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Comparison of open-access databases for clinical variant interpretation in cancer: a case study of MDS/AML

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: We give an overview of existing databases and evaluate their benefit in practical appl...

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Main Authors: Banck, Henrik (Author) , Dugas, Martin (Author) , Müller-Tidow, Carsten (Author) , Sandmann, Sarah (Author)
Format: Article (Journal)
Language:English
Published: February 19, 2021
In: Cancer genomics & proteomics
Year: 2021, Volume: 18, Issue: 2, Pages: 157-166
ISSN:1790-6245
DOI:10.21873/cgp.20250
Online Access:Verlag, lizenzpflichtig, Volltext: https://doi.org/10.21873/cgp.20250
Verlag, lizenzpflichtig, Volltext: https://cgp.iiarjournals.org/content/18/2/157
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Author Notes:Henrik Banck, Martin Dugas, Carsten Müller-Tidow and Sarah Sandmann

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520 |a 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: 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: 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: 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. 
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