Integration of proteomics with genomics and transcriptomics increases the diagnostic rate of Mendelian disorders

By lack of functional evidence, genome-based diagnostic rates cap at approximately 50% across diverse Mendelian diseases. Here we demonstrate the effectiveness of combining genomics, transcriptomics, and, for the first time, proteomics and phenotypic descriptors, in a systematic diagnostic approach to discover the genetic cause of mitochondrial diseases. On fibroblast cell lines from 145 individuals, tandem mass tag labelled proteomics detected approximately 8,000 proteins per sample and covered over 50% of all Mendelian disease-associated genes. By providing independent functional evidence, aberrant protein expression analysis allowed validation of candidate protein-destabilising variants and of variants leading to aberrant RNA expression. Overall, our integrative computational workflow led to genetic resolution for 21% of 121 genetically unsolved cases and to the discovery of two novel disease genes. With increasing democratization of high-throughput omics assays, our approach and code provide a blueprint for implementing multi-omics based Mendelian disease diagnostics in routine clinical practice.