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Updated: May 31, 2026
Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
Published on: June 21, 2018
Multiplex mutation screening by mass spectrometry evaluation of 820 cases from a personalized cancer medicine
Carol Beadling1, Michael C Heinrich, Andrea Warrick
1Division of Hematology/Oncology, Oregon Health & Science University, Portland, Oregon, USA.
Abstract:
There is an immediate and critical need for a rapid, broad-based genotyping method that can evaluate multiple mutations simultaneously in clinical cancer specimens and identify patients most likely to benefit from targeted agents now in use or in late-stage clinical development. We have implemented a prospective genotyping approach to characterize the frequency and spectrum of mutations amenable to drug targeting present in urothelial, colorectal, endometrioid, and thyroid carcinomas and in melanoma. Cancer patients were enrolled in a Personalized Cancer Medicine Registry that houses both clinical information and genotyping data, and mutation screening was performed using a multiplexed assay panel with mass spectrometry-based analysis to detect 390 mutations across 30 cancer genes. Formalin fixed, paraffin-embedded specimens were evaluated from 820 Registry patients. The genes most frequently mutated across multiple cancer types were BRAF, PIK3CA, KRAS, and NRAS. Less common mutations were also observed in AKT1, CTNNB1, FGFR2, FGFR3, GNAQ, HRAS, and MAP2K1. Notably, 48 of 77 PIK3CA-mutant cases (62%) harbored at least one additional mutation in another gene, most often KRAS. Among melanomas, only 54 of 73 BRAF mutations (74%) were the V600E substitution. These findings demonstrate the diversity and complexity of mutations in druggable targets among the different cancer types and underscore the need for a broad-spectrum, prospective genotyping approach to personalized cancer medicine.
Insights
A new multiplexed genotyping assay identifies multiple cancer gene mutations simultaneously. This approach is crucial for matching patients with targeted therapies and advancing personalized cancer medicine.
Area of Science:
- Oncology
- Genetics
- Molecular Biology
Background:
- There is a critical need for rapid, broad-based genotyping methods to identify cancer patients who can benefit from targeted therapies.
- Simultaneous evaluation of multiple mutations in clinical cancer specimens is essential for personalized medicine.
Purpose of the Study:
- To implement and evaluate a prospective genotyping approach for characterizing drug-targetable mutations in various cancer types.
- To determine the frequency and spectrum of mutations in urothelial, colorectal, endometrioid, and thyroid carcinomas, and melanoma.
Main Methods:
- A multiplexed assay panel with mass spectrometry was used to screen for 390 mutations across 30 cancer genes.
- Formalin-fixed, paraffin-embedded specimens from 820 patients in a Personalized Cancer Medicine Registry were analyzed.
- Clinical information and genotyping data were housed in the registry.
Main Results:
- BRAF, PIK3CA, KRAS, and NRAS were the most frequently mutated genes across multiple cancer types.
- Less common mutations were identified in AKT1, CTNNB1, FGFR2, FGFR3, GNAQ, HRAS, and MAP2K1.
- Notably, 62% of PIK3CA-mutant cases had additional mutations, often in KRAS. 74% of melanoma BRAF mutations were the V600E substitution.
Conclusions:
- The study highlights the diversity and complexity of mutations in druggable targets across different cancer types.
- A broad-spectrum, prospective genotyping approach is essential for effective personalized cancer medicine.
- This method aids in identifying patients likely to benefit from targeted cancer agents.
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