Keywords
Introduction
Points to Consider for Clinical Laboratory Professionals
Testing Approaches
Testing method | Sample required | PGPV covered in the test | Confirmatory germline testing |
---|---|---|---|
Tumor-only testing | Tumor specimen | May be inferred | Yes |
Tumor-normal paired testing with germline variant subtraction | Both tumor and nontumor specimens | Masked | Unlikely |
Tumor-normal paired testing with a set of cancer predisposition genes in germline data deliberately analyzed | Both tumor and nontumor specimens | Detected based on test design | No if germline results validated as a germline test |
AlDubayan SH. Leveraging clinical tumor-profiling programs to achieve comprehensive germline-inclusive precision cancer medicine. JCO Precis Oncol. 2019 May 23; https://doi.org/10.1200/PO.19.00108 [Epub ahead of print].
Features of PGPVs
Box 1 A 7-year-old Child was Diagnosed with a Rhabdomyosarcoma of The Jaw
Reporting of PGPV
Points to Consider for Clinical Laboratory Professionals
- •There are three tumor testing strategies: tumor-only testing, tumor-normal paired testing with germline variant subtraction, or tumor-normal paired testing with full analysis of the germline data from a subset of genes associated with cancer predisposition.
- •Tumor-normal paired testing is not a substitute for dedicated germline testing unless the germline application was designed, validated, and implemented as part of the tumor-normal paired testing protocol.
- •A known founder variant in a cancer predisposition gene detected on tumor-only testing is almost always germline, but still merits orthogonal confirmation.
- •Copy-number variation and variant characteristics such as large indels or homopolymers may affect variant allele frequencies and may require specialized testing methods to report.
- •Clinical data such as tumor type, age at cancer onset, bilateral or multiple tumors, and family history of cancer can help inform the evaluation of PGPVs.
- •Using “normal” adjacent tissue in tumor-normal paired testing should be discouraged to avoid the risk of false positives/negatives due to field “cancerization” effects.
- •Clonal hematopoiesis of indeterminate potential (CHIP) and aberrant clonal expansion (ACE) should be factored into genomic analyses, to minimize false-positive germline results or false-negative somatic results.
Points to Consider for Clinical Professionals
Pretest Considerations
- Bashford M.T.
- Kohlman W.
- Everett J.
- Parrott A.
- Pollin T.I.
Patient Education and Informed Consent
Box 2 A 45-year-old Male Presented to his Primary care Physician with History of Change in Stool Pattern and an at-home Fecal Occult Blood Test Positive Three Times Over The Past Month
Box 3 A 23-year-old Woman Developed Nonspecific Abdominal Pain and Progressive Hirsutism
Box 4 A 17-year-old Previously Healthy Male without a Significant Family Cancer History Developed a Ewing Sarcoma
Disclosure of Results
Points to Consider for Clinical Professionals
- •Individuals undergoing tumor testing should undergo informed consent of the possibility that a PGPV might be discovered. However, if there is clinical indicator for germline cancer predisposition, then dedicated germline testing should be ordered.
- •Patient choice and autonomy (opt-out of PGPV result return) should be respected.
- •When automated methods are used for pre- and post-testing education and counseling, clinicians with experience in cancer genetics should be available to answer specific questions.
- •Patients should be informed that discovery of a PGPV would prompt referral for genetic consultation and the possibility of confirmatory germline testing.
- •Confirmatory germline testing should be performed in a clinical laboratory that has adequate resources and expertise in conducting germline testing and interpreting and reporting the test results.
- •Positive germline test results should be returned by qualified and experienced clinicians (e.g., oncologists with genetics expertise, geneticists, and genetic counselors).
Summary and Future Directions
Ethics declarations
Disclosure
Additional information
Disclaimer:
References
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