Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC)

PURPOSE

Several professional societies have published guidelines for the clinical interpretation of somatic variants, which specifically address diagnostic, prognostic, and therapeutic implications. Although these guidelines for the clinical interpretation of variants include data types that may be used to determine the oncogenicity of a variant (eg, population frequency, functional, and in silico data or somatic frequency), they do not provide a direct, systematic, and comprehensive set of standards and rules to classify the oncogenicity of a somatic variant. This insufficient guidance leads to inconsistent classification of rare somatic variants in cancer, generates variability in their clinical interpretation, and, importantly, affects patient care. Therefore, it is essential to address this unmet need.

METHODS

Clinical Genome Resource (ClinGen) Somatic Cancer Clinical Domain Working Group and ClinGen Germline/Somatic Variant Subcommittee, the Cancer Genomics Consortium, and the Variant Interpretation for Cancer Consortium used a consensus approach to develop a standard operating procedure (SOP) for the classification of oncogenicity of somatic variants.

RESULTS

This comprehensive SOP has been developed to improve consistency in somatic variant classification and has been validated on 94 somatic variants in 10 common cancer-related genes.

CONCLUSION

The comprehensive SOP is now available for classification of oncogenicity of somatic variants.

Theory utilization in current communication of cancer genetic testing research: Identified gaps and opportunities

BACKGROUND

Effective communication of cancer-related genetic and genomic testing (CGT) with patients and the public is paramount to transforming and managing cancer prevention, detection, and care. Behavioral and social science theories could improve communication effectiveness and, in turn, health outcomes.

METHODS

In this study, we characterized the use of theory in recent research on communication about CGT from 2010 to 2017.

RESULTS

Of 513 empirical papers focusing on communication about CGT, only 119 (23%) utilized any theory in the study design. Behavior change and health psychology/cognitive representation theories (24.2% and 21.9%, respectively) were the most commonly used with minimal use of communication theories (3%). Theories were primarily used to guide hypotheses or research question development (73.9%), and for selecting measures or codes (68.9%). Approximately half of the papers (48.3%) related their study findings to the referenced theory. Fewer papers (14.3%) discussed implications of the findings for the theory.

CONCLUSIONS

While theories are being utilized to inform study design, few discuss their results in the context of theoretical implications and thus decrease potential generalizability. Greater use of theory could help scholars to identify and develop theories suited to this clinical context and inform our understanding of related communication processes more broadly.

Inequities in multi-gene hereditary cancer testing: lower diagnostic yield and higher VUS rate in individuals who identify as Hispanic, African or Asian and Pacific Islander as compared to European

The identification of germline pathogenic/likely pathogenic (P/LP) variants in cancer predisposition genes can guide treatment and management decisions for the individual being tested and potentially at-risk relatives. Prior studies have raised concerns of racial/ethnic disparities in the detection rates of P/LP variants and variants of uncertain significance (VUSs). In 2018, Color Genomics™, a commercial laboratory, made de-identified, aggregate genetic and clinical information from 50,000 individuals who completed testing for 30 cancer predisposition genes publicly available. It is the largest publicly available database of its kind from a single laboratory. An analysis of individuals from this database with a negative personal history of cancer that identify as European (n = 31,920), Hispanic (n = 1700), African (n = 462) or Asian and Pacific Islander (n = 2602), demonstrated that the VUS rate in the hereditary breast and ovarian cancer syndrome and Lynch syndrome genes was higher for all non-European groups as compared to the European group; Hispanic (7.1% vs. 5.8%; p = 0.029), African (12.3% vs. 5.8%; p < 0.001), Asian and Pacific Islander (13.1% vs. 5.8%; p < 0.001). In the other cancer genes (OCGs), the P/LP rate was lower; Hispanic (5.1% vs. 7.6%; p < 0.001), African (2.4% vs. 7.6%; p < 0.001), and Asian and Pacific Islander (4.3% vs. 7.6%; p < 0.001). The VUS rate was also higher in the OCGs; Hispanic (16.2% vs. 12.2%; p < 0.001), African (21.6% vs. 12.2%; p < 0.001), Asian and Pacific Islander (24.4% vs. 12.2%; p < 0.001). Our study emphasizes the reality of disparities in the results of cancer genetic testing and highlights factors that propagate these inequities.

Development of a Tool to Guide Parents Carrying a BRCA1/2 Mutation Share Genetic Results with Underage Children

Although most parents carrying a BRCA1/2 genetic mutation share their test result with their underage children, they report needing support to decide if, when, and how to share risk information and what reactions to expect from their children. We developed a tool to guide parents carrying a BRCA1/2 mutation share their genetic result with underage children. Here, we report on the development of this tool using a qualitative methodology. A tool prototype was developed based on the International Patient Decision Aids Standards Collaboration framework. Content was assessed using feedback from focus groups, individual interviews, and a 12-item reading grid. Participants were nine BRCA1/2 mutation carriers with underage children and three cancer genetics health professionals. Thematic content analysis was conducted on interview transcripts. The tool was developed using an iterative process until saturation of data. An independent advisory committee was involved in all steps of tool development until reaching consensus. Rather than a decision aid per se (to communicate or not), the parents wanted a more comprehensive tool to help them communicate genetic test result to their children. To meet parents' needs, a communication guidance booklet was developed, setting out the pros and cons of communication, steps to prepare sharing the test result, communication tips, and parents' testimonies. This communication tool responds to a significant unmet need faced by parents carrying a genetic predisposition to cancer. Future studies are needed to assess how the information from the parent's genetic test result impacts the child's development, health behaviors, and relationship with the parent.

Cancer Genetic Counseling and Testing in an Era of Rapid Change

The impacts of the Association for Molecular Pathology vs. Myriad Supreme Court decision regarding patenting DNA segments and multi-gene testing on cancer genetic counseling practice have not been well described. We aimed to assess genetic counselors' perceptions of how their genetic testing-related practices for hereditary breast and/or ovarian cancer (HBOC) changed after these events. One-hundred fifty-two genetic counselors from the National Society of Genetic Counselors Cancer Special Interest Group completed an anonymous, online, mixed-methods survey in November 2013. The survey presented four hypothetical patients and asked about changes in testing practice. Across the vignettes, a majority of participants reported specific changes in testing decisions following Association for Molecular Pathology vs. Myriad and availability of multi-gene testing. Ninety-three percent of participants reported changing the types of first- and second-line tests they order for HBOC; the degree of change varied geographically. Qualitative analysis indicated that some counselors have altered the counseling session content, trading depth of information for breadth and spending more time counseling about uncertainty. This study shows that cancer genetic counselors are adapting quickly to genetic testing changes, but with wide variability. Findings suggest future research to elucidate clinicians' and patients' preferences for guidance on the clinical implementation of next-generation sequencing.