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Accuracy of somatic variant detection in multiregional tumor sequencing data

https://doi.org/10.1101/655605
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What this work says

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

inferredcites →https://doi.org/10.1002/cpbi.20openalex-snapshot
cgpCaVEManWrapper: Simple Execution of CaVEMan in Order to Detect Somatic Single Nucleotide Variants in NGS Data
inferredcites →https://doi.org/10.1002/path.4270openalex-snapshot
Implications of intratumour heterogeneity for treatment stratification
inferredcites →https://doi.org/10.1016/j.csbj.2018.01.003openalex-snapshot
A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data
inferredcites →https://doi.org/10.1038/nature08489openalex-snapshot
Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution
inferredcites →https://doi.org/10.1038/nature09515openalex-snapshot
Distant metastasis occurs late during the genetic evolution of pancreatic cancer
inferredcites →https://doi.org/10.1038/nature10762openalex-snapshot
Clonal evolution in 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/ng.2891openalex-snapshot
Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing
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.3886openalex-snapshot
Subclonal diversification of primary breast cancer revealed by multiregion sequencing
inferredcites →https://doi.org/10.1038/nm.3984openalex-snapshot
Pan-cancer analysis of the extent and consequences of intratumor heterogeneity
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/nrclinonc.2017.166openalex-snapshot
Tumour heterogeneity and resistance to cancer therapies
inferredcites →https://doi.org/10.1038/s41467-019-09027-xopenalex-snapshot
Deep convolutional neural networks for accurate somatic mutation detection
inferredcites →https://doi.org/10.1038/s41467-019-09406-4openalex-snapshot
Systematic benchmarking of omics computational tools
inferredcites →https://doi.org/10.1038/s41467-019-12926-8openalex-snapshot
Rapid evolution and biogeographic spread in a colorectal cancer
inferredcites →https://doi.org/10.1038/s41592-018-0051-xopenalex-snapshot
Strelka2: fast and accurate calling of germline and somatic variants
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/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btr509openalex-snapshot
A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from 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/bioinformatics/btr708openalex-snapshot
ART: a next-generation sequencing read simulator
inferredcites →https://doi.org/10.1093/bioinformatics/btt183openalex-snapshot
Shimmer: detection of genetic alterations in tumors using next-generation sequence data
inferredcites →https://doi.org/10.1093/bioinformatics/btu755openalex-snapshot
SNV-PPILP: refined SNV calling for tumor data using perfect phylogenies and ILP
inferredcites →https://doi.org/10.1093/nar/gkv135openalex-snapshot
multiSNV: a probabilistic approach for improving detection of somatic point mutations from multiple related tumour samples
inferredcites →https://doi.org/10.1093/nar/gkw227openalex-snapshot
VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research
inferredcites →https://doi.org/10.1101/191759openalex-snapshot
MuClone: Somatic mutation detection and classification through probabilistic integration of clonal population structure
inferredcites →https://doi.org/10.1101/201178openalex-snapshot
Scaling accurate genetic variant discovery to tens of thousands of samples
inferredcites →https://doi.org/10.1101/gr.129684.111openalex-snapshot
VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing
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/scitranslmed.3008665openalex-snapshot
Demystifying Disease, Democratizing Health Care
inferredcites →https://doi.org/10.1186/s12864-016-3281-2openalex-snapshot
SNooPer: a machine learning-based method for somatic variant identification from low-pass next-generation sequencing
inferredcites →https://doi.org/10.1371/journal.pone.0186175openalex-snapshot
Comprehensive benchmarking of SNV callers for highly admixed tumor data
inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot
Cutadapt removes adapter sequences from high-throughput sequencing reads

What points at this work

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

inferred← citeshttps://doi.org/10.1007/978-3-030-35210-3_4openalex-snapshot
Accurate and Flexible Bayesian Mutation Call from Multi-regional Tumor Samples
inferred← citeshttps://doi.org/10.1007/978-3-030-64511-3_9openalex-snapshot
Theoretical Foundation of the Performance of Phylogeny-Based Somatic Variant Detection
inferred← citeshttps://doi.org/10.1089/cmb.2022.0357openalex-snapshot
Testing for Phylogenetic Signal in Single-Cell RNA-Seq Data
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