Edward D. Esplin

Expanded Gene Panel Use for Women With Breast Cancer: Identification and Intervention Beyond Breast Cancer Risk

BackgroundClinicians ordering multi-gene next-generation sequencing panels for hereditary breast cancer risk have a variety of test panel options. Many panels include lesser known breast cancer genes or genes associated with other cancers. The authors hypothesized that using broader gene panels increases the identification of clinically significant findings, some relevant and others incidental to the testing indication. They examined clinician ordering patterns and compared the yield of pathogenic or likely pathogenic (P/LP) variants in non-BRCA genes of female breast cancer patients.MethodsThis study analyzed de-identified personal and family histories in 1085 breast cancer cases with P/LP multi-gene panel findings in non-BRCA cancer genes and sorted them into three groups by the panel used for testing: group A (breast cancer genes only), group B (commonly assessed cancers: breast, gynecologic, and gastrointestinal), and group C (a more expanded set of tumors). The frequency of P/LP variants in genes with established management guidelines was compared and evaluated for consistency with personal and family histories.ResultsThis study identified 1131 P/LP variants and compared variants in clinically actionable genes for breast and non-breast cancers. Overall, 91.5% of these variants were in genes with management guidelines. Nearly 12% were unrelated to personal or family history.ConclusionBroader panels were used for 85.6% of our cohort (groups B and C). Although pathogenic variants in non-BRCA genes are reportedly rare, the study found that most were in clinically actionable genes. Expanded panel testing improved the identification of hereditary cancer risk. Small, breast-limited panels may miss clinically relevant findings in genes associated with other heritable cancers.

Conflicts of interest in genetic counseling: addressing and delivering

To the Editor:We read with interest the commentary by Stoll et al.1 entitled “Conflicts of Interest in Genetic Counseling: Acknowledging and Accepting,” discussing conflicts of interest (COI) in genetic counseling pertaining to patient care. We agree that acknowledging and mitigating COI is imperative, not only among laboratory-based genetic counselors (lab-based GCs) but in any clinical environment. We also support the development of a publicly accessible database via the National Society of Genetic Counselors (NSGC)/American Board of Genetic Counseling, as suggested by Stoll et al.1 The importance of the topic addressed by their commentary is undisputed, which compels us, as practicing lab-based GCs actively engaged in patient care, to respond. Stoll and colleagues’ commentary implies a lack of acknowledgment and acceptance of COI in the field of genetic counseling. However, the NSGC has developed COI awareness resources including a Reference Sheet, Guiding Questions, and a Checklist to “help GCs recognize COI they may have, which in turn can give them confidence in assessing, disclosing, and managing this COI in their professional interactions” (http://www.nsgc.org/page/ethicsandcoi). The NSGC has put extensive effort into the development of these tools to assist not only lab-based GCs but any GC who may face COI through participation on advisory committees, acceptance of honoraria, or numerous other professional interactions with commercial entities. There has been a limited number of blog posts, newspaper articles, and journal commentaries suggesting that lab-based GCs are too conflicted to provide patient care.1 However, there remains a paucity of evidence supporting these assertions. Such suppositions, when unsupported by peerreviewed data, diminish and distract from the excellent work accomplished by this growing sector of our profession. The field of genetic counseling demands that our everyday practice be informed by the available evidence, and the discussion regarding COI should be informed in the same way. Stoll et al.1 contend that lab-based GCs may be conflicted between following practice guidelines and serving the interests of their for-profit employer (e.g., by providing pretest counseling). The authors point out that some insurers require non-lab-based pretest genetic counseling; however, this requirement was recently rescinded by one large payer (www.uhcprovider.com/content/ dam/provider/docs/public/policies/comm-medical-drug/genetictesting-hereditary-breast-ovarian-cancer-syndrome.pdf). Furthermore, our study, presented at the NSGC 2016 annual conference, demonstrated that for a cohort of 129 patients in a community clinic who underwent lab-based pretest genetic counseling, a recommendation was made to alter the genetic testing order 16% of the time. This resulted in the cancelation of testing for 9 of the 21 patients, because they either had a relative more appropriate for testing or had already tested negative. For an additional 4 of the 21 patients, the number of genes ordered was reduced, most often because of the discovery of a previously identified familial mutation after pedigree assessment by the lab-based GC.2 The authors further posit that the mere availability of posttest lab-based genetic counseling encourages nongenetics providers to order additional, unnecessary testing beyond their scope of practice. However, in a peer-to-peer consultation model involving lab-based GCs and breast surgeons, we found that test selection was altered in 21% of cases (37 of 170) after lab-based GC consultation. A substantial proportion of modified orders resulted in a reduction in the number of genes requested.3 Stoll et al.1 surmise that in the posttest setting, lab-based GCs may not be “as open to discussing the potential weaknesses and failures of tests as they would be if they were independently employed.” Our experience contradicts this supposition. For example, early in our lab’s history we offered hereditary cancer genetic testing but at the time were unable to disambiguate certain pathogenic variants in PMS2 from pseudogene sequences. Our lab-based GCs proactively communicated this limitation, which was documented in the test reports, to both clinicians and patients, instructing those for whom PMS2 analysis was indicated to obtain genetic testing elsewhere. The authors propose that COI concerns may be mitigated by excluding lab-based GCs from providing direct patient care. However, it is important to recognize that lab-based GCs can play a critical role in providing clinical care at this time of provider scarcity (https://www.nsgc.org/page/workforce). Lab-based GCs have the capacity to substantially alleviate GC shortages because of the unique nature of the delivery model; service is typically provided through telephoneor video-based counseling. This enables genetic counseling to be conveniently provided to patients nearly anywhere, significantly reducing wait times and improving access to services. In our laboratory, several measures have been implemented to mitigate COI with regard to genetic counseling services. First, all of our GCs, regardless of whether they interact directly with patients, are required to annually review the NSGC Genetic Counselor Code of Ethics, as a guiding code for our profession (http://www.nsgc.org/p/cm/ld/fid= 12). Second, we disclose GC laboratory employment with our patients at three separate touch points: online at the time their appointment is scheduled, verbally at the start of the telephone genetic counseling session, and in writing as part of the clinical documentation sent to both patients and referring providers.

Germline hemizygous deletion of CDKN2A–CDKN2B locus in a patient presenting with Li–Fraumeni syndrome

Li–Fraumeni syndrome (LFS) is a rare cancer predisposition syndrome usually associated with TP53 germline alterations. Its genetic basis in TP53 wild-type pedigrees is less understood. Using whole-genome sequencing, we identified a germline hemizygous deletion ablating CDKN2A–CDKN2B in a TP53 wild-type patient presenting with high-grade sarcoma, laryngeal squamous cell carcinoma and a family history suggestive of LFS. Patient-derived cells demonstrated reduced basal gene and protein expression of the CDKN2A-encoded tumour suppressors p14ARF and p16INK4A with concomitant decrease in p21 and faster cell proliferation, implying potential deregulation of p53-mediated cell cycle control. Review of 13 additional patients with pathogenic CDKN2A variants suggested associations of germline CDKN2A mutations with an expanded spectrum of non-melanoma familial cancers. To our knowledge, this is the first report of a germline gross deletion of the CDKN2A–CDKN2B locus in an LFS family. These findings highlight the potential contribution of germline CDKN2A deletions to cancer predisposition and the importance of interrogating the full extent of CDKN2A locus in clinical testing gene panels.

Secondary findings on virtual panels: opportunities, challenges, and potential for preventive medicine

We read with interest the commentary by Dr. Biesecker entitled “Secondary findings in exome slices, virtual panels and anticipatory sequencing,“ proposing the demarcation and return of secondary findings as outlined by the American College of Medical Genetics and Genomics (ACMG), identified through multigene panels, exome slices, and anticipatory sequencing. We agree that this is a key issue for the ACMG to address and wish to contribute to the discussion of this important topic. In the virtual panels section, Dr. Biesecker succinctly describes the potential for return of secondary findings across clinical areas (ACMG59 cancer and cardiovascular findings when an epilepsy panel is ordered), when the data is generated with a common molecular process/platform. Does a variant in an unrequisitioned gene represent a secondary finding if the gene belongs to the clinical area for which the testing was initially indicated? Specifically, healthcare professionals (HCPs) often order a narrow panel for patients based on clinical indication. For example, in a patient with personal or family history of breast cancer, an HCP may order BRCA1 and BRCA2 only, or an 11-gene guidelinesbased breast cancer panel (e.g., ATM, BRCA1, BRCA2, CDH1, CHEK2, NBN, NF1, PALB2, PTEN, STK11, and TP53). At the same time, data may be generated for some or all of the hereditary cancer syndrome (HCS) genes on the ACMG59, including such genes as MLH1, MSH2, MSH6, PMS2, EPCAM, APC, MEN1, and RET, among others. On the one hand, one might argue that variants in these other HCS genes are not secondary findings because other providers might have ordered them for the same indication because they prefer broader panels. On the other hand, the same would not be true for patients undergoing clinically indicated genetic testing for a cardiovascular condition, such as familial hypercholesterolemia (FH). Here, an HCP may order an FH-focused panel (e.g., LDLR, APOB, PCSK9, and LDLRAP1). At the same time, data may be generated for some or all of the cardiovascular genes on the ACMG59, including such genes as FBN1, TGFBR1, TGFBR2, MYH7, RYR2, PKP2, KCNQ1, and SCN5A, among others, that would not ordinarily be examined in a patient with a dyslipidemia. Although it is not always obvious what constitutes an expanded panel and what is a true secondary finding, these examples represent additional opportunities for patients to obtain information valuable to their health in the ACMG59 genes. It could be suggested that secondary findings should not be offered in conjunction with multigene panels/exome slices because the physicians ordering the panels are doing so for a specific clinical indication and are not interested in, or do not want the possibility of, secondary findings. However, the same was said of physicians ordering exome sequencing or genome sequencing (ES/GS) at the time of release of the original ACMG56 guidelines. In fact, studies conducted at the time of the original ACMG56 guidelines release showed that there were both primary care clinicians as well as genetics professionals who opposed even the offering of actionable incidental findings to adult patients undergoing ES/GS, let alone the mandatory release of secondary findings as originally recommended by the ACMG. One of the reasons for this opposition could have been related to the potential that “[a]n IF [incidental finding] may fall outside the expertise of the clinician who ordered the test, and referral to others may be necessary.” However, despite this clinician reluctance, the ACMG proceeded with release of the 2013 ACMG56 recommendations, which have, over time, gained broad acceptance. Similarly, we would advocate that the ACMG consider recommending the option of secondary findings in conjunction with multigene panels/exome slices/ anticipatory sequencing despite potential physician apprehension related to implementation. Finally, Dr. Biesecker raises the hypothetical construct in which a patient has suffered harm due to the “...lack of an opportunity to receive secondary findings.” This statement suggests that the offering of secondary findings represents a potential benefit, in the form of personalized preventive medicine, to patients who engage in this opportunity, with which we would agree. In fact, the impact of this benefit population-wide would be significantly increased if secondary findings were offered from multigene panels/exome slices/ anticipatory sequencing. Let’s consider a hypothetical case where in addition to ES, secondary findings are offered from multigene panels and exome slices classified as panels. According to insurance claim clearinghouse data, recent estimates indicate that clinical ES (as represented by Current Procedural Terminology [CPT] codes 81415, 81416) is ordered annually nationwide for over 1600 patients (this could represent up to 4800 patients if all were trios). The same insurance claim clearinghouse data indicate that the number of clinical multigene panels/exome slices ordered for hereditary breast and ovarian cancer (HBOC) and hereditary colon cancer (CRC) alone (as represented by CPT codes 81162, 81211 and codes 81435, 81436, respectively) is over 90,000 annually. This suggests the potential for a 50-fold increased magnitude of additional positive impact to patients’ preventive health care, through opportunistic screening of individuals, if

Misattributed parentage as an unanticipated finding during exome/genome sequencing: current clinical laboratory practices and an opportunity for standardization

PurposeClinical laboratories performing exome or genome sequencing (ES/GS) are familiar with the challenges associated with proper consenting for and reporting of medically actionable secondary findings based on recommendations from the American College of Medical Genetics and Genomics (ACMG). Misattributed parentage is another type of unanticipated finding a laboratory may encounter during family-based ES/GS; however, there are currently no professional recommendations related to the proper consenting for and reporting of misattributed parentage encountered during ES/GS.MethodsWe surveyed 10 clinical laboratories offering family-based ES/GS regarding their consent language, discovery, and reporting of misattributed parentage.ResultsMany laboratories have already developed their own practices/policies for these issues, which do not necessarily agree with those from other labs.ConclusionThere are several other possibilities besides true misattributed parentage that could result in similar laboratory findings, and laboratories often feel they lack sufficient information to make formal conclusions on a report regarding the true genetic relatedness of the submitted samples. However, understanding the genetic relatedness (or lack thereof) of the samples submitted for family-based ES/GS has medical relevance. Therefore, professional recommendations for the appropriate handling of suspected misattributed parentage encountered during ES/GS are needed to help standardize current clinical laboratory practices.

Underdiagnosis of Hereditary Breast and Ovarian Cancer in Medicare Patients: Genetic Testing Criteria Miss the Mark

BackgroundAn estimated 5–10% of breast and ovarian cancers are due to hereditary causes such as hereditary breast and ovarian cancer (HBOC) syndrome. Medicare, the third-party payer that covers 44 million patients in the United States, has implemented a set of clinical criteria to determine coverage for the testing of the BRCA1 and BRCA2 genes. These criteria, developed to identify carriers of BRCA1/2 variants, have not been evaluated in the panel testing era. This study investigated a series of Medicare patients undergoing genetic testing for HBOC to determine the efficacy of genetic testing criteria in identifying patients with hereditary risk.MethodsThis study retrospectively examined de-identified data from a consecutive series of Medicare patients undergoing genetic testing based on personal and family history of breast and gynecologic cancer. Ordering clinicians indicated whether patients did or did not meet established criteria for BRCA1/2 genetic testing. The genetic test results were compared between the group that met the criteria and the group that did not. Patients in families with known pathogenic (P) or likely pathogenic (LP) variants were excluded from the primary analysis.ResultsAmong 4196 unique Medicare patients, the rate of P/LP variants for the patients who met the criteria for genetic testing was 10.5%, and for those who did not, the rate was 9% (p = 0.26).ConclusionsThe results of this study indicate that a substantial number of Medicare patients with clinically actionable genetic variants are being missed by current testing criteria and suggest the need for significant expansion and simplification of the testing criteria for HBOC.

MG-115 Colorectal cancer patients with BRCA1 and BRCA2 mutations: Preparing for unexpected results

Background A new paradigm in genetic panel testing for hereditary colorectal cancer (CRC) has emerged. CRC association with BRCA1/2 has been suggested, but guidelines do not include CRC in Hereditary Breast and Ovarian Cancer syndrome (HBOC). Objectives We describe 6 patients with CRC and germline mutations in BRCA1 or BRCA2, detected by multi-gene panels, to highlight actionable findings that would have been missed by traditional CRC genetic testing. Design/method 585 patients with a personal history of CRC and/or gastrointestinal (GI) polyps were tested. Variants were identified using an NGS-based cancer gene panel with CRC genes and BRCA1/2. Germline variants were classified using a point-based system based on ACMG guidelines. Clinical histories from test request forms were de-identified for analysis. Results Hereditary cancer panel testing found Pathogenic (P) or Likely Pathogenic (LP) variants in 92 of 585 (15%) patients. Of the 92 mutation carriers, 69 (75%) had a P/LP variant in a CRC gene, while 6 (6%) had a P/LP variant in BRCA1/2. None of the patients with BRCA1/2 mutations reported Ashkenazi Jewish ancestry. The 4 male patients did not meet HBOC testing guidelines. Conclusions In this series, a substantial minority of P/LP variants were in non-canonical CRC genes. BRCA1/2 pathogenic variants’ prevalence in the general population is insufficiently elevated to account for these findings. More research is needed to link CRC and BRCA1/2, and clinicians need to prepare themselves and their patients to deal with unexpected, potentially actionable.