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Detection of elusive DNA copy-number variations in hereditary disease and cancer through the use of noncoding and off-target sequencing reads

Publicated to:American Journal Of Human Genetics. 111 (4): 701-713 - 2024-04-04 111(4), DOI: 10.1016/j.ajhg.2024.03.001

Authors: Quinodoz M; Kaminska K; Cancellieri F; Han JH; Peter VG; Celik E; Janeschitz-Kriegl L; Schärer N; Hauenstein D; György B; Calzetti G; Hahaut V; Custódio S; Sousa AC; Wada Y; Murakami Y; Fernández AA; Hernández CR; Minguez P; Ayuso C; Nishiguchi KM; Santos C; Santos LC; Tran VH; Vaclavik V; Scholl HPN; Rivolta C

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Abstract

Copy-number variants (CNVs) play a substantial role in the molecular pathogenesis of hereditary disease and cancer, as well as in normal human interindividual variation. However, they are still rather difficult to identify in mainstream sequencing projects, especially involving exome sequencing, because they often occur in DNA regions that are not targeted for analysis. To overcome this problem, we developed OFF-PEAK, a user-friendly CNV detection tool that builds on a denoising approach and the use of “off-target” DNA reads, which are usually discarded by sequencing pipelines. We benchmarked OFF-PEAK on data from targeted sequencing of 96 cancer samples, as well as 130 exomes of individuals with inherited retinal disease from three different populations. For both sets of data, OFF-PEAK demonstrated excellent performance (>95% sensitivity and >80% specificity vs. experimental validation) in detecting CNVs from in silico data alone, indicating its immediate applicability to molecular diagnosis and genetic research.

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