A missing link in the bench-to-bedside paradigm: engaging regulatory stakeholders in clinical genomics research

Optimising clinical care through CDH1-specific germline variant curation: improvement of clinical assertions and updated curation guidelines

BACKGROUND

Germline pathogenic variants in CDH1 are associated with increased risk of diffuse gastric cancer and lobular breast cancer. Risk reduction strategies include consideration of prophylactic surgery, thereby making accurate interpretation of germline CDH1 variants critical for physicians deciding on these procedures. The Clinical Genome Resource (ClinGen) CDH1 Variant Curation Expert Panel (VCEP) developed specifications for CDH1 variant curation with a goal to resolve variants of uncertain significance (VUS) and with ClinVar conflicting interpretations and continues to update these specifications.

METHODS

CDH1 variant classification specifications were modified based on updated genetic testing clinical criteria, new recommendations from ClinGen and expert knowledge from ongoing CDH1 variant curations. The CDH1 VCEP reviewed 273 variants using updated CDH1 specifications and incorporated published and unpublished data provided by diagnostic laboratories.

RESULTS

Updated CDH1-specific interpretation guidelines include 11 major modifications since the initial specifications from 2018. Using the refined guidelines, 97% (36 of 37) of variants with ClinVar conflicting interpretations were resolved to benign, likely benign, likely pathogenic or pathogenic, and 35% (15 of 43) of VUS were resolved to benign or likely benign. Overall, 88% (239 of 273) of curated variants had non-VUS classifications. To date, variants classified as pathogenic are either nonsense, frameshift, splicing, or affecting the translation initiation codon, and the only missense variants classified as pathogenic or likely pathogenic have been shown to affect splicing.

CONCLUSIONS

The development and evolution of CDH1-specific criteria by the expert panel resulted in decreased uncertain and conflicting interpretations of variants in this clinically actionable gene, which can ultimately lead to more effective clinical management recommendations.

Queensland Genomics: an adaptive approach for integrating genomics into a public healthcare system

The establishment of genomics in health care systems has been occurring for the past decade. It is recognised that implementing genomics within a health service is challenging without a system-wide approach. Globally, as clinical genomics implementation programs have matured there is a growing body of information around program design and outcomes. Program structures vary depending on local ecosystems including the health system, politics and funding availability, however, lessons from other programs are important to the design of programs in different jurisdictions. Here we describe an adaptive approach to the implementation of genomics into a publicly funded health care system servicing a population of 5.1 million people. The adaptive approach enabled flexibility to facilitate substantial changes during the program in response to learnings and external factors. We report the benefits and challenges experienced by the program, particularly in relation to the engagement of people and services, and the design of both individual projects and the program as a whole.

A case for expert curation: an overview of cancer curation in the Clinical Genome Resource (ClinGen)

We describe the Clinical Genome Resource (ClinGen) cancer-related curation activities and the importance of curation to the evolving state of variant interpretation in a clinical context for both pediatric and adult cancer patients. We highlight specific examples from the CDH1 and PTEN Variant Curation Expert Panels (VCEPs) of the FDA-recognized process by which ClinGen VCEPs specify the American College of Medical Genetics and Genomics/Association of Molecular Pathology evidence code to develop variant classifications. We also review gene curations performed within the Hereditary Cancer Clinical Domain. We describe the parallel efforts for curation of somatic cancer variants from the Somatic Cancer Working Group. The ClinGen Germline/Somatic Committee is working to improve incorporation of both hereditary and somatic variant data to aid clinical interpretation. These ClinGen efforts rely on broad data sharing and detailed phenotypic and molecular information from published case studies to provide expert-curated variant interpretation to the cancer community.