Exome sequencing as a first-tier test for copy number variant detection: retrospective evaluation and prospective screening in 2418 cases

Abstract

BackgroundDespite 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.MethodsThis 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.ResultsOn 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.ConclusionCombining 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.

Exome copy number variant detection, analysis and classification in a large cohort of families with undiagnosed rare genetic disease

“…The additional 2.6% solve rate of exome CNV calling identified in this cohort is comparable to previously reported diagnostic yield in other cohorts. 12–16 In this cohort, most causal CNVs were deletions. Duplications were more common in the callset, but are less likely to disrupt gene function and also typically require more functional investigation to confirm a deleterious effect.…”

“…The reported additional diagnostic yield of CNV calling on exome data, most commonly used as a second-line test after CMA, on various cohorts of patients with suspected rare genetic diseases varies between 1 to 2%. [12][13][14][15][16] The widespread implementation of CMA and exome/genome sequencing is expanding the types and numbers of CNVs identified in both clinical and research settings, and it can be challenging to determine the impact of these CNVs on human health. Several resources have been or are being developed to address this challenge.…”

“…The reported additional diagnostic yield of CNV calling on exome data, most commonly used as a second-line test after CMA, on various cohorts of patients with suspected rare genetic diseases varies between 1 to 2%. 12–16…”

Quality assurance for next-generation sequencing diagnostics of rare neurological diseases in the European Reference Network

“…Therefore, an appropriate interpretation and reporting of results considering these limitations should be ensured by the ERN-RND quality assessment scheme. Recent publications report an increasingly expanding mutational spectrum detectable by NGS-based genetic testing [21,22]. Although initially, NGS has been primarily aimed at detecting sequence variants, attempts have been undertaken to detect CNVs [22,23], repeat expansions [24], mitochondrial variants (if included in the enrichment) [22] and uniparental disomy [25].…”

Novel maternal duplication of 6p22.3-p25.3 with subtelomeric 6p25.3 deletion: new clinical findings and genotype–phenotype correlations

“…However, WES-CNV could not detect regions beyond the exons. When compared, although the limited resolution of CNV-seq is not allowed to detect deletion or duplication regions smaller than 100 kb, CNV-seq can not only be evaluated at the genome level for contiguous deletions or duplications in exonic regions but also in intron regions [ 21 – 23 ]. Therefore, the different advantages and limitations of WES-CNV and CNV-seq are the major reason why the CNVs detected via WES-CNV and CNV-seq have discrepancies.…”