| Author/Editor | Ellingford, Jamie M; Campbell, Christopher; Barton, Stephanie J.; Bhaskar, Sanjeev S; Gupta, Saurabh; Taylor, Rachel L.; Sergouniotis, Panagiotis I.; Horn, Bradley; Lamb, Janine A; Michaelides, Michel | |
| Title | Validation of copy number variation analysis fornext-generation sequencing diagnostics | |
| Type | članek | |
| Vol. and No. | Letnik iss. 6, št. Vol. 25 | |
| Publication year | 2017 | |
| Volume | str. 719-724 | |
| ISSN | 1018-4813 - European journal of human genetics : EJHG | |
| Language | eng | |
| Abstract | Although a common cause of disease, copy number variants (CNVs) have not routinely been identified from next-generation sequencing (NGS) data in a clinical context. This study aimed to examine the sensitivity and specificity of a widely used software package, ExomeDepth, to identify CNVs from targeted NGS data sets. We bench marked the accuracy of CNV detectionusing ExomeDepth v1.1.6 applied to targeted NGS data sets by comparison to CNV events detected through whole-genome sequencing for 25 individuals and determined the sensitivity and specificity of ExomeDepth applied to these targeted NGS datasets to be 100% and 99.8%, respectively. To define quality assurance metrics for CNV surveillance through ExomeDepth, weundertook simulation of single-exon (n=1000) and multiple-exon heterozygous deletion events (n=1749), determining asensitivity of 97% (n=2749). We identified that the extent of sequencing coverage, the inter- and intra-sample variability in thedepth of sequencing coverage and the composition of analysis regions are all important determinants of successful CNV surveillance through ExomeDepth. We then applied these quality assurance metrics during CNV surveillance for 140 individual sacross 12 distinct clinical areas, encompassing over 500 potential rare disease diagnoses. All 140 individuals lacked molecular diagnoses after routine clinical NGS testing, and by application of ExomeDepth, we identified 17 CNVs contributing to the cause ofa Mendelian disorder. Ourfindings support the integration of CNV detection using ExomeDepth v1.1.6 with routine targeted NGSdiagnostic services for Mendelian disorders. Implementation of this strategy increases diagnostic yields and enhances clinical care. | |
| Keywords | sequencing validation genome sekvenciranje validacija genom |