Beginner’s guide to single-gene testing in gynecologic care

Illustration shows dramatization of extraction of DNA from a blood test. Chromosomes 17 and 13 show the location of BRCA mutation leading to double DNA breaks, the most common cause of hereditary breast and ovarian cancer

Introduction

Improved knowledge of genomic alterations in cancer has changed the landscape of cancer diagnosis, treatment, and prevention. At the forefront of this revolution are gynecologic malignancies, including ovarian and uterine cancers, which are most commonly associated with hereditary breast and ovarian cancer (HBOC) and hereditary non-polyposis colorectal cancer (HNPCC) or Lynch, respectively. The importance of these discoveries cannot be understated because they have resulted in practice-changing evidence that informs prognosis and treatment for those affected by cancer and enables risk reduction strategies for women who are affected and unaffected.

Ideally, mutation carriers should be identified before cancer develops when preventative surgery can be performed at the appropriate age. Testing women already affected by these cancers, however, is often the earliest opportunity to identify these mutations in the remainder of their blood relatives. Therefore, gynecologists and gynecologic oncologists are both positioned to identify candidates for hereditary cancer testing. Moreover, in cancer patients, hereditable and non-heritable mutations are informative for cancer treatment.

This article reviews the two most common cancer syndromes in addition to aspects of “genetic” testing that can be tricky for a clinician to navigate when treating and counseling these women. Patient information resources we recommend are listed in Table 1.

Hereditary breast and ovarian cancer syndrome

Deleterious mutations in the BRCA1 and BRCA2 genes are the most common cause of HBOC, accounting for 15% to 20% of ovarian cancer cases.¹ A deleterious mutation in the BRCA1 or BRCA2 gene will increase a woman’s risk of ovarian cancer to 40% or 11% to 17%, respectively, by age 70.² Risk-reducing removal of the fallopian tubes and ovaries has been shown to reduce lifetime risks of breast cancer by 50% and of ovarian and tubal cancer by 80%.³ These approaches serendipitously led to the discovery of BRCA1/2 –related fallopian tube cancer and serous tubal intraepithelial carcinoma (STIC) lesions^4,5 which are found in about 5% of cases.⁶ When cancer is not prevented, mutated BRCA1 and BRCA2 proteins, critical in the pathway for homologous DNA repair, still confer higher sensitivity to treatments such as platinum-based chemotherapy and newly approved poly-adenosine ribose polymerase (PARP) inhibitors.⁷

Current guidelines recommend that all women who are diagnosed with ovarian cancer, tubal cancer, or primary peritoneal cancer be tested for germline mutations of cancer-causing genes, regardless of age or family history,^1,7-9

Lynch syndrome

Lynch syndrome is an autosomal-dominant condition of high penetrance that is the leading cause of hereditary uterine cancer. Incidence of Lynch syndrome in women who present with a primary endometrial cancer is 2.3%, although in women under age 50 who present with endometrial cancer, it is 5% to 9%.^10,11 Lynch syndrome is caused by a mutation in one of the four mismatch (MMR) repair genes, MLH1, MSH2, MSH6, and PMS2 or in the EPCAM gene. In addition to increasing a woman’s lifetime risk of endometrial and colon cancer to 40%, Lynch syndrome also increases risk of ovarian cancer to 7% to 10%, and also confers high risk of developing gastric, small bowel, hepatobiliary, ureteral, breast, brain and skin cancers.¹² The molecular hallmark of Lynch syndrome is microsatellite instability (MSI). This results from failure of MMR genes to correct errors in single and dinucleotide repeats within coding and non-coding regions of the genome. MSI not only predisposes to cancer, but also is a marker for response to cancer immunotherapy by anti-PD-1 checkpoint inhibitors such as US Food and Drug Administration-approved pembrolizumab.¹³

Germline and somatic tumor mutations

Understanding the difference between germline and somatic tumor mutations is of key importance when managing hereditary cancer syndromes. Germline mutations are those present in germ cells at birth, which therefore can be transmitted to one’s offspring. Somatic mutations are those that occur after fertilization and are not hereditable in nature. Somatic mutations are present only in a certain cell lineage or tumor. In patients with cancer, tumors harboring germline and/or somatic mutations usually share the same phenotype in terms of biologic behavior and sensitivity to novel treatment. For example, PARP inhibitors have very similar efficacy in women with somatic or germline BRCA1 and BRCA2 mutations.¹⁴ Therefore, distinguishing germline from somatic mutations is most relevant for testing the blood relatives of someone with a known germline mutation, which is known as cascade testing. Cascade testing is only necessary when germline mutations are diagnosed, and it is not indicated when somatic mutations are found only in the tumor.⁷

Tumor tissue testing and serum testing

Cancer mutations can be found in serum and/or tumor tissue. Where the mutation is detected helps determine the germline or somatic nature of it. Because somatic mutations are found only within certain tissues, or within the cancer itself, tissue testing is necessary to identify these mutations. This may be performed on the initial tumor specimen or on biopsy specimens following a diagnosed recurrence. However, if a mutation is identified within a tumor sample that may be hereditary and the patient has not yet been tested for a germline mutation, she must be appropriately counseled that she may have a hereditary condition and will need confirmatory serum testing. Serum, and sometimes salivary, lymphocyte DNA testing can be performed at any time and will only identify germline mutation. Therefore, germline mutations currently can only be confirmed with serum or saliva testing, whereas somatic mutations are diagnosed on tissue testing, which is capable of detecting germline mutations but not sufficient for that.

The utility of tumor testing for diagnosing germline mutations currently differs between HBOC and Lynch syndromes. Tumor testing is most relevant for Lynch syndrome. Unlike women with ovarian cancer, not all women with endometrial cancer should be directly referred for genetic testing. Evaluation should begin with the tumor specimen itself, rather than germline blood testing.^15,16 The tumor is tested with immunohistochemistry (IHC) connoting the four MMR repair proteins (MLH1, MSH2, MSH6 and PMS2). If IHC testing does not identify loss of expression of any of these proteins, the patient has essentially tested negative for Lynch syndrome. However, if testing is negative but clinical suspicion is very high, the patient should still be referred for further microsatellite instability and germline testing.

If IHC defined testing does show absence of MLH1, PMS2, or both, the tumor should be tested for hypermethylation of the MLH1 promoter, as this may cause lack of expression of either protein.¹⁵ If hypermethylation is present, this essentially rules out presence of Lynch syndrome. If hypermethylation is absent, or if IHC identifies lack of expression of MSH2 or MSH6, the patient should be referred for germline testing.

For the purposes of cancer treatment, all somatic and germline forms of MSI including MMR deficiency and hypermethylation, in any tumor type, qualify patients for immunotherapy, however, this is typically not prescribed until cancer recurs after first-line chemotherapy.

Multigene panel testing and single-gene testing

In women who qualify for HBOC testing, BRCA1 and BRCA2 are the most frequently mutated genes. However, with the discovery of an increasing number of hereditary cancer genes, multi-panel genetic testing is also an option. This includes sequencing of RAD51C, RAD51D, BRIP1, PALB2, BARD1, and the MMR genes. Multipanel testing may identify mutations that are responsible for up to 4% of hereditary cancers that might have been missed if single-gene testing were employed.^17-19 However, when an increased number of genes are tested, the likelihood of discovering a variant of unknown significance is also increased, with rates as high as 25% to 41%.^20,21 Although logical, the strategy of testing common mutations first, and only testing for rare mutations if the initial testing is negative, can be cost-prohibitive and might not be covered by insurance.

Referral to genetic counseling is often the best first step to evaluate which type of testing is best for each individual patient. In centers in which genetic referral is not available, recommending appropriate testing is at the provider’s discretion. This can also prevent delays in testing and streamline care. However, before ordering any genetic testing, providers should feel comfortable with counseling, and ensure availability of appropriate post-test counseling. This includes knowledge regarding management of variants of unknown
significance and management of cascade testing, if indicated.²²

Deleterious mutations and variants of uncertain significance

A deleterious mutation in a cancer-causing gene is a mutation that is known to be associated with increased cancer risk. When a deleterious mutation is identified in a patient who has undergone genetic testing, the management strategy is straightforward. She should be counseled regarding her personal risk of developing other associated cancers and referred to appropriate specialists for screening and prevention strategies. In addition, she should be informed of the risk of transmission to her offspring, and the risk of inheritance in her siblings. Family members who may be affected are then eligible for genetic testing limited to the mutation identified in the patient. There is no general recommended age at which cascade testing should be performed, although it is not recommended for minors. It is recommended that testing be performed by age 35 at the latest.

Variants of uncertain significance (VUS) are unclassified changes in the DNA sequence that may or may not result in a meaningful change in the encoded protein. In general, the rate of VUS has decreased in BRCA testing from 13% to 2.1% over the last 10 years, most variants being reclassified as not clinically significant. Panel testing increases risk of VUS results. When a VUS is encountered during genetic testing, individuals with this (heterozygous) variant should not be considered at risk or referred for risk-reducing surgery or even surveillance. The testing laboratory and online databases can monitor specific variants for cancer association and better characterization over time.²² A VUS, however, should be interpreted within the context of the patient’s history. In a patient with a strong family history and a VUS, the provider should use his or her discretion in recommending appropriate screening, risk reduction, and cascade testing, if indicated. Although this recommendation might seem straightforward in theory, the uncertainty with regard to cancer risk in women with a VUS can be particularly anxiety-provoking for patients.

Conclusion

When hereditary cancer syndromes were first discovered, genetic testing was limited to patients with an extensive family history of cancer, or for those who presented at a very young age. As our understanding of cancer genetics grows, an increasing number of tests are becoming available to a growing population of cancer patients. It is important to understand the benefits and limitations of testing to appropriately counsel patients and ensure that each of them receives the appropriate workup and management when genetic testing identifies a familial cancer syndrome. As cancer therapeutics continues to expand, and precision medicine identifies an increasing number of targeted therapies, the importance of cancer genetics will only continue to grow. 

Disclosures:

The authors report no potential conflicts of interest with regard to this article.

References:

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