Variomes

Variomes

Introduction

Precision oncology relies on the use of treatments targeting specific genetic variants. However, identifying clinically actionable variants as well as relevant information likely to be used to treat a patient with a given cancer is a labor-intensive task, which includes searching the literature for a large set of variants. The lack of universally adopted standard nomenclature for variants requires the development of variant-specific literature search engines. We develop a system to perform triage of publications relevant to support an evidence-based decision. Together with providing a ranked list of articles for a given variant, the system is also able to prioritize variants, as found in a Variant Calling Format, assuming that the clinical actionability of a genetic variant is correlated with the volume of literature published about the variant. Our system ¹ searches within four pre-annotated document collections: MEDLINE abstracts, PubMed Central full-text articles, supplementary materials associated with publications, and ClinicalTrials.gov clinical trials. A variant synonym generator is used to increase the comprehensiveness of the set of retrieved documents. We then apply different strategies to rank the publications.

API

See the dedicated page