ArticleOncoTargets and therapy2015
Evaluation and comparison of two commercially available targeted next-generation sequencing platforms to assist oncology decision making.
Article in OncoTargets and therapy, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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
19 citing papers in PubMed, 37 citations in OpenAlex.
- Emerging Strategies Targeting the PI3K/AKT/mTOR Pathway in HR+/HER2- Advanced Breast Cancer.Drugs · 2026Review
- Genomic innovations in cancer prevention, diagnosis, prognosis and precision therapeutics.Frontiers in genetics · 2026Review
- Association of the Genomic Profile of Medullary Thyroid Carcinoma with Tumor Characteristics and Clinical Outcomes in an International Multicenter Study.Thyroid : official journal of the American Thyroid Association · 2024Article
- Samples from patients with AML show high concordance in detection of mutations by NGS at local institutions vs central laboratories.Blood advances · 2023Article
- Personalized matched targeted therapy in advanced pancreatic cancer: a pilot cohort analysis.NPJ genomic medicine · 2023Article
- Challenges and Obstacles in Applying Therapeutical Indications Formulated in Molecular Tumor Boards.Cancers · 2022Review
- Validation of a Circulating Tumor DNA-Based Next-Generation Sequencing Assay in a Cohort of Patients with Solid tumors: A Proposed Solution for Decentralized Plasma Testing.The oncologist · 2021Article
- Fibroblast growth factor receptor 2 (FGFR2) fusions in Japanese patients with intrahepatic cholangiocarcinoma.Japanese journal of clinical oncology · 2021Observational
- An Interactive Pipeline for Quantitative Histopathological Analysis of Spatially Defined Drug Effects in Tumors.Journal of pathology informatics · 2021Article
- Genomics-based immuno-oncology: bridging the gap between immunology and tumor biology.Human molecular genetics · 2020Review
- Next-Generation Sequencing May Discriminate Extreme Long-term versus Short-term Survival in Patients with Metastatic Small Cell Lung Cancer (SCLC).Translational oncology · 2019Article
- A machine learning approach for somatic mutation discovery.Science translational medicine · 2018Article
- MERIT reveals the impact of genomic context on sequencing error rate in ultra-deep applications.BMC bioinformatics · 2018Article
- Value-based genomics.Oncotarget · 2018Review
- Article
- Clinicopathologic Features of Non-Small-Cell Lung Cancer Harboring anJCO precision oncology · 2018Article
- Comparison of 2 Commercially Available Next-Generation Sequencing Platforms in Oncology.JAMA oncology · 2017Article
- Practical aspects of NGS-based pathways analysis for personalized cancer science and medicine.Oncotarget · 2016Review
- Comparing two assays for clinical genomic profiling: the devil is in the data.OncoTargets and therapy · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIt is widely acknowledged that there is value in examining cancers for genomic aberrations via next-generation sequencing (NGS). How commercially available NGS platforms compare with each other, and the clinical utility of the reported actionable results, are not well known. During the course of the current study, the Foundation One (F1) test generated data on a combination of somatic mutations, insertion and deletion polymorphisms, chromosomal abnormalities, and deoxyribonucleic acid (DNA) copy number changes at ~250× coverage, while the Paradigm Cancer Diagnostic (PCDx) test generated the same type of data at >5,000× coverage, plus provided messenger RNA (mRNA) expression levels. We sought to compare and evaluate paired formalin-fixed paraffin-embedded tumor tissue using these two platforms.
methodsSamples from patients with advanced solid tumors were submitted to both the F1 and PCDx vendors for NGS analysis. Turnaround time (TAT) was calculated. Biomarkers were considered clinically actionable if they had a published association with treatment response in humans and were assigned to the following categories: commercially available drug (CA), clinical trial drug (CT), or neither option (hereafter referred to as "None").
resultsThe demographics of the 21 unique patient tumor samples included ten men and eleven women, with a median age of 56 years. Due to insufficient archival tissue from the same collection period, in one case, we used samples from different collections. PCDx reported first results faster than F1 in 20 cases. When received at both vendors on the same day, PCDx reported first results for 14 of 15 cases, with a median TAT of 9 days earlier than F1 (P<0.0001). Categorization of CA compared to CT and none significantly favored PCDx (P=0.012).
conclusionIn the current analysis, commercially available NGS platforms provided clinically relevant actionable targets (CA or CT) in 47%-67% of diverse cancer types. In the samples analyzed, PCDx significantly outperformed F1 in TAT, and had statistically significant higher clinically relevant actionable targets categorized as CA.
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.