org/10.1038/nature14347openalex-snapshot
The evolutionary history of lethal metastatic prostate cancer
inferredcites →https://doi.org/10.1038/nature20788openalex-snapshot
Genomic hallmarks of localized, non-indolent prostate cancer
inferredcites →https://doi.org/10.1038/nature22364openalex-snapshot
Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution
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/ncomms13671openalex-snapshot
Germline BRCA2 mutations drive prostate cancers with distinct evolutionary trajectories
inferredcites →https://doi.org/10.1038/ncomms3997openalex-snapshot
Heterogeneity of genomic evolution and mutational profiles in multiple myeloma
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.3221openalex-snapshot
Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue
inferredcites →https://doi.org/10.1038/ng.3315openalex-snapshot
Spatial genomic heterogeneity within localized, multifocal prostate 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/nmeth.2883openalex-snapshot
PyClone: statistical inference of clonal population structure in cancer
inferredcites →https://doi.org/10.1038/nmeth.3407openalex-snapshot
Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection
inferredcites →https://doi.org/10.1038/s41586-019-1907-7openalex-snapshot
The evolutionary history of 2,658 cancers
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/10.1056/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.1009843107openalex-snapshot
Allele-specific copy number analysis of tumors
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/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot
BEDTools: a flexible suite of utilities for comparing genomic features
inferredcites →https://doi.org/10.1093/bioinformatics/btr446openalex-snapshot
ContEst: estimating cross-contamination of human samples in next-generation sequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/btr629openalex-snapshot
Feature-based classifiers for somatic mutation detection in tumour–normal paired sequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/btr665openalex-snapshot
SomaticSniper: identification of somatic point mutations in whole genome sequencing data
inferredcites →https://doi.org/10.1093/gigascience/giw015openalex-snapshot
Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes
inferredcites →https://doi.org/10.1093/nar/29.1.308openalex-snapshot
dbSNP: the NCBI database of genetic variation
inferredcites →https://doi.org/10.1093/nar/gkm226openalex-snapshot
g:Profiler—a web-based toolset for functional profiling of gene lists from large-scale experiments
inferredcites →https://doi.org/10.1093/nar/gkq603openalex-snapshot
ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
inferredcites →https://doi.org/10.1093/nar/gku1075openalex-snapshot
COSMIC: exploring the world's knowledge of somatic mutations in human cancer
inferredcites →https://doi.org/10.1093/nar/gkw520openalex-snapshot
FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing
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/cshperspect.a026625openalex-snapshot
Principles of Reconstructing the Subclonal Architecture of Cancers
inferredcites →https://doi.org/10.1101/gr.107524.110openalex-snapshot
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
inferredcites →https://doi.org/10.1101/gr.1239303openalex-snapshot
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
inferredcites →https://doi.org/10.1101/gr.180281.114openalex-snapshot
TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data
inferredcites →https://doi.org/10.1186/1471-2105-12-35openalex-snapshot
VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R
inferredcites →https://doi.org/10.1186/1471-2105-15-35openalex-snapshot
Inferring clonal evolution of tumors from single nucleotide somatic mutations
inferredcites →https://doi.org/10.1186/gb-2009-10-3-r25openalex-snapshot
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
inferredcites →https://doi.org/10.1186/gb-2013-14-7-r80openalex-snapshot
THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data
inferredcites →https://doi.org/10.1186/s12859-019-2610-2openalex-snapshot
BPG: Seamless, automated and interactive visualization of scientific data
inferredcites →https://doi.org/10.1186/s13015-019-0155-6openalex-snapshot
Implications of non-uniqueness in phylogenetic deconvolution of bulk DNA samples of tumors
inferredcites →https://doi.org/10.1186/s13029-016-0059-5openalex-snapshot
A bedr way of genomic interval processing
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/10.1371/journal.pcbi.1003118openalex-snapshot
Software for Computing and Annotating Genomic Ranges
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.pcbi.1003703openalex-snapshot
Inferring Clonal Composition from Multiple Sections of a Breast Cancer

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1038/s41467-020-14351-8openalex-snapshot
Inferring structural variant cancer cell fraction
inferred← citeshttps://doi.org/10.1038/s41592-020-01013-2openalex-snapshot
A practical guide to cancer subclonal reconstruction from DNA sequencing
inferred← citeshttps://doi.org/10.1371/journal.pone.0224143openalex-snapshot
Assessing reliability of intra-tumor heterogeneity estimates from single sample whole exome sequencing data
inferred← citeshttps://doi.org/10.31799/1684-8853-2020-6openalex-snapshot
inferred← citeshttps://doi.org/10.31799/1684-8853-2020-6-50-59openalex-snapshot
Building and evaluation of bioinformatic pipeline for determination of clonal profiles in myelodysplastic syndrome
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