ArticleJCO clinical cancer informatics2020
Reliable Analysis of Clinical Tumor-Only Whole-Exome Sequencing Data.
Article in JCO clinical cancer informatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
22 citing papers in PubMed.
- Mutational Signature-Based Biomarker for Phase II Trial of Olaparib Maintenance in Advanced High-Grade Ovarian Cancer.Cancer science · 2026Trial
- Evolution of the tumor immune landscape during treatment with tebentafusp, a T cell receptor-CD3 bispecific.Cell reports. Medicine · 2025Trial
- Combined PD-1, BRAF and MEK inhibition in advanced BRAF-mutant melanoma: safety run-in and biomarker cohorts of COMBI-i.Nature medicine · 2020Trial
- Somatic likelihood tiering: an interpretable post-calling triage protocol for tumor-only whole-exome variant review.Briefings in bioinformatics · 2026Article
- Whole-Exome Sequencing Identifies Candidate Genomic Features Associated with Response to Platinum-Based Chemotherapy and Ixabepilone-Based Treatment in Ovarian Cancer.International journal of molecular sciences · 2026Article
- Energetics of whole genome doubling and genomic instability.Cancer letters · 2025Review
- Precise identification of somatic and germline variants in the absence of matched normal samples.Briefings in bioinformatics · 2024Article
- Validation and Implementation of a Somatic-Only Tumor Exome for Routine Clinical Application.The Journal of molecular diagnostics : JMD · 2024Article
- The enrichment of Fanconi anemia/homologous recombination pathway aberrations in ATM/ATR-mutated NSCLC was accompanied by unique molecular features and poor prognosis.Journal of translational medicine · 2023Article
- Potential value of ctDNA monitoring in metastatic HR + /HER2 - breast cancer: longitudinal ctDNA analysis in the phase Ib MONALEESASIA trial.BMC medicine · 2023Article
- Cell-Free DNA Extracted from CSF for the Molecular Diagnosis of Pediatric Embryonal Brain Tumors.Cancers · 2023Article
- Rare mutation-dominant compound EGFR-positive NSCLC is associated with enriched kinase domain-resided variants of uncertain significance and poor clinical outcomes.BMC medicine · 2023Article
- Impact of Whole Genome Doubling on Detection of Circulating Tumor DNA in Colorectal Cancer.Cancers · 2023Article
- Fast, accurate, and racially unbiased pan-cancer tumor-only variant calling with tabular machine learning.NPJ precision oncology · 2023Article
- Genetic Ancestry Inference from Cancer-Derived Molecular Data across Genomic and Transcriptomic Platforms.Cancer research · 2023Article
- Gene signatures associated with prognosis and chemotherapy resistance in glioblastoma treated with temozolomide.Frontiers in genetics · 2023Article
- Co-occurrence CDK4/6 amplification serves as biomarkers of de novo EGFR TKI resistance in sensitizing EGFR mutation non-small cell lung cancer.Scientific reports · 2022Article
- Systematic assessment and optimizing algorithm of tumor mutational burden calculation and their implications in clinical decision-making.Frontiers in oncology · 2022Article
- TOSCA: an automated Tumor Only Somatic CAlling workflow for somatic mutation detection without matched normal samples.Bioinformatics advances · 2022Article
- Altered Signaling Pathways Revealed by Comprehensive Genomic Profiling in Patients With Unknown Primary Tumors.Frontiers in oncology · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
purposeAllele-specific copy number alteration (CNA) analysis is essential to study the functional impact of single-nucleotide variants (SNVs) and the process of tumorigenesis. However, controversy over whether it can be performed with sufficient accuracy in data without matched normal profiles and a lack of open-source implementations have limited its application in clinical research and diagnosis.
methodsWe benchmark allele-specific CNA analysis performance of whole-exome sequencing (WES) data against gold standard whole-genome SNP6 microarray data and against WES data sets with matched normal samples. We provide a workflow based on the open-source PureCN R/Bioconductor package in conjunction with widely used variant-calling and copy number segmentation algorithms for allele-specific CNA analysis from WES without matched normals. This workflow further classifies SNVs by somatic status and then uses this information to infer somatic mutational signatures and tumor mutational burden (TMB).
resultsApplication of our workflow to tumor-only WES data produces tumor purity and ploidy estimates that are highly concordant with estimates from SNP6 microarray data and matched normal WES data. The presence of cancer type-specific somatic mutational signatures was inferred with high accuracy. We also demonstrate high concordance of TMB between our tumor-only workflow and matched normal pipelines.
conclusionThe proposed workflow provides, to our knowledge, the only open-source option with demonstrated high accuracy for comprehensive allele-specific CNA analysis and SNV classification of tumor-only WES. An implementation of the workflow is available on the Terra Cloud platform of the Broad Institute (Cambridge, MA).
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.