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A framework for automated gene selection in genomic applications

Abstract

Purpose

An efficient framework to identify disease-associated genes is needed to evaluate genomic data for both individuals with an unknown disease etiology and those undergoing genomic screening. Here, we propose a framework for gene selection used in genomic analyses, including applications limited to genes with strong or established evidence levels and applications including genes with less or emerging evidence of disease association.

Methods

We extracted genes with evidence for gene–disease association from the Human Gene Mutation Database, OMIM, and ClinVar to build a comprehensive gene list of 6,145 genes. Next, we applied stringent filters in conjunction with computationally curated evidence (DisGeNET) to create a restrictive list limited to 3,929 genes with stronger disease associations.

Results

When compared to manual gene curation efforts, including the Clinical Genome Resource, genes with strong or definitive disease associations are included in both gene lists at high percentages, while genes with limited evidence are largely removed. We further confirmed the utility of this approach in identifying pathogenic and likely pathogenic variants in 45 genomes.

Conclusion

Our approach efficiently creates highly sensitive gene lists for genomic applications, while remaining dynamic and updatable, enabling time savings in genomic applications.

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Fig. 1: Overview of comprehensive and restrictive gene list.
Fig. 2: Comprehensive and restrictive gene lists compared to the GDA classifications assigned by six resources.

Data availability

The gene lists and data used to develop the lists can be found at https://Broad.io/genelist.

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Acknowledgements

Funding support was partly provided by grant 5R01HL143295 from the National Institutes of Health/National Heart, Lung, and Blood Institute (L.L.d.l.V., C.L.B.Z., R.C.G., H.L.R., M.S.L.). The authors would like to thank the Gene Curation Coalition (GenCC) for generating curated content used in this project. GenCC’s curated content was obtained at www.thegencc.org (13 March 2021) and includes contributions from the following organizations: Invitae, Illumina, Myriad Women’s Health, Ambry Genetics, and TGMI/G2P.

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Authors

Contributions

Conceptualization: M.S.L., K.M,. C.A.A.T., H.M.S. Data curation: W.Y., L.H. Formal analysis: L.L.d.l.V., W.Y. Funding acquisition: R.C.G. Investigation: L.L.d.l.V., K.M. Methodology: M.S.L., H.L.R. Project administration: C.L.B.Z. Software: W.Y., L.H. Supervision: M.S.L. Visualization: W.Y., L.L.d.l.V. Writing—original draft: L.L.d.l.V., M.S.L. Writing—review and editing: H.L.R., C.L.B.Z., R.C.G., C.A.A.T., H.M.S. All authors reviewed and approved the final manuscript.

Corresponding author

Correspondence to M. S. Lebo.

Ethics declarations

Ethics declaration

This project has been reviewed and approved by the Mass General Brigham institutional review board (IRB). All individuals consented for clinical genomic screening and all individual data was de-identified.

Competing interests

M.S.L., L.L.d.l.V., and C.L.B.Z. report grants from the National Institutes of Health (NIH) during the conduct of the study. H.L.R. reports grants from NIH during the conduct of the study; she also reports personal fees from Genome Medical outside the submitted work. R.C.G. reports grants from NIH during the conduct of the study; he also reports personal fees from AIA, SavvySherpa, Verily, and Wamberg, all outside the submitted work. The other authors declare no competing interests.

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Lazo de la Vega, L., Yu, W., Machini, K. et al. A framework for automated gene selection in genomic applications. Genet Med (2021). https://doi.org/10.1038/s41436-021-01213-x

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