1. CNV Detection from Exome Sequencing Data in Routine Diagnostics of Rare Genetic Disorders: Opportunities and Limitations
- Author
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Katarina Cisarova, Beryl Royer-Bertrand, Heidi Fodstad, Andrea Superti-Furga, Lauréane Mittaz-Crettol, and Florence Niel-Bütschi
- Subjects
Adult ,Male ,copy number variations (CNVs) ,congenital, hereditary, and neonatal diseases and abnormalities ,Adolescent ,DNA Copy Number Variations ,endocrine system diseases ,Computational biology ,QH426-470 ,Biology ,Genome ,Article ,Cohort Studies ,Young Adult ,Exon ,Rare Diseases ,Gene panel ,Exome Sequencing ,mental disorders ,Genetics ,Humans ,In patient ,Genetic Testing ,Multiplex ligation-dependent probe amplification ,Copy-number variation ,Child ,next-generation sequencing (NGS) ,Gene ,Genetics (clinical) ,Exome sequencing ,Aged ,Aged, 80 and over ,Diagnostic Tests, Routine ,High-Throughput Nucleotide Sequencing ,Infant ,Sequence Analysis, DNA ,Middle Aged ,MLPA ,rare and undiagnosed disease ,exome sequencing (ES) ,Child, Preschool ,arrayCGH (aCGH) ,structural variation (SV) ,Female ,Switzerland - Abstract
To assess the potential of detecting copy number variations (CNVs) directly from exome sequencing (ES) data in diagnostic settings, we developed a CNV-detection pipeline based on ExomeDepth software and applied it to ES data of 450 individuals. Initially, only CNVs affecting genes in the requested diagnostic gene panels were scored and tested against arrayCGH results. Pathogenic CNVs were detected in 18 individuals. Most detected CNVs were larger than 400 kb (11/18), but three individuals had small CNVs impacting one or a few exons only and were thus not detectable by arrayCGH. Conversely, two pathogenic CNVs were initially missed, as they impacted genes not included in the original gene panel analysed, and a third one was missed as it was in a poorly covered region. The overall combined diagnostic rate (SNVs + CNVs) in our cohort was 36%, with wide differences between clinical domains. We conclude that (1) the ES-based CNV pipeline detects efficiently large and small pathogenic CNVs, (2) the detection of CNV relies on uniformity of sequencing and good coverage, and (3) in patients who remain unsolved by the gene panel analysis, CNV analysis should be extended to all captured genes, as diagnostically relevant CNVs may occur everywhere in the genome.
- Published
- 2021
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