ArticlePloS one2018
Performance of next-generation sequencing on small tumor specimens and/or low tumor content samples using a commercially available platform.
Article in PloS one, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 22 papers.
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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.
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Who cites it
22 citing papers in PubMed.
- Performance and Clinical Benefit of Comprehensive Genomic Profiling of GI Tumors in a Comprehensive Cancer Center.JCO precision oncology · 2026Article
- Pre-Analytical and Analytical Challenges in Whole-Exome Sequencing of Formalin-Fixed Paraffin-Embedded Breast and Prostate Cancer Tissue: A Real-World Multicenter Study.Diagnostics (Basel, Switzerland) · 2026Article
- Gene testing and prognosis in post-operative recurrent non-small-cell lung cancer: subgroup analyses of WJOG15421L.ESMO open · 2026Observational
- The Growth Modulation Index (GMI) as an Efficacy Outcome in Cancer Clinical Trials: A Scoping Review with Suggested Reporting Guidelines.Current oncology reports · 2025Article
- Next-Generation Sequencing Analysis on Image-Guided Biopsy Samples in Early-Stage Lung Cancer: Feasibility Study and Comparison With Surgical Samples.JTO clinical and research reports · 2025Article
- Genetic Uncertainties Fueling Cholangiocarcinoma Progression.Current genomics · 2025Review
- Concordance in the estimation of tumor percentage in non-small cell lung cancer using digital pathology.Scientific reports · 2024Article
- The Health Inequality Impact of Liquid Biopsy to Inform First-Line Treatment of Advanced Non-Small Cell Lung Cancer: A Distributional Cost-Effectiveness Analysis.Value in health : the journal of the International Society for Pharmacoeconomics and Outcomes Research · 2023Article
- Evaluation of appropriate conditions for Oncomine DxTT testing of FFPE specimens for driver gene alterations in non-small cell lung cancer.Thoracic cancer · 2023Article
- Impact of tissue-agnostic approvals for patients with gastrointestinal malignancies.Trends in cancer · 2023Review
- Accuracy of next-generation sequencing for molecular profiling of small specimen of lung cancer: a prospective pilot study of side-by-side comparison.Diagnostic pathology · 2022Article
- Reliable Detection of Somatic Mutations for Pancreatic Cancer in Endoscopic Ultrasonography-Guided Fine Needle Aspirates with Next-Generation Sequencing: Implications from a Prospective Cohort Study.Journal of gastrointestinal surgery : official journal of the Society for Surgery of the Alimentary Tract · 2021Article
- Association Between Medicare's National Coverage Determination and Utilization of Next-Generation Sequencing.JCO oncology practice · 2021Article
- An analysis of research biopsy core variability from over 5000 prospectively collected core samples.NPJ precision oncology · 2021Article
- Real-World Performance of a Comprehensive Genomic Profiling Test Optimized for Small Tumor Samples.JCO precision oncology · 2021Observational
- Utility of Endoscopic Ultrasound with Bronchoscope-guided Fine-needle Aspiration for Detecting Driver Oncogenes in Non-small-cell Lung Cancer during Emergency Situations: Case Series.Internal medicine (Tokyo, Japan) · 2021Article
- The expression patterns and prognostic significance of pleckstrin homology-like domain family A (PHLDA) in lung cancer and malignant mesothelioma.Journal of thoracic disease · 2021Article
- Tissue surface area and tumor cell count affect the success rate of the Oncomine Dx Target Test in the analysis of biopsy tissue samples.Thoracic cancer · 2021Article
- Article
- Next-Generation Sequencing May Discriminate Extreme Long-term versus Short-term Survival in Patients with Metastatic Small Cell Lung Cancer (SCLC).Translational oncology · 2019Article
Corrections and comments
- Erratum issued
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNext generation sequencing tests (NGS) are usually performed on relatively small core biopsy or fine needle aspiration (FNA) samples. Data is limited on what amount of tumor by volume or minimum number of FNA passes are needed to yield sufficient material for running NGS. We sought to identify the amount of tumor for running the PCDx NGS platform.
methods2,723 consecutive tumor tissues of all cancer types were queried and reviewed for inclusion. Information on tumor volume, success of performing NGS, and results of NGS were compiled. Assessment of sequence analysis, mutation calling and sensitivity, quality control, drug associations, and data aggregation and analysis were performed.
results6.4% of samples were rejected from all testing due to insufficient tumor quantity. The number of genes with insufficient sensitivity make definitive mutation calls increased as the percentage of tumor decreased, reaching statistical significance below 5% tumor content. The number of drug associations also decreased with a lower percentage of tumor, but this difference only became significant between 1-3%. The number of drug associations did decrease with smaller tissue size as expected. Neither specimen size or percentage of tumor affected the ability to pass mRNA quality control. A tumor area of 10 mm2 provides a good margin of error for specimens to yield adequate drug association results.
conclusionsSpecimen suitability remains a major obstacle to clinical NGS testing. We determined that PCR-based library creation methods allow the use of smaller specimens, and those with a lower percentage of tumor cells to be run on the PCDx NGS platform.
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