Improving diagnostic yield of exome sequencing with RNA sequencing

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, University of Groningen researchers use RNA-seq data from 31,499 samples to predict which genes cause specific disease phenotypes, and develop GeneNetwork Assisted Diagnostic Optimization (GADO). They 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.

Schematic overview of GADO

rna-seq

a Per patient, GADO requires a set of phenotypic features (encoded using HPO terms) and a list of candidate genes (gene names either entered using HGNC symbols or Ensembl IDs). This gene list should contain genes in which rare variants have been observed for the patient. It then ascertains whether any of these genes have been predicted to cause the phenotypic features, observed in the patient. These HPO phenotypes predictions per gene are based on observed co-regulation with sets of genes that are already known to be associated with these phenotypes. b Overview of how disease symptoms are predicted using gene expression data from 31,499 human RNA-seq samples. A principal component analysis on the co-expression matrix results in the identification of 1588 significant principal components. For each HPO term we investigate every component: per component we test whether there is a significant difference between eigenvector coefficients of genes known to cause a specific phenotype and a background set of genes. This results in a matrix that indicates which principal components are informative for every HPO term. By correlating this matrix to the eigenvector coefficients of every individual gene, it is possible to infer the likely HPO disease phenotype term that would be the result of a pathogenic variant in that gene

Availability – All analyses described in this paper can be performed using the online toolbox at www.genenetwork.nl. A standalone command line version of GADO that can easily be integrating in a bioinformatics pipeline is available at: https://github.com/molgenis/systemsgenetics/wiki/GADO-Command-line

Deelen P et al. (2019) Improving the diagnostic yield of exome- sequencing by predicting gene-phenotype associations using large-scale gene expression analysis. Nat Commun 10(1):2837. [article]

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