Variomes: a high recall search engine to support the curation of genomic variants.
Bioinformatics
; 38(9): 2595-2601, 2022 04 28.
Article
em En
| MEDLINE
| ID: mdl-35274687
ABSTRACT
MOTIVATION Identification and interpretation of clinically actionable variants is a critical bottleneck. Searching for evidence in the literature is mandatory according to ASCO/AMP/CAP practice guidelines; however, it is both labor-intensive and error-prone. We developed a system to perform triage of publications relevant to support an evidence-based decision. The system is also able to prioritize variants. Our system searches within pre-annotated collections such as MEDLINE and PubMed Central. RESULTS:
We assess the search effectiveness of the system using three different experimental settings literature triage; variant prioritization and comparison of Variomes with LitVar. Almost two-thirds of the publications returned in the top-5 are relevant for clinical decision-support. Our approach enabled identifying 81.8% of clinically actionable variants in the top-3. Variomes retrieves on average +21.3% more articles than LitVar and returns the same number of results or more results than LitVar for 90% of the queries when tested on a set of 803 queries; thus, establishing a new baseline for searching the literature about variants. AVAILABILITY AND IMPLEMENTATION Variomes is publicly available at https//candy.hesge.ch/Variomes. Source code is freely available at https//github.com/variomes/sibtm-variomes. SynVar is publicly available at https//goldorak.hesge.ch/synvar. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Genômica
/
Ferramenta de Busca
Tipo de estudo:
Guideline
/
Prognostic_studies
Idioma:
En
Revista:
Bioinformatics
Ano de publicação:
2022
Tipo de documento:
Article