Scott M. Weissman

Pathogenic and likely pathogenic variant prevalence among the first 10,000 patients referred for next-generation cancer panel testing

Purpose:Germ-line testing for panels of cancer genes using next-generation sequencing is becoming more common in clinical care. We report our experience as a clinical laboratory testing both well-established, high-risk cancer genes (e.g., BRCA1/2, MLH1, MSH2) as well as more recently identified cancer genes (e.g., PALB2, BRIP1), many of which have increased but less well-defined penetrance.Methods:Clinical genetic testing was performed on over 10,000 consecutive cases referred for evaluation of germ-line cancer genes, and results were analyzed for frequency of pathogenic or likely pathogenic variants, and were stratified by testing panel, gene, and clinical history.Results:Overall, a molecular diagnosis was made in 9.0% of patients tested, with the highest yield in the Lynch syndrome/colorectal cancer panel. In patients with breast, ovarian, or colon/stomach cancer, positive yields were 9.7, 13.4, and 14.8%, respectively. Approximately half of the pathogenic variants identified in patients with breast or ovarian cancer were in genes other than BRCA1/2.Conclusion:The high frequency of positive results in a wide range of cancer genes, including those of high penetrance and with clinical care guidelines, underscores both the genetic heterogeneity of hereditary cancer and the usefulness of multigene panels over genetic tests of one or two genes.Genet Med 18 8, 823–832.

Genetic Counseling Considerations in the Evaluation of Families for Lynch Syndrome—A Review

Lynch syndrome is the most common hereditary colorectal cancer syndrome and the most common cause of hereditary endometrial cancer. Identifying and evaluating families for Lynch syndrome is increasing in complexity due to the recognition that: family history-based clinical criteria lack sensitivity and specificity; genetic testing for Lynch syndrome continues to evolve as understanding of the molecular mechanisms underlying it evolves; and the Lynch syndrome phenotype encompasses multiple organ systems and demonstrates overlap with other hereditary cancer syndromes. This document is a summary of considerations when evaluating individuals and families for Lynch syndrome, including information on cancer risks, diagnostic criteria, tumor and genetic testing strategies, and the management of individuals with this condition.

Diagnostic Exome Sequencing Identifies a Novel Gene, EMILIN1, Associated with Autosomal‐Dominant Hereditary Connective Tissue Disease

Heritable connective tissue diseases are a highly heterogeneous family of over 200 disorders that affect the extracellular matrix. While the genetic basis of several disorders is established, the etiology has not been discovered for a large portion of patients, likely due to rare yet undiscovered disease genes. By performing trio‐exome sequencing of a 55‐year‐old male proband presenting with multiple symptoms indicative of a connective disorder, we identified a heterozygous missense alteration in exon 1 of the Elastin Microfibril Interfacer 1 (EMILIN1) gene, c.64G>A (p.A22T). The proband presented with ascending and descending aortic aneurysms, bilateral lower leg and foot sensorimotor peripheral neuropathy, arthropathy, and increased skin elasticity. Sanger sequencing confirmed that the EMILIN1 alteration, which maps around the signal peptide cleavage site, segregated with disease in the affected proband, mother, and son. The impaired secretion of EMILIN‐1 in cells transfected with the mutant p.A22T coincided with abnormal protein accumulation within the endoplasmic reticulum. In skin biopsy of the proband, we detected less EMILIN‐1 with disorganized and abnormal coarse fibrils, aggregated deposits underneath the epidermis basal lamina, and dermal cells apoptosis. These findings collectively suggest that EMILIN1 may represent a new disease gene associated with an autosomal‐dominant connective tissue disorder.

Managing hereditary gastrointestinal cancer syndromes: the partnership between genetic counselors and gastroenterologists.

A standard of care for the recognition and management of patients and families with hereditary gastrointestinal cancer syndromes is emerging, and both gastroenterologists and genetic counselors have an important role. This Review considers these roles and outlines the partnership needed between gastroenterologists and genetic counselors. The role of the gastroenterologist involves careful sampling of polyps and tumors, and requires a basic working knowledge of the features of hereditary gastrointestinal cancer syndromes. The role of the genetic counselor is to gather and synthesize family history and pathology information, formulate a genetic differential diagnosis, determine a genetic testing strategy, guide medical management and help patients communicate information to their relatives. Managing the complex logistics of testing the best candidate in the family, facilitating informed consent, outlining costs to patients and interpreting test results are also responsibilities assumed by genetic counselors. In addition, genetic counselors help physicians meet their ethical and medicolegal obligations with respect to patient management and family communication. Referral schemata for patients with polyposis and nonpolyposis features are presented in this Review, along with comprehensive tables that outline the features of well-known and rare syndromes that heighten the risk of gastrointestinal malignancy.

Code of Ethics of the National Society of Genetic Counselors: Explication of Revisions

The Code of Ethics (COE) of the National Society of Genetic Counselors (NSGC) was adopted in 1992. In 2004, the NSGC leadership appointed the Code of Ethics Work Group (COEWG) to consider revisions to the NSGC COE based on advice from the NSGC legal counsel, and to consider additional changes given growth in the scope of genetic counseling practice since the adoption of the original COE. After input from the NSGC membership, changes to the COE addressing the recommendations of the NSGC legal counsel were approved in December 2004. The COEWG then reviewed ethical codes and codes of professional conduct from 22 professional organizations, deemed to have similar goals and philosophies to the NSGC, searching for themes that encompassed genetic counseling practice that might not yet be addressed in the NSGC COE. Additional revisions to the COE were proposed, and after feedback from the NSGC membership, the revised COE was approved in January 2006 by majority vote of full members of the NSGC. The explications for the 2004 and 2006 revisions are presented.

FDA Approval of PARP Inhibitors and the Impact on Genetic Counseling and Genetic Testing Practices

In December 2014, the FDA approved olaparib, a poly(ADP-ribose) polymerase inhibitor (PARPi) for ovarian cancer patients who have failed three or more lines of chemotherapy and have a germline BRCA1/2 mutation identified through a companion diagnostic test (BRACAnalysis CDx™ (CDx™)) offered exclusively by Myriad Genetic Laboratories. This study explored the impact of PARPi/CDx™ on genetic counselors’ (GCs) counseling and testing practices. One hundred twenty three GCs responded to an online survey regarding pre- and post-FDA approval referral patterns, testing strategies/influences, and anecdotal experiences with insurance coverage of PARPi for BRCA1/2 positive patients through a non-CDx™ platform. Following PARPi approval, 40% of respondents reported an increase in overall referrals of ovarian cancer patients and 20% had an increase in post-test counseling only referrals. The majority (61.9%) of respondents reported no change in genetic testing strategy, and there was no change in factors influencing choice of testing laboratory. Nearly all (98.1%) respondents who had experience with insurance covering PARPi indicated approval with mutations identified via non-CDx™ testing. Respondents indicated an increase in referral volume following FDA approval of PARPi/CDx™, but did not report changes in testing practices. Respondents were not aware of PARPi insurance coverage denial in the absence of CDx™.

Evaluation of laboratory perspectives on hereditary cancer panels

Genetic counseling and testing for hereditary cancer susceptibility is a rapidly evolving field and partly a result of next-generation sequencing (NGS) allowing analysis of multiple cancer susceptibility genes simultaneously. This qualitative study explored laboratory perspectives on hereditary cancer panels. Semi-structured interviews were conducted with representatives of clinical laboratories offering hereditary cancer panels via NGS. Several themes emerged from the responses pertaining to hereditary cancer panel development, the importance of communication of panel properties with patients, variant reporting policies, and the future of hereditary cancer gene testing. Clinical utility was discussed as primary consideration during panel development. In addition, while participants indicated gene and syndrome overlap prompted panel development in general, laboratories differed in their opinions of whether phenotypic overlap warrants offering pan-cancer panels only versus cancer specific panels. Participants stressed the importance of patients understanding implications of panel testing, including what is tested for and limitations of testing. While all laboratories discussed the limitations of a variant of uncertain significance result, they differed significantly in their reporting methods. This study provides healthcare providers information on the laboratory approach to panel testing, highlighting both commonalities and differences in laboratory approaches, and may allow providers to make more informed decisions when ordering hereditary cancer panels.

Identifying Women at High Risk of Breast Cancer: Understanding the Risk Models

Breast cancer risk assessment is increasingly becoming part of routine medical care. For women who have not been affected with breast cancer, identifying those that have personal and/or family history risk factors increasing their risk can benefit from increased screening with breast MRI, chemoprevention with tamoxifen, and/or prophylactic bilateral mastectomy, especially in women found to have a hereditary susceptibility to breast cancer [1–5]. Similarly, women who have already been affected with breast cancer can benefit in the same fashion for the same reasons with respect to developing an ipsi- or contralateral tumor, in addition to the potential of recognizing other sites in the body that may be at increased risk for tumor development (e.g., ovarian, gastric, endometrium). One integral tool in assessing breast cancer risk is the incorporation of one or more breast cancer risk models.