Evidence map›Paper›PMID 39682116›Full record

ArticleCancers2024

Analytical Validation and Performance Evaluation of Amplicon-Based Next-Generation Sequencing Assays for Detecting

Ekaterina Olkhov-Mitsel, Danny Chan, Kenneth J Craddock, August Lin, Grace Luk, Rashmi S Goswami, Hong Wang, Anna Plotkin, Sharon Nofech-Mozes, David M Hwang and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cancers, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Current oncology (Toronto, Ont.) · 2026
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors.

Ekaterina Olkhov-MitselPrecision Diagnostics and Therapeutics Program, Division of Anatomic Pathology, Department of Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada.
Danny ChanPrecision Diagnostics and Therapeutics Program, Division of Anatomic Pathology, Department of Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada.
Kenneth J CraddockPrecision Diagnostics and Therapeutics Program, Division of Anatomic Pathology, Department of Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada.
August LinBiological Sciences Platform, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada.ORCID 0009-0002-9994-1558
Grace LukPrecision Diagnostics and Therapeutics Program, Division of Anatomic Pathology, Department of Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada.
Rashmi S GoswamiPrecision Diagnostics and Therapeutics Program, Division of Anatomic Pathology, Department of Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada.ORCID 0000-0001-6037-5582
Hong WangGenetics Program, North York General Hospital, Toronto, ON M2K 1E1, Canada.
Anna PlotkinPrecision Diagnostics and Therapeutics Program, Division of Anatomic Pathology, Department of Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada.
Sharon Nofech-MozesPrecision Diagnostics and Therapeutics Program, Division of Anatomic Pathology, Department of Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada.
David M HwangPrecision Diagnostics and Therapeutics Program, Division of Anatomic Pathology, Department of Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada.
Weei-Yuarn HuangPrecision Diagnostics and Therapeutics Program, Division of Anatomic Pathology, Department of Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada.ORCID 0009-0001-3604-9645

Funding

Internal departmental funding - Department of Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre (Toronto, ON, Canada). N/A
6 · The paper itself

Abstract

backgroundTargeted next-generation sequencing (NGS) panels are increasingly being utilized to identify actionable gene amplifications (copy number > 4) among solid tumors.

methodsThis study validated the analytical performance of two amplicon-based NGS assays, the Oncomine Comprehensive Panel (OCAv3) and the Oncomine Focus Assay (OFA), for detecting gene amplification in formalin-fixed paraffin-embedded (FFPE) tumors of varying cellularity. OCAv3 was assessed for amplification detection in 756 FFPE samples comprising various tumor types.

resultsWe demonstrated that with standardized quality control metrics, including median absolute pairwise difference score, these assays can achieve a near-perfect positive predictive value, although their sensitivity for detecting amplifications significantly decreased in tumors with cellularity below 30%. Stratifying tumor cellularity into 10-30%, 31-60%, and 61-95% groups revealed significantly higher gene amplification detection rates in the 31-60% and 61-95% groups

conclusionsThis study highlights the strengths and limitations of amplicon-based NGS assays in detecting amplifications using real-world data.

Indexed as

amplicon based next-generation sequencingamplicon-based panelscopy number variationERBB2 amplificationfluorescence in situ hybridizationgene amplificationmolecular pathologysolid tumors

Identifiers

PMID39682116
PMCPMC11640679

What OpenQuestion holds

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Registered trials

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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.