Related Experiment Video
Updated: Oct 5, 2025
Comparative Lesions Analysis Through a Targeted Sequencing Approach
Published on: November 5, 2019
Comprehensive assessment of germline pathogenic variant detection in tumor-only sequencing
Background:
Tumor-only sequencing, implemented for the identification of somatic variants, is oftentimes used for the detection of actionable germline variants. We sought to determine whether tumor-only sequencing assays are suitable for detection of actionable germline variants, given their importance for the delivery of targeted therapies and risk-reducing measures.
Patients And Methods:
The detection of germline variants affecting moderate- and high-penetrance cancer susceptibility genes (CSGs) by tumor-only sequencing was compared to clinical germline testing in 21 333 cancer patients who underwent tumor and germline testing using the Food and Drug Administration (FDA)-authorized Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Targets (MSK-IMPACT) assay. Seven homologous recombination deficiency (HRD), two DNA damage response (DDR) and four mismatch repair (MMR) genes, as well as NF1, RB1 and TP53 were included in the analysis. FDA-authorized and New York State Department of Health-approved sequencing methods for germline, tumor/normal and tumor-only sequencing assays and analytical pipelines were employed.
Results:
In patients who underwent tumor and germline sequencing, as compared to clinical genetic testing, tumor-only sequencing failed to detect 10.5% of clinically actionable pathogenic germline variants in CSGs, including 18.8%, 12.8% and 7.3% of germline variants in MMR, DDR and HRD genes, respectively. The sensitivity for detection of pathogenic germline variants by tumor-only sequencing was 89.5%. Whilst the vast majority of pathogenic germline exonic single-nucleotide variants (SNVs) and small indels were detected by tumor-only sequencing, large percentages of germline copy number variants, intronic variants and repetitive element insertions were not detected.
Conclusions:
Tumor-only sequencing is adequate for the detection of clinically actionable germline variants, particularly for SNVs and small indels; however, a small subset of alterations affecting HRD, DDR and MMR genes may not be detected optimally. Therefore, for high-risk patients with negative tumor-only sequencing results, clinical genetic testing could be considered given the impact of these variants on therapy and genetic counseling.
Insights
Tumor-only sequencing can detect many actionable germline variants, but misses some, especially in DNA repair genes. Clinical genetic testing may be needed for high-risk patients with negative results.
Area of Science:
- Genomic Medicine
- Cancer Genetics
- Molecular Diagnostics
Background:
- Tumor-only sequencing is commonly used for somatic variant identification but also for detecting germline variants.
- Actionable germline variants are crucial for targeted therapies and risk management.
Purpose of the Study:
- To evaluate the suitability of tumor-only sequencing for detecting actionable germline variants.
- To compare tumor-only sequencing with clinical germline testing in a large patient cohort.
Main Methods:
- Compared tumor-only sequencing results with clinical germline testing in 21,333 cancer patients.
- Utilized FDA-authorized MSK-IMPACT assay and approved sequencing methods.
- Analyzed variants in cancer susceptibility genes (CSGs), including HRD, DDR, MMR, NF1, RB1, and TP53.
Main Results:
- Tumor-only sequencing missed 10.5% of actionable germline variants in CSGs.
- Sensitivity for detecting pathogenic germline variants was 89.5%.
- Missed variants included a significant proportion of copy number variants, intronic variants, and repetitive element insertions, particularly in MMR, DDR, and HRD genes.
Conclusions:
- Tumor-only sequencing is largely adequate for detecting actionable germline single-nucleotide variants and small indels.
- A subset of alterations in HRD, DDR, and MMR genes may not be optimally detected.
- Clinical genetic testing should be considered for high-risk patients with negative tumor-only results due to implications for therapy and counseling.
More Related Videos
11:02Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
Published on: October 18, 2013
13:24Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies
Published on: April 11, 2016
Related Concept Videos
01:05Cancer-Critical Genes II: Tumor Suppressor Genes
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
Such genes that act...
01:12Loss of Tumor Suppressor Gene Functions
When the tumor suppressor genes develop mutations or are lost, cells start growing out of control, leading to cancer. However, a single functional copy of the tumor suppressor gene is enough for the cells to maintain their normal functions and cell...
02:21Cancers Originate from Somatic Mutations in a Single Cell