*It is important to note that although somatic tumor tests are not intended to find germline variants, it is a possible outcome of this testing. In fact, up to 12% of somatic tumor tests identify a germline variant (3).
Hallmark signs that a somatic finding may be a germline variant:
- The variant allele frequency, (AF). This is how often the variant was seen in the tested tumor sample. AF provides insights to how predominant the variant may be in the tumor sample; however, the AF only provides information about the cells tested, not the entire tumor. Allele frequencies in the 20% to 70% range may be indicative of a germline variant (3,4). Germline variants are typically observed at around a 50% AF, as the variant is one of two inherited alleles.
- Founder mutations or well-characterized variants. There are common germline variants seen at a higher frequency in a distinct population, referred to as founder mutations. If a founder mutation is present in a tumor sample, it may be an indication the variant is also present in the germline. Common examples of founder mutations are the three BRCA Ashkenazi Jewish founder mutations, and the Polish CHEK2 c.1100delC variant (4).
- The gene where the variant is present. Some genes are more commonly altered in tumors than others. For example, TP53 variants are frequently seen in tumor specimens, but most of those individuals do not have a germline TP53 variant, or Li Fraumeni Syndrome. Other examples of genes commonly seen with variants in tumors include APC, MEN1, RET, RB1, STK11, and PTEN. On the other hand, genes that can be more suspicious for a germline variant include BRCA1, BRCA2, PALB2, any of the Lynch Syndrome genes (MLH1, MSH2, MSH6, PMS2, EPCAM), especially if the personal and/or family history is consistent with the gene’s phenotype (1). In addition, some genes frequently analyzed in tumors have no hereditary cancer germline associations, such as KRAS, and are therefore less likely to need follow-up testing.
- Report comments. Most laboratories include a brief comment if the noted variant is suspected to be germline. Often, labs use their own internal guidelines or follow medical society guidelines like the “ACMG Recommendations for Reporting of Secondary Findings in Clinical Exome and Genome Sequencing” list. This provides a guide for the laboratory; however, the list is not exhaustive, and may miss some genes relevant to hereditary cancer such as CHEK2, ATM, RAD51C and RAD51D (2).
Next steps if a germline variant is suspected
If there is suspicion that a somatic variant may be germline based on the information shared above, follow-up steps are needed for confirmation. To begin, germline testing should be ordered to look for the variant in question. In many cases, it is recommended that germline testing not only be limited to analysis of the somatic variant but rather include testing of multiple relevant genes at once (multi gene panel) based upon the patient’s personal and family history. The reason for this is that, as mentioned above, somatic tumor testing is not intended to detect germline variants. Therefore, germline testing using a multi gene panel provides more comprehensive information for the patient. In most cases a blood, saliva, or buccal (cheek swab) sample can be used. However, for patients with an active hematologic malignancy, an alternative tissue type may be recommended such as fibroblasts from a skin punch biopsy. For those patients, the blood and saliva may be contaminated by circulating tumor cells and may not yield an accurate result. Quest Diagnostics accepts fibroblasts and cultured cells, and our genetic counselors are available to help coordinate this testing.
Next steps if a suspected germline variant is not identified
For patients who have undergone somatic tumor testing without any potential germline variants identified, a hereditary predisposition to cancer is not ruled out. If the somatic result you are reviewing indicates germline testing was completed at the same time, follow-up germline testing may still be warranted. If the germline testing was completed on the same platform as the next generation sequencing (NGS) somatic test, germline variants may have been missed. These platforms were not designed to be diagnostic germline tests, and their coverage often misses certain types of variants (large deletions and duplications, indels, and variants that involve the noncoding regions like the promotor region or introns). Empiric data suggests approximately 8% to 10% of germline pathogenic variants are missed on tumor testing (1,6). If the concurrent test was run as a separate diagnostic germline test, often resulted in a separate report, additional follow-up testing may not be necessary. It is also important to note that the somatic variant classification, or whether the finding is considered significant or not (pathogenic, uncertain, benign), is not necessarily the same as the variant classification for germline variants. For example, a somatic report may call a variant “pathogenic,” and a germline report may call it “uncertain.
Germline testing should still be considered for patients, regardless of prior somatic tumor testing if they meet certain genetic testing criteria based on their personal and family history. The most common guidelines referenced when determining whether germline testing should be pursued are the National Comprehensive Cancer Network (NCCN) Guidelines (5). In general, reasons to consider germline testing in a patient include the following:
- Early age of onset for cancer in the family, such as under age 50 for breast or colon cancers
- Multiple relatives on the same side of the family with the same type of cancer, or cancer types that can be seen together in certain hereditary cancer syndromes (eg breast and ovarian cancers in the BRCA1/2 genes, or uterine and colon cancers in Lynch syndrome)
- Individuals with multiple separate cancer diagnoses in their lifetime
- Individuals with rare tumor types that have a considerable risk of heredity (eg epithelial ovarian cancer and exocrine pancreatic cancer)
It is always best to consult a genetics professional such as a genetic counselor regarding genetic test selection. For more information on test options for your patients visit www.QuestHereditaryCancer.com or call our team of genetic counselors at 1.866.436.3463.
References:
- Lincoln SE, Nussbaum RL, Kurian AW, et al. Yield and Utility of Germline Testing Following Tumor Sequencing in Patients With Cancer. JAMA Netw Open. 2020;3(10):e2019452. Published 2020 Oct 1. doi:10.1001/jamanetworkopen.2020.19452
- Miller DT, Lee K, Abul-Husn NS, Amendola LM, Brothers K, Chung WK, Gollob MH, Gordon AS, Harrison SM, Hershberger RE, Klein TE, Richards CS, Stewart DR, Martin CL; ACMG Secondary Findings Working Group. Electronic address: documents@acmg.net. ACMG SF v3.1 list for reporting of secondary findings in clinical exome and genome sequencing: A policy statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med. 2022 Jul;24(7):1407-1414. doi: 10.1016/j.gim.2022.04.006. Epub 2022 Jun 17. PMID: 35802134
- Raymond VM, Gray SW, Roychowdhury S, et al. Germline findings in tumor-only sequencing: Points to consider for clinicians and laboratories. J Natl Cancer Inst 108:djv351. 2015
- DeLeonardis K, Hogan L, Cannistra SA, Rangachari D, Tung N. When Should Tumor Genomic Profiling Prompt Consideration of Germline Testing? J Oncol Pract. 2019 Sep;15(9):465-473. doi: 10.1200/JOP.19.00201 PMID: 31509718
- National Comprehensive Cancer Network®. NCCN Clinical Practice Guidelines in Oncology. Genetic/Familial High-Risk Assessment: Breast, Ovarian, and Pancreatic. V2.2024. www.NCCN.org
- Terraf P, Pareja F, Brown DN, et al. Comprehensive assessment of germline pathogenic variant detection in tumor-only sequencing. Ann Oncol 2022; 33:426-433.
