Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing
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Updated: May 6, 2026
Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
Published on: October 18, 2013
Garrett M Frampton1, Alex Fichtenholtz, Geoff A Otto
11] Foundation Medicine, Cambridge, Massachusetts, USA. [2].
Abstract:
As more clinically relevant cancer genes are identified, comprehensive diagnostic approaches are needed to match patients to therapies, raising the challenge of optimization and analytical validation of assays that interrogate millions of bases of cancer genomes altered by multiple mechanisms. Here we describe a test based on massively parallel DNA sequencing to characterize base substitutions, short insertions and deletions (indels), copy number alterations and selected fusions across 287 cancer-related genes from routine formalin-fixed and paraffin-embedded (FFPE) clinical specimens. We implemented a practical validation strategy with reference samples of pooled cell lines that model key determinants of accuracy, including mutant allele frequency, indel length and amplitude of copy change. Test sensitivity achieved was 95-99% across alteration types, with high specificity (positive predictive value >99%). We confirmed accuracy using 249 FFPE cancer specimens characterized by established assays. Application of the test to 2,221 clinical cases revealed clinically actionable alterations in 76% of tumors, three times the number of actionable alterations detected by current diagnostic tests.
Insights
A new DNA sequencing test identifies actionable cancer alterations in 76% of tumors, significantly improving upon current diagnostic methods. This comprehensive genomic profiling test aids in matching cancer patients with targeted therapies.
Area of Science:
- Genomic Medicine
- Cancer Genomics
- Molecular Diagnostics
Background:
- Increasing identification of clinically relevant cancer genes necessitates advanced diagnostic tools.
- Current diagnostic assays face challenges in optimizing and validating comprehensive genomic interrogation.
Purpose of the Study:
- To develop and validate a massively parallel DNA sequencing test for comprehensive genomic profiling.
- To assess the test's ability to detect various alterations in formalin-fixed and paraffin-embedded (FFPE) specimens.
Main Methods:
- Massively parallel DNA sequencing of 287 cancer-related genes.
- Characterization of base substitutions, insertions/deletions (indels), copy number alterations, and fusions.
- Validation using reference cell line samples and 249 FFPE cancer specimens.
Main Results:
- Achieved 95-99% sensitivity and >99% specificity across alteration types.
- Confirmed accuracy against established assays in FFPE samples.
- Identified clinically actionable alterations in 76% of 2,221 tested clinical cases.
Conclusions:
- The developed sequencing test provides comprehensive genomic profiling from FFPE samples.
- It detects three times more actionable alterations compared to current diagnostic tests.
- This approach enhances precision oncology by enabling better patient-therapy matching.
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