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Published on: April 11, 2016
Mutation Yield of a 34-Gene Solid Tumor Panel in Community-Based Tumor Samples
Heather Sanders1, Kevin Qu2, Hairong Li2
1Department of Hematology and Oncology, Quest Diagnostics Nichols Institute, 33608 Ortega Highway, San Juan Capistrano, CA, 92675, USA. heather.r.sanders@questdiagnostics.com.
Background:
Several targeted therapies have been approved for treatment of solid tumors. Identification of gene mutations that indicate response to these therapies is rapidly progressing. A 34-gene next-generation sequencing (NGS) panel, developed and validated by us, was evaluated to detect additional mutations in community-based cancer specimens initially sent to our reference laboratory for routine molecular testing.
Methods:
Consecutive de-identified clinical specimens (n = 121) from melanoma cases (n = 31), lung cancer cases (n = 27), colorectal cancer cases (n = 33), and breast cancer cases (n = 30) were profiled by NGS, and the results were compared with routine molecular testing.
Results:
Upon initial mutation testing, 20 % (24/121) were positive. NGS detected ≥1 additional mutation not identified by routine testing in 74 % of specimens (90/121). Of the specimens with additional mutations, 16 harbored mutations in National Comprehensive Cancer Network guideline genes. These various additional mutations were in gene regions not routinely covered, in genes not routinely tested, and/or present at low allele frequencies. Moreover, NGS yielded no false negatives. Overall, NGS detected mutations in 59 % of the genes (20/34) included in the panel, 75 % of which (15/20) were detected in multiple tumor types. Mutations in TP53 were found in 51 % of tumors tested (62/121). Mutations in at least one other (non-TP53) gene present in the panel were detected in 64 % of cases (77/121).
Conclusion:
This assay provides improved breadth and sensitivity for profiling clinically relevant genes in these prevalent solid tumor types.
Insights
A novel 34-gene next-generation sequencing (NGS) panel identified additional mutations in 74% of solid tumor specimens. This comprehensive profiling enhances detection of clinically relevant gene mutations for targeted cancer therapies.
Area of Science:
- Oncology
- Molecular Biology
- Genetics
Background:
- Targeted therapies are approved for solid tumors, with gene mutation identification rapidly advancing.
- Routine molecular testing has limitations in detecting all relevant mutations.
Purpose of the Study:
- To evaluate a 34-gene next-generation sequencing (NGS) panel for detecting additional mutations in community-based solid tumor specimens.
- To compare NGS performance against routine molecular testing.
Main Methods:
- 121 de-identified clinical specimens from melanoma, lung, colorectal, and breast cancer cases were profiled using the 34-gene NGS panel.
- NGS results were compared with initial routine molecular testing findings.
Main Results:
- NGS detected at least one additional mutation in 74% of specimens (90/121) not found by routine testing.
- 16 specimens had additional mutations in National Comprehensive Cancer Network guideline genes.
- TP53 mutations were found in 51% of tumors, and other gene mutations in 64% of cases.
Conclusions:
- The developed NGS assay offers improved breadth and sensitivity for profiling clinically relevant genes in common solid tumors.
- This enhanced profiling aids in identifying patients who may benefit from targeted therapies.
