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Achieving reproducibility and accuracy in cancer mutation detection with whole-genome and whole-exome sequencing

https://doi.org/10.1101/626440
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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.cels.2015.08.015openalex-snapshot
Optimizing Cancer Genome Sequencing and Analysis
inferredcites →https://doi.org/10.1016/j.jmoldx.2013.05.003openalex-snapshot
Clinical Validation of a Next-Generation Sequencing Screen for Mutational Hotspots in 46 Cancer-Related Genes
inferredcites →https://doi.org/10.1038/483531aopenalex-snapshot
Raise standards for preclinical cancer research
inferredcites →https://doi.org/10.1038/nature08645openalex-snapshot
Complex landscapes of somatic rearrangement in human breast cancer genomes
inferredcites →https://doi.org/10.1038/nbt.2403openalex-snapshot
Assuring the quality of next-generation sequencing in clinical laboratory practice
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/nbt.2696openalex-snapshot
Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing
inferredcites →https://doi.org/10.1038/nbt.2786openalex-snapshot
Clinical development success rates for investigational drugs
inferredcites →https://doi.org/10.1038/nbt.2835openalex-snapshot
Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls
inferredcites →https://doi.org/10.1038/ncomms10001openalex-snapshot
A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing
inferredcites →https://doi.org/10.1038/nm.2580openalex-snapshot
Functionally recurrent rearrangements of the MAST kinase and Notch gene families in breast 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/s42003-018-0023-9openalex-snapshot
Genome-wide somatic variant calling using localized colored de Bruijn graphs
inferredcites →https://doi.org/10.1038/sdata.2016.25openalex-snapshot
Extensive sequencing of seven human genomes to characterize benchmark reference materials
inferredcites →https://doi.org/10.1038/srep24607openalex-snapshot
A somatic reference standard for cancer genome 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/btr665openalex-snapshot
SomaticSniper: identification of somatic point mutations in whole genome sequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/bts271openalex-snapshot
Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/bioinformatics/btv290openalex-snapshot
BFC: correcting Illumina sequencing errors
inferredcites →https://doi.org/10.1093/nar/gks1443openalex-snapshot
Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation
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/10.1101/250647openalex-snapshot
TNscope: Accurate Detection of Somatic Mutations with Haplotype-based Variant Candidate Detection and Machine Learning Filtering
inferredcites →https://doi.org/10.1101/gr.186114.114openalex-snapshot
INTEGRATE: gene fusion discovery using whole genome and transcriptome data
inferredcites →https://doi.org/10.1126/science.aai8690openalex-snapshot
DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification
inferredcites →https://doi.org/10.1136/bmj.39590.732037.47openalex-snapshot
What is missing from descriptions of treatment in trials and reviews?
inferredcites →https://doi.org/10.1186/1471-2164-15-244openalex-snapshot
Comparison of somatic mutation calling methods in amplicon and whole exome sequence data
inferredcites →https://doi.org/10.1186/1755-8794-7-20openalex-snapshot
Analytical validation of whole exome and whole genome sequencing for clinical applications
inferredcites →https://doi.org/10.1186/1756-0500-7-864openalex-snapshot
Comparison of insertion/deletion calling algorithms on human next-generation sequencing data
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/gm495openalex-snapshot
Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers
inferredcites →https://doi.org/10.1186/s12967-017-1125-8openalex-snapshot
Towards standardization of next-generation sequencing of FFPE samples for clinical oncology: intrinsic obstacles and possible solutions
inferredcites →https://doi.org/10.1186/s13059-015-0758-2openalex-snapshot
An ensemble approach to accurately detect somatic mutations using SomaticSeq
inferredcites →https://doi.org/10.1186/s13073-017-0424-2openalex-snapshot
Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden
inferredcites →https://doi.org/10.1309/ajcpmwgwgo34egodopenalex-snapshot
Clinical Validation of KRAS, BRAF, and EGFR Mutation Detection Using Next-Generation Sequencing
inferredcites →https://doi.org/10.1371/journal.pbio.1002165openalex-snapshot
The Economics of Reproducibility in Preclinical Research
inferredcites →https://doi.org/10.1371/journal.pcbi.1004274openalex-snapshot
Genome Modeling System: A Knowledge Management Platform for Genomics
inferredcites →https://doi.org/10.1373/clinchem.2014.223040openalex-snapshot
Sequence Artifacts in DNA from Formalin-Fixed Tissues: Causes and Strategies for Minimization
inferredcites →https://doi.org/10.1593/neo.12914openalex-snapshot
Gene Fusions Associated with Recurrent Amplicons Represent a Class of Passenger Aberrations in Breast Cancer
inferredcites →https://doi.org/10.2217/bmm.15.81openalex-snapshot
Biomarker-Based Drug Safety Assessment in the Age of Systems Pharmacology: From Foundational to Regulatory Science
inferredcites →https://doi.org/10.5858/arpa.2013-0710-oaopenalex-snapshot
Validation of a Next-Generation–Sequencing Cancer Panel for Use in the Clinical Laboratory
inferredcites →https://doi.org/10.7717/peerj.148openalex-snapshot
On the reproducibility of science: unique identification of research resources in the biomedical literature

What points at this work

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

inferred← citeshttps://doi.org/10.1038/s41587-020-00748-9openalex-snapshot
A multicenter study benchmarking single-cell RNA sequencing technologies using reference samples
inferred← citeshttps://doi.org/10.1038/s41597-021-00809-xopenalex-snapshot
A multi-center cross-platform single-cell RNA sequencing reference dataset
inferred← citeshttps://doi.org/10.1093/bioinformatics/btaa051openalex-snapshot
BioSeqZip: a collapser of NGS redundant reads for the optimization of sequence analysis
inferred← citeshttps://doi.org/10.1101/2021.02.18.431906openalex-snapshot
Comprehensive Assessment of Somatic Copy Number Variation Calling Using Next-Generation Sequencing Data
inferred← citeshttps://doi.org/10.1101/2021.04.09.438252openalex-snapshot
Personalized genome assembly for accurate cancer somatic mutation discovery using cancer-normal paired reference samples
inferred← citeshttps://doi.org/10.1101/667261openalex-snapshot
Robust Cancer Mutation Detection with Deep Learning Models Derived from Tumor-Normal Sequencing Data
inferred← citeshttps://doi.org/10.1177/2472630320931794openalex-snapshot
Role of Digital Microfluidics in Enabling Access to Laboratory Automation and Making Biology Programmable
inferred← citeshttps://doi.org/10.1186/s13059-021-02315-0openalex-snapshot
Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions
inferred← citeshttps://doi.org/10.1186/s13059-021-02316-zopenalex-snapshot
A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency
inferred← citeshttps://doi.org/10.3389/fgene.2022.981269openalex-snapshot
TLsub: A transfer learning based enhancement to accurately detect mutations with wide-spectrum sub-clonal proportion
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