A one-stop shop for clinical interpretation of variants in oncology
The Swiss Variant Interpretation Platform for Oncology (SVIP-O) aims at providing a centralized, joint, and curated database for clinical somatic variants coming from Swiss hospitals and related institutions (e.g. pathology institutes).
An infrastructure development project of SPHN and BioMedIT
Clinicians in oncology and hemato-oncology are daily confronted with the challenge of interpreting genetic variants using an increasing number of public knowledge sources, which provide information of heterogeneous quality.
Swiss hospitals and SIB have decided to join forces to develop a common infrastructure allowing hospitals to share and unify the clinical interpretation of the genetic variants identified in their patients all over Switzerland.
This consensus annotation of variants will also be accessible to researchers, as having access to variants detected in patients with well-characterized and clinically-validated phenotypic information is critical to better understand disease aetiology and reliably identify new drug targets.
The SVIP project was launched in 2017, with the support of the Swiss Personalized Health Network (SPHN, www.sphn.ch) and BioMedIT initiatives.
The principle of the project is that hospitals feed the system with all variants they identify in their patients when using NGS for diagnosis. For variants already annotated in the database, annotations will be merged, and discrepancies will be solved by a clinical panel composed of experts from the partnering hospitals. For variants without previous annotation, manual curation supported by bioinformatics tools will provide a draft annotation and likely clinical interpretation, which will also be validated by the clinical expert panel.
Shared between all partner hospitals with single point of entry
To avoid unnecessary manual labor and increase efficiency
By manual curation (SIB) and clinical experts consensus (hospitals)
Approved by all partners, ensuring consistent assessment of pathogenicity
To solve conflicting annotations between labs when new variants are identified
In case pathogenicity changes over time
SVIP will incorporate variant information from other similar projects such as ClinVar, ClinGen, CIViC, OncoKB, and PMKB, to facilitate the prioritization of variants by molecular pathologists, to become the Swiss one-stop shop for the interpretation of somatic variants, enabling faster and more robust prioritisation.
The consensus annotation of variants will also be accessible to researchers, as having access to variants detected in patients with well-characterized and clinically-validated phenotypic information is critical to better understand disease aetiology and reliably identify new drug targets.
A national network of medical institutions committed to a joint goal
This program has been made possible thanks to the commitment and strong support of Swiss hospitals, institutes and medical societies who have agreed to share their know-how and expertise for the benefit of the patients.
Valérie Barbié is head of Clinical Bioinformatics at SIB, which objectives are to harmonize bioinformatics diagnosis practices for omics data across Swiss hospitals. The group also collaborates with Swiss hospitals or institutions to jointly develop tailored diagnosis pipelines in NGS. She is co-leading the SIB Somatic Mutation Calling WG.
Daniel Stekhoven is head of the Clinical Bioinformatics Unit at NEXUS – a biomedical core facility of ETH Zurich aiming at translating computational methods and tools to clinical application. CBU is among the first to use comprehensive NGS in cancer diagnostics. He is group leader of SIB and co-leader of the Somatic Mutation Calling WG.
Patrick Ruch is professor and chairman of the Information Sciences department of the University of Applied Sciences Western Switzerland (HES-SO) in Geneva. He is also leader of the SIB Text Mining group, which maintains text analytics services to support the curation of SIB databases such as Swiss-Prot and neXtprot.
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