Comparison of Open-access Databases for Clinical Variant Interpretation in Cancer: A Case Study of MDS/AML.
Variant interpretation
mutation databases
somatic variants in cancer
Journal
Cancer genomics & proteomics
ISSN: 1790-6245
Titre abrégé: Cancer Genomics Proteomics
Pays: Greece
ID NLM: 101188791
Informations de publication
Date de publication:
Historique:
received:
29
12
2020
revised:
23
01
2021
accepted:
29
01
2021
entrez:
20
2
2021
pubmed:
21
2
2021
medline:
29
9
2021
Statut:
ppublish
Résumé
Recently, guidelines for variant interpretation in cancer have been established. However, these guidelines do not mention which databases are most suited to performing this task. We give an overview of existing databases and evaluate their benefit in practical application. We compared three meta-databases and 12 databases for a dataset of patients with myelodysplastic syndrome or acute myeloid leukemia. Clinical implications were found for 13% of all variants. One-third of variants with therapeutic implications were uniquely contained in one database. The VICC meta-database was the most extensive source of information, featuring 92% of variants with a drug association. However, a comparison of meta-databases and original sources indicated that some variants are missing in those meta-databases. Public databases provide decision support for interpreting variants but there is still need for manual curation. Meta-databases facilitate the use of multiple resources but should be interpreted with caution.
Sections du résumé
BACKGROUND
BACKGROUND
Recently, guidelines for variant interpretation in cancer have been established. However, these guidelines do not mention which databases are most suited to performing this task.
MATERIALS AND METHODS
METHODS
We give an overview of existing databases and evaluate their benefit in practical application. We compared three meta-databases and 12 databases for a dataset of patients with myelodysplastic syndrome or acute myeloid leukemia.
RESULTS
RESULTS
Clinical implications were found for 13% of all variants. One-third of variants with therapeutic implications were uniquely contained in one database. The VICC meta-database was the most extensive source of information, featuring 92% of variants with a drug association. However, a comparison of meta-databases and original sources indicated that some variants are missing in those meta-databases.
CONCLUSION
CONCLUSIONS
Public databases provide decision support for interpreting variants but there is still need for manual curation. Meta-databases facilitate the use of multiple resources but should be interpreted with caution.
Identifiants
pubmed: 33608312
pii: 18/2/157
doi: 10.21873/cgp.20250
pmc: PMC7943210
doi:
Types de publication
Case Reports
Journal Article
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
157-166Informations de copyright
Copyright© 2021, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.
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