AMP case report: A patient with an unexpected cancer predisposition syndrome—somatic tumor mutation testing and germline mutation testing complement each other

Create PDF

When tumor tissue is tested, it can be difficult to distinguish somatic mutations from germline mutations as most laboratories only sequence the tumor. Correlating the VAF in the tumor with the tumor cell percentage can be helpful to distinguish between the two; however, the VAF is not always included in reports. Theoretically, the VAF of a driver mutation should be approximately 50 percent of the tumor cell percentage, and in a tumor with high tumor cell percentage it might be around 50 percent. Loss of heterozygosity (LOH), copy neutral LOH, or gene amplification might distort this relationship and the estimation of the tumor cell percentage may be inaccurate. A germline mutation, however, is also expected to show a VAF of around 50 percent. It is impossible to distinguish with certainty between a somatic mutation and a germline mutation when only tumor tissue is tested. In our patient, two mutations in one cancer-predisposing gene, MLH1, in the colon cancer raise suspicion for a possible germline mutation and a second somatic inactivating mutation. Therefore, germline testing is necessary to prove the germline mutation status,¹³ as a similar molecular profile could also be found in “Lynch-like” tumors with high microsatellite instability, where both alleles of an MMR gene are inactivated by somatic mutations.¹⁴

Although molecular testing of tumors is not performed with the purpose of detecting an underlying cancer predisposition syndrome, it is important to note that molecular findings in a tumor interpreted in the context of the clinical history may be suggestive of cancer predisposition syndromes. Cancer genetic evaluation should be offered in those instances, as germline test results might have a significant impact on patient management and surveillance.^15,16

Conclusion. In this patient with a history of multiple primary cancers, somatic biomarker testing identified immunotherapy as an option for the lung cancer based on the PD-L1 expression and for the colorectal cancer based on the MMR deficiency. Molecular testing also identified a previously unsuspected germline mutation in BRCA2 that will guide future medical care for this patient as well as her family and could provide options for future therapy with PARP inhibitors in the right clinical context.

Although initial somatic molecular characterization of the patient’s colon cancer and her clinical history of urothelial cancer suggested a possible germline MMR defect in MLH1 (Lynch syndrome), the collaborative and multidisciplinary investigative efforts of her oncologist, molecular pathologist, and genetic counselors urged germline testing, which ultimately led to the discovery of a germline BRCA2 mutation (HBOC), which likely caused the breast cancer 20 years ago. The mismatch-repair–deficient colon cancer and the metastatic lung cancer were likely unrelated to the patient’s HBOC. Of note, further breast imaging revealed new calcifying breast lesions that were diagnosed as invasive ductal carcinoma and resected. Given the germline mutation in BRCA2, a prophylactic bilateral mastectomy could have been considered. However, the patient ultimately opted for close surveillance because of her age and poor cardiac status. In addition, identification of the germline BRCA2 mutation has led to cascade testing of family members, highlighting the clinical utility/significance of identifying this mutation.

1. National Comprehensive Cancer Network. NCCN Practice Guidelines in Oncology: Genetic/Familial High Risk Assessment: Colorectal. Version 1.2021. May 11, 2021. www.nccn.org/professionals/physician_gls/pdf/genetics_colon.pdf.
2. Aisner DL, Marshall CB. Molecular pathology of non-small cell lung cancer: a practical guide. Am J Clin Pathol. 2012;138(3):332–346.
3. Herbst RS, Aisner DL, Sonett JR, Turk AT, Weintraub JL, Lindeman NI. Practical considerations relating to routine clinical biomarker testing for non–small cell lung cancer: focus on testing for RET fusions. Front Med. 2021;7:562480. doi:10.3389/fmed.2020.562480.
4. Yu TM, Morrison C, Gold EJ, Tradonsky A, Layton AJ. Multiple biomarker testing tissue consumption and completion rates with single-gene tests and investigational use of Oncomine Dx Target Test for advanced non-small-cell lung cancer: a single-center analysis. Clin Lung Cancer. 2018;20(1):20–29.
5. Lindeman NI, Cagle PT, Beasley MB, et al. Molecular testing guideline for selection of lung cancer patients for EGFR and ALK tyrosine kinase inhibitors: guideline from the College of American Pathologists, International Association for the Study of Lung Cancer, and Association for Molecular Pathology. J Thorac Oncol. 2013;8(7):823–859.
6. Lindeman NI, Cagle PT, Aisner DL, et al. Updated molecular testing guideline for the selection of lung cancer patients for treatment with targeted tyrosine kinase inhibitors: guideline from the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology. Arch Pathol Lab Med. 2018;142(3):321–346.
7. National Comprehensive Cancer Network. NCCN Practice Guidelines in Oncology: Non-Small Cell Lung Cancer. Version 6.2021. Sept. 30, 2021. www.nccn.org/professionals/physician_gls/pdf/nscl.pdf.
8. Stanislaw C, Xue Y, Wilcox WR. Genetic evaluation and testing for hereditary forms of cancer in the era of next-generation sequencing. Cancer Biol Med. 2016;13(1):55–67.
9. National Comprehensive Cancer Network. NCCN Practice Guidelines in Oncology: Genetic/Familial High Risk Assessment: Breast, Ovarian, and Pancreatic. Version 1.2022. Aug. 11, 2021. www.nccn.org/professionals/physician_gls/pdf/genetics_bop.pdf.
10. Ricker C, Culver JO, Lowstuter K, et al. Increased yield of actionable mutations using multi-gene panels to assess hereditary cancer susceptibility in an ethnically diverse clinical cohort. Cancer Gen. 2016;209(4):130–137.
11. Susswein LR, Marshall ML, Nusbaum R, et al. Pathogenic and likely pathogenic variant prevalence among the first 10,000 patients referred for next-generation cancer panel testing. Genet Med. 2016;18(8):823–832.
12. Tung N, Domchek SM, Stadler Z, et al. Counselling framework for moderate-penetrance cancer-susceptibility mutations. Nat Rev Clin Oncol. 2016;13(9):581–588.
13. Haraldsdottir S, Hampel H, Tomsic J, et al. Colon and endometrial cancers with mismatch repair deficiency can arise from somatic, rather than germline, mutations. Gastroenterology. 2014;147(6):1308–1316.
14. Carethers JM. Differentiating Lynch-like from Lynch syndrome. Gastroenterology. 2014;146(3):602–604.
15. Kipp BR. Differentiating germline vs somatic variants in cancer tissue: are large-panel genetic tests helping or hurting the cancer patient? Clin Chem. 2015;61(9):1215–1216.
16. Catenacci DVT, Amico AL, Nielsen SM, et al. Tumor genome analysis includes germline genome: are we ready for surprises? Int J Cancer. 2015;136(7):1559–1567.

Dr. Barnes is an anesthesiology resident, Yale New Haven Hospital; Dr. Young is an associate professor of medicine at Cooper Medical School of Rowan University, and in the Department of Medicine, Hematology and Oncology, MD Anderson Cancer Center at Cooper, Cooper University Health Care; Kristin Mattie and Kathryn Zarnawski are genetic counselors in the William G. Rohrer Cancer Genetics Program, MD Anderson Cancer Center at Cooper, Cooper University Health Care; and Dr. Edmonston is in the Department of Pathology and Laboratory Services, Cooper University Health Care, and professor of pathology, Cooper Medical School of Rowan University.

Test yourself

Here are three questions taken from the case report.

1. In this case, loss of MLH1 and PMS2 detected by immunohistochemistry in the patient’s colon tumor was explained by:
a. A germline mutation in MLH1 (Lynch syndrome).
b. MLH1 promoter methylation.
c. Two somatic mutations in MLH1.
d. A germline mutation in BRCA2.

2. This case demonstrates all of the following except:
a. Distinguishing somatic mutations from germline mutations can be challenging.
b. Somatic testing is superior to germline testing.
c. Paired (both somatic and germline) testing may be needed to gain the full clinical picture for both a patient and their family members.
d. Individuals with germline BRCA2 mutations can have primary cancer types outside of the traditional HBOC tumor spectrum (breast, ovarian, prostate, pancreatic).

3. Which of the following is not a benefit of the NGS multi-gene panel approach to genetic testing?
a. Increased frequency of identifying genetic variants of unknown significance or pathogenic variants in genes for which there are no current clinical management guidelines.
b. Most cost-effective way to test for mutations in multiple genes.
c. Identification of mutations in genes that were not expected based on clinical presentation.
d. Fastest way to test for mutations in multiple genes.

Answers are also online now at www.amp.org/casereports.