ArticleJCO precision oncology2020
Comparison of Annotation Services for Next-Generation Sequencing in a Large-Scale Precision Oncology Program.
Article in JCO precision oncology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers, 1 of them a synthesis that pooled it.
What it found
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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
17 citing papers in PubMed, 1 synthesis or guideline pooled it, 31 citations in OpenAlex.
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- Genomics and integrative clinical data machine learning scoring model to ascertain likely Lynch syndrome patients.BJC reports · 2025Article
- Impact of molecular diagnostics and targeted cancer therapy on patient outcomes (MODIFY): a retrospective study of the implementation of precision oncology.Molecular oncology · 2025Article
- Digital twins for health: a scoping review.NPJ digital medicine · 2024Article
- Clinical reporting for personalized cancer genomics requires extensive access to subscription-only literature.Journal of the Medical Library Association : JMLA · 2023Article
- Mutational profiles of head and neck squamous cell carcinomas based upon human papillomavirus status in the Veterans Affairs National Precision Oncology Program.Journal of cancer research and clinical oncology · 2023Article
- Introducing AI to the molecular tumor board: one direction toward the establishment of precision medicine using large-scale cancer clinical and biological information.Experimental hematology & oncology · 2022Review
- Artificial Intelligence-Assisted Serial Analysis of Clinical Cancer Genomics Data Identifies Changing Treatment Recommendations and Therapeutic Targets.Clinical cancer research : an official journal of the American Association for Cancer Research · 2022Article
- Findings from precision oncology in the clinic: rare, novel variants are a significant contributor to scaling molecular diagnostics.BMC medical genomics · 2022Article
- A clinician's handbook for using ctDNA throughout the patient journey.Molecular cancer · 2022Review
- MET D1228N and D1246N are the Same Resistance Mutation in MET Exon 14 Skipping.The oncologist · 2021Article
- Liquid biopsy enters the clinic - implementation issues and future challenges.Nature reviews. Clinical oncology · 2021Review
- An online compendium of treatable genetic disorders.American journal of medical genetics. Part C, Seminars in medical genetics · 2021Article
- Genetic Alteration Profiling of Chinese Lung Adenocarcinoma and Its Effect on Targeted Therapy Efficacy.Frontiers in oncology · 2021Article
- Article
- VA National Precision Oncology Program.Federal practitioner : for the health care professionals of the VA, DoD, and PHS · 2020Article
- Comparison of Open-access Databases for Clinical Variant Interpretation in Cancer: A Case Study of MDS/AML.Cancer genomics & proteomicsReview
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
purposeNext-generation sequencing (NGS) multigene panel testing has become widespread, including the Veterans Affairs (VA), through the VA National Precision Oncology Program (NPOP). The interpretation of genomic alterations remains a bottleneck for realizing precision medicine. We sought to examine the concordance for pathogenicity determination and clinical actionability of annotation services in NPOP.
methodsUnique gene variants were generated from NGS gene panel results using two sequencing services. For each unique gene variant, annotations were provided through N-of-One (NoO), IBM Watson for Genomics (WfG), and OncoKB. Annotations for pathogenicity (all three sources) and actionability (WfG and OncoKB) were examined for concordance. Cohen's kappa statistic was calculated to measure agreement between annotation services.
resultsAmong 1,227 NGS results obtained between 2015 and 2017, 1,388 unique variants were identified in 117 genes. The genes with the largest number of variants included
conclusionThere is substantial variability in pathogenicity assessment of NGS variants in solid tumors by annotation services. In addition, there was only moderate agreement in level 1 therapeutic actionability recommendations between WfG and OncoKB. Improvement in the precision of NGS multigene panel annotation is needed.
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.