Comprehensive reanalysis for CNVs in exome sequencing data from unsolved rare disease cases results in new diagnoses

Abstract We report the diagnostic results of a comprehensive copy number variant (CNV) reanalysis of 9,171 exome sequencing (ES) datasets from 5,757 families, including 6,143 individuals affected by a rare disease (RD). The data analysed was extremely heterogeneous, having been generated using 28 different exome enrichment kits, and sequenced on multiple short-read sequencing platforms, by 42 different research groups across Europe partnering in the Solve-RD project. Each of these research groups had previously undertaken their own analysis of the ES data but had failed to identify disease-causing variants. We applied three CNV calling algorithms to maximise sensitivity: ClinCNV, Conifer, and ExomeDepth. Rare CNVs overlapping genes of interest in custom lists provided by one of four partner European Reference Networks (ERN) were identified and taken forward for interpretation by clinical experts in RD. To facilitate interpretation, Integrative Genomics Viewer (IGV) screenshots incorporating a variety of custom-made tracks were generated for all prioritised CNVs. These analyses have resulted in a molecular diagnosis being provided for 51 families in this sample, with ClinCNV performing the best of the three algorithms in identifying disease-causing CNVs. We also identified pathogenic CNVs that are partially explanatory of the proband’s phenotype in a further 34 individuals. This work illustrates the value of reanalysing ES cold cases for CNVs even where analyses had been undertaken previously. Crucially, identification of these previously undetected CNVs has resulted in the conclusion of the diagnostic odyssey for these RD families, some of which had endured decades.