Exome sequencing as a first-tier test for copy number variant detection: retrospective evaluation and prospective screening in 2418 cases
Quentin Testard, Xavier Vanhoye, Kévin Yauy, Marie-Emmanuelle Naud, Gaëlle Vieville, Francis Rousseau, Benjamin Dauriat, Valentine Marquet, Sylvie Bourthoumieu, David Geneviève, Vincent Gâtinois, Constance Wells, Marjolaine Willems, Christine Coubes, Lucile Pinson, Rodolphe Dard, Aude Tessier, Bérénice Herve, François Vialard, Inès Harzallah, Renaud Touraine, Benjamin Cogné, Wallid Deb, Thomas Besnard, Olivier Pichon, Béatrice Laudier, Laurent Mesnard, Alice Doreille, Tiffany Busa, Chantal Missirian, Véronique Satre, Charles Coutton, Tristan Celse, Radu Harbuz, Laure Raymond, Jean-François Taly, Julien Thévenon
Abstract
BACKGROUND: Despite the availability of whole exome (WES) and genome sequencing (WGS), chromosomal microarray (CMA) remains the first-line diagnostic test in most rare disorders diagnostic workup, looking for copy number variations (CNVs), with a diagnostic yield of 10%-20%. The question of the equivalence of CMA and WES in CNV calling is an organisational and economic question, especially when ordering a WGS after a negative CMA and/or WES. METHODS: This study measures the equivalence between CMA and GATK4 exome sequencing depth of coverage method in detecting coding CNVs on a retrospective cohort of 615 unrelated individuals. A prospective detection of WES-CNV on a cohort of 2418 unrelated individuals, including the 615 individuals from the validation cohort, was performed. RESULTS: On the retrospective validation cohort, every CNV detectable by the method (ie, a CNV with at least one exon not in a dark zone) was accurately called (64/64 events). In the prospective cohort, 32 diagnoses were performed among the 2418 individuals with CNVs ranging from 704 bp to aneuploidy. An incidental finding was reported. The overall increase in diagnostic yield was of 1.7%, varying from 1.2% in individuals with multiple congenital anomalies to 1.9% in individuals with chronic kidney failure. CONCLUSION: Combining single-nucleotide variant (SNV) and CNV detection increases the suitability of exome sequencing as a first-tier diagnostic test for suspected rare Mendelian disorders. Before considering the prescription of a WGS after a negative WES, a careful reanalysis with updated CNV calling and SNV annotation should be considered.