Improving the diagnostic yield of exome- sequencing by predicting gene–phenotype associations using large-scale gene expression analysis
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Abstract
The diagnostic yield of exome and genome sequencing remains low (8–70%), due to incomplete knowledge on the genes that cause disease. To improve this, we use RNA-seq data from 31,499 samples to predict which genes cause specific disease phenotypes, and develop GeneNetwork Assisted Diagnostic Optimization (GADO). We show that this unbiased method, which does not rely upon specific knowledge on individual genes, is effective in both identifying previously unknown disease gene associations, and flagging genes that have previously been incorrectly implicated in disease. GADO can be run on www.genenetwork.nl by supplying HPO-terms and a list of genes that contain candidate variants. Finally, applying GADO to a cohort of 61 patients for whom exome-sequencing analysis had not resulted in a genetic diagnosis, yields likely causative genes for ten cases.
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Novel metrics based on gene co-regulation networks can predict whether genes function within a disease-relevant pathway.
“Furthermore, novel metrics based on gene co-regulation networks can predict whether genes function within a disease-relevant pathway33.”
From Evidence for 28 genetic disorders discovered by combining healthcare and research data (2020) · cites this paper as [33]
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- Authors
- Deelen, P., van Dam, S., Herkert, J. C., Karjalainen, J. M., Brugge, H., Abbott, K. M., van Diemen, C. C., van der Zwaag, P. A., Gerkes, E. H., Zonneveld-Huijssoon, E., Boer-Bergsma, J. J., Folkertsma, P., Gillett, T., van der Velde, K. J., Kanninga, R., van den Akker, P. C., Jan, S. Z., Hoorntje, E. T., te Rijdt, W. P., Vos, Y. J., Jongbloed, J. D. H., van Ravenswaaij-Arts, C. M. A., Sinke, R., Sikkema-Raddatz, B., Kerstjens-Frederikse, W. S., Swertz, M. A., & Franke, L.
- Affiliations
- University Medical Center Groningen (NL)
- Corresponding author
- Franke, Lude
- ORCID
- Deelen, Patrick
- Herkert, Johanna C.
- Karjalainen, Juha M.
- Abbott, Kristin M.
- Zonneveld-Huijssoon, Evelien
- Boer-Bergsma, Jelkje J.
- Folkertsma, Pytrik
- Gillett, Tessa
- Jan, Sabrina Z.
- Hoorntje, Edgar T.
- te Rijdt, Wouter P.
- Jongbloed, Jan D. H.
- Sinke, Richard
- Kerstjens-Frederikse, Wilhelmina S.
- Swertz, Morris A.
- Franke, Lude
- Venue
- Nature Communications
- Published
- 2019-06-28
- Volume
- 10
- Issue
- 1
- Pages
- 2837-2837
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC6599066
- OpenAlex
- W2953983664
- Cited by
- 138
- References
- 57
- Citations by year
- 2026: 6 · 2025: 7 · 2024: 15 · 2023: 17 · 2022: 26 · 2021: 38 · 2020: 18 · 2019: 9 · 2018: 2
- FWCI
- 13.67
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (acceptedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, cc-by)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion)
- Funders
- University of Groningen
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
- Keywords
- exome sequencing, diagnostic yield, genotype-phenotype correlation, RNA-seq, gene expression, disease gene discovery, Human Phenotype Ontology, candidate variants, genetic diagnosis
- MeSH terms
- Gene Expression Regulation, Humans, Models, Genetic, Software, User-Computer Interface, Sequence Analysis, RNA, Genetic Predisposition to Disease, Principal Component Analysis, Databases, Nucleic Acid, Transcriptome
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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