Lost in translation: returning germline genetic results in genome-scale cancer research

Background The return of research results (RoR) remains a complex and well-debated issue. Despite the debate, actual data related to the experience of giving individual results back, and the impact these results may have on clinical care and health outcomes, is sorely lacking. Through the work of the Australian Pancreatic Cancer Genome Initiative (APGI) we: (1) delineate the pathway back to the patient where actionable research data were identified; and (2) report the clinical utilisation of individual results returned. Using this experience, we discuss barriers and opportunities associated with a comprehensive process of RoR in large-scale genomic research that may be useful for others developing their own policies. Methods We performed whole-genome (n = 184) and exome (n = 208) sequencing of matched tumour-normal DNA pairs from 392 patients with sporadic pancreatic cancer (PC) as part of the APGI. We identified pathogenic germline mutations in candidate genes (n = 130) with established predisposition to PC or medium–high penetrance genes with well-defined cancer associated syndromes or phenotypes. Variants from candidate genes were annotated and classified according to international guidelines. Variants were considered actionable if clinical utility was established, with regard to prevention, diagnosis, prognostication and/or therapy. Results A total of 48,904 germline variants were identified, with 2356 unique variants undergoing annotation and in silico classification. Twenty cases were deemed actionable and were returned via previously described RoR framework, representing an actionable finding rate of 5.1%. Overall, 1.78% of our cohort experienced clinical benefit from RoR. Conclusion Returning research results within the context of large-scale genomics research is a labour-intensive, highly variable, complex operation. Results that warrant action are not infrequent, but the prevalence of those who experience a clinical difference as a result of returning individual results is currently low. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0430-4) contains supplementary material, which is available to authorized users.


Variant Details
Various nomenclature (genomic coordinates, nucleotide and amino acid level); Consequence (e.g. frameshift, missense, splice site etc.); Current classification (Class 5--1); Sequencing depth (whole genome, exome, panel, targeted); Previous reports and classification in mutation databases (e.g. ClinVar, HGMD Professional, InSiGHT, LOVD, BIC); Links to primary and supporting literature 3. Proposed Actions Additional genomic data that may be useful for further decision-making (e.g. somatic data or functional evidence); Accredited laboratory details and sample specifications for external validation; Scientific or clinical contacts for additional expert advice 4. Summary Date of meeting; Final consensus variant classification; Justification of no RoR; Action plan if RoR.

Outcome
Progress and outcomes of each case are chronologically documented here.

Molecular MDT Meeting
The Molecular MDT working group includes research and clinical personnel with particular expertise, such as genetic pathologists, medical oncologists, pathologists, bioinformaticians and genetic counsellors. The group meets in person on a monthly basis for 1--2 hours, with a maximum of 3 cases discussed each meeting. The Case Reports (Sections 1--3) are circulated one week prior, to provide the opportunity for familiarization and independent literature review as allocated.
The minutes for each case are documented in Section 4 of the Case Report. The final variant classification is decided upon once all evidence is presented. The clinical significance and personal utility of the variant is assessed in the unique context of the participant. If the consensus recommends returning the result, an action plan is outlined including independent validation and recommended strategy for result communication (i.e. directly to clinician, participant or next of kin). If no further action is deemed, this rationale is clearly stated in Section 4 of the Case Report. Updates of cases with results to return are provided in subsequent Molecular MDT meetings and recorded in Section 5. Case Reports are attached to the participant's research file.

APPENDICES Appendix 1 -Variant Classification Schema
Variant ranking Initial bioinformatic classification

Final classification Class 5 = pathogenic
Genomic coordinates fed to VEP on ENSEMBL 75: "splice_donor_variant" "splice_acceptor_variant" "stop_gained" "frameshift_variant" Transcript abrogating variants (nonsense, frameshift, consensus splice site) with previous reports of pathogenicity Missense variants with functional characterisation demonstrating a functional effect relevant to the disease phenotype and multiple independent reports of pathogenicity. Class 4 = likely pathogenic "stop_lost" "initiator_codon_variant" "inframe_insertion" "inframe_deletion" "missense variant" and 1000 genomes project combined MAF < 0.01 and VEST3 call deleterious Previously unreported variants predicted to lead to protein truncation (nonsense, frameshift, consensus splice site, initiator codon, non-stop). Variants predicted to abrogate the transcript but occurring in the last exon were called class 3 unless a functional effect or pathogenicity had been previously demonstrated.
Missense variants with supporting functional evidence, but lacking multiple independent reports of pathogenicity.

Class 3 = uncertain significance
MAF < 0.01 and "splice_region_variant" "incomplete_terminal_codon_vari ant" "missense variant" and 1000 genomes project combined MAF < 0.01 and VEST3 call not available Class 3 variants all have a minor allele frequency <0.01 and include in-frame indels, splice region variants and missense variants with predicted deleterious consequence according to VEST3 or conflicting reports of pathogenicity.

Class 2 = probable nonpathogenic
1000 genomes combined MAF > 0.01 and/or "missense variant" and VEST3 call tolerated Class 1 and class 2 variants are comprised of mmissense variants which either have a MAF < 0.01 but are predicted to be benign or a MAF ≥0.01, synonymous variants and non-coding variants (intronic, UTR, down-and up-stream).