Diagnostic genome sequencing improves diagnostic yield: a prospective single-centre study in 1000 patients with inherited eye diseases
Nicole Weisschuh, Pascale Mazzola, Theresia Zuleger, Karin Schaeferhoff, Laura Kühlewein, Friederike Kortüm, Dennis Witt, Alexandra Liebmann, Ruth Falb, Lisa Pohl, Milda Reith, Lara G. Stühn, Miriam Bertrand, Amelie J. Müller, Nicolas Casadei, Olga Kelemen, Carina Kelbsch, Christoph Kernstock, Paul Richter, Françoise Sadler, German Demidov, Leon Schütz, Jakob Admard, Marc Sturm, Ute Grasshoff, Felix Tonagel, T. Heinrich, Fadi Nasser, Bernd Wissinger, Stephan Ossowski, Susanne Kohl, Olaf Rieß, Katarína Štingl, Tobias B. Haack
Abstract
PURPOSE: Genome sequencing (GS) is expected to reduce the diagnostic gap in rare disease genetics. We aimed to evaluate a scalable framework for genome-based analyses 'beyond the exome' in regular care of patients with inherited retinal degeneration (IRD) or inherited optic neuropathy (ION). METHODS: PCR-free short-read GS was performed on 1000 consecutive probands with IRD/ION in routine diagnostics. Complementary whole-blood RNA-sequencing (RNA-seq) was done in a subset of 74 patients. An open-source bioinformatics analysis pipeline was optimised for structural variant (SV) calling and combined RNA/DNA variation interpretation. RESULTS: A definite genetic diagnosis was established in 57.4% of cases. For another 16.7%, variants of uncertain significance were identified in known IRD/ION genes, while the underlying genetic cause remained unresolved in 25.9%. SVs or alterations in non-coding genomic regions made up for 12.7% of the observed variants. The RNA-seq studies supported the classification of two unclear variants. CONCLUSION: GS is feasible in clinical practice and reliably identifies causal variants in a substantial proportion of individuals. GS extends the diagnostic yield to rare non-coding variants and enables precise determination of SVs. The added diagnostic value of RNA-seq is limited by low expression levels of the major IRD disease genes in blood.