Structural variant calling and clinical interpretation in 6224 unsolved rare disease exomes
German Demidov, Steven Laurie, Annalaura Torella, Giulio Piluso, Marcello Scala, Manuela Morleo, Vincenzo Nigro, Holm Graeßner, Siddharth Banka, Alfons Macaya, Belén Pérez-Dueñas, Adam Jackson, Giovanni Stévanin, Jean‐Madeleine de Sainte Agathe, Markéta Havlovičová, Rita Horváth, Michele Pinelli, Nienke J.H. van Os, Bart P.C. van de Warrenburg, Anne‐Sophie Denommé‐Pichon, Marco Savarese, Mridul Johari, Bruno Dallapiccola, Marco Tartaglia, Martje G. Pauly, Anna Katharina Sommer, Tobias B. Haack, Ana Töpf, Didier Lacombe, Chiara Fallerini, Alessandra Renieri, Patrick F. Chinnery, Daniel Natera‐de Benito, A. Nascimento, Aurélien Trimouille, Francina Munell, Anna Marcé‐Grau, Ben Yaou Rabah, Gisèle Bonne, Liedewei Van de Vondel, Katja Lohmann, Stephan Ossowski
Abstract
Structural variants (SVs), including large deletions, duplications, inversions, translocations, and more complex events have the potential to disrupt gene function resulting in rare disease. Nevertheless, current pipelines and clinical decision support systems for exome sequencing (ES) tend to focus on small alterations such as single nucleotide variants (SNVs) and insertions-deletions shorter than 50 base pairs (indels). Additionally, detection and interpretation of large copy-number variants (CNVs) are frequently performed. However, detection of other types of SVs in ES data is hampered by the difficulty of identifying breakpoints in off-target (intergenic or intronic) regions, which makes robust identification of SVs challenging. In this paper, we demonstrate the utility of SV calling in ES resulting in a diagnostic yield of 0.4% (23 out of 5825 probands) for a large cohort of unsolved patients collected by the Solve-RD consortium. Remarkably, 8 out of 23 pathogenic SV were not found by comprehensive read-depth-based CNV analysis, resulting in a 0.13% increased diagnostic value.