CIViC partners are generally those organizations and individuals who are engaged in reciprocal collaboration that leads to substantial improvements of the CIViC codebase, application and/or curated content. CIViC is actively working with these organizations to advance our mission of improving clinical interpretation of variants for cancer. In some cases specific feature developments or research questions may be supported by co-funded grants.
ClinGen Somatic Working Group¶
The mission of the ClinGen Cancer Somatic Workgroup (SWG) is to facilitate the development of data curation interfaces and standards for interpretation of somatic changes and their clinical actionability in order to enhance the usability, dissemination and implementation of cancer somatic changes in the ClinGen resource to improve healthcare. The Cancer Somatic Workgroup aims to collaborate with expert groups to develop processes that support accurate determination of clinical relevance of somatic changes for use by physicians, clinical laboratories, researchers, and guideline-developing groups. The Cancer Somatic Workgroup, under the leadership of Dr Subha Madhavan and Dr Shashikant Kulkarni, has adopted use of the CIViC curation platform for several of its task teams and Variant Curation Expert Panels (VCEP; in development). CIViC is working closely with SWG experts to develop their VCEP curation process and automate submission of somatic variant interpretations to ClinVar.
Personalized Oncogenomics at BC Cancer Agency¶
The BC Cancer Agency’s Personalized Onco-Genomics (POG) program is a clinical research initiative that is embedding genomic sequencing into real-time treatment planning for BC patients with incurable cancers. Cancer is a complex biological process. The POG program categorizes cancers according to their site of origin (e.g. lung, breast, liver, colon) as each one is different, but even within these groupings there are subtypes with differences in response to treatment and overall behaviour. The POG program is a collaborative research study including many BCCA oncologists, pathologists and other clinicians along with the Genome Sciences Centre (GSC), which aims to decode the genome – the entire DNA and RNA inside the cell – of each patient’s cancer, to understand what is enabling it to grow. Using this genomic data in clinical decision-making should allow the development of treatment strategies to block its growth, identify clinical trials that the patient may benefit from and potentially identify less toxic and more effective therapeutic options. The POG program, under the leadership of Dr Steven Jones and Dr Janessa Laskin, have partnered with CIViC to study the impact of including CIViC interpretations in our clinical decision making.
Variant Interpretation for Cancer Consortium¶
The field of precision medicine aspires to a future in which a cancer patient’s molecular information can be used to inform diagnosis, prognosis and treatment options most likely to benefit that individual patient. Many groups have created knowledgebases to annotate cancer genomic mutations associated with evidence of pathogenicity or relevant treatment options. However, clinicians and researchers are unable to fully utilize the accumulated knowledge derived from such efforts. Integration of the available knowledge is currently infeasible because each group (often redundantly) curates their own knowledgebase without adherence to any interoperability standards. Therefore, there is a clear need to standardize and coordinate clinical-genomics curation efforts, and create a public community resource able to query the aggregated information. The Variant Interpretation for Cancer Consortium (VICC) was founded to bring together the leading institutions that are independently developing comprehensive cancer variant interpretation databases. CIViC is a founding member of the VICC.
Alissa Clinical Informatics Platform at Agilent Technologies¶
To widen the reach and visibility of CIViC, and to enable its use as a valuable resource to the community of diagnostic labs, a partnership was set up with Agilent Technologies. The CIViC database has been integrated into their Alissa Clinical Informatics Platform. This cloud-based, clinical-grade software platform is geared towards routine diagnostic labs and allows molecular pathologists to automate their variant filtration and classification workflow, and draft lab reports. As of version 5.0 of Bench Lab, labs can automate their variant assessment protocol to assess the molecular profile of a sample and automatically flag presence of prognostic, diagnostic and therapeutic evidence in the CIViC database. Users are able to restrict the CIViC search to relevant tumor and tissue type. Secondly, the variant review tools in the platform now allow users to review the CIViC content and assess and select relevant portions for inclusion into draft lab reports. Discussions are underway to support the submission of new interpretation, developed by Alissa users, back to the CIViC knowledgebase.
VHL Variant Curation Expert Panel¶
The ClinGen VHL Variant Curation Expert Panel, under the leadership of Dr Raymond Kim, is an Expert Panel for VHL as part of the ClinGen Clinical Domain Working Groups. This panel consists of expert clinicians, clinical laboratory diagnosticians, and researchers working to implement VHL specific standards and protocols for assessing VHL variant pathogenicity. CIViC is working with the VHL Expert panel to develop these rules, catalogue published evidence for VHL variant pathogenicity, and submit exemplar variants to ClinVar for use in the ClinGen curation process.