An Extended Targeted Copy Number Variation Detection Array Including 187 Genes for the Diagnostics of Neuromuscular Disorders

Abstract

Background:Our previous array, the Comparative Genomic Hybridisation design (CGH-array) for nemaline myopathy (NM), named the NM-CGH array, revealed pathogenic copy number variation (CNV) in the genes for nebulin (NEB) and tropomyosin 3 (TPM3), as well as recurrent CNVs in the segmental duplication (SD), i.e. triplicate, region of NEB (TRI, exons 82–89, 90–97, 98–105). In the light of this knowledge, we have designed and validated an extended CGH array, which includes a selection of 187 genes known to cause neuromuscular disorders (NMDs).Objective:Our aim was to develop a reliable method for CNV detection in genes related to neuromuscular disorders for routine mutation detection and analysis, as a much-needed complement to sequencing methods.Methods:We have developed a novel custom-made 4×180 k CGH array for the diagnostics of NMDs. It includes the same tiled ultra-high density coverage of the 12 known or putative NM genes as our 8×60 k NM-CGH-array but also comprises a selection of 175 additional genes associated with NMDs, including titin (TTN), at a high to very high coverage. The genes were divided into three coverage groups according to known and potential pathogenicity in neuromuscular disorders.Results:The array detected known and putative CNVs in all three gene coverage groups, including the repetitive regions of NEB and TTN.Conclusions:The targeted neuromuscular disorder 4×180 k array-CGH (NMD-CGH-array v1.0) design allows CNV detection for a broader spectrum of neuromuscular disorders at a high resolution.

Targeted gene panel use in 2249 neuromuscular patients: the Australasian referral center experience

“…The higher read‐depth facilitated CNV detection, and detection of variants within the triplicated regions of TTN and NEB without need for an additional Comparative Genomic Hybridisation array . Within our study, 4% of genetically diagnosed probands harbored a CNV. Although megabase scale CNVs may have been detected by aCGH, the others are likely too small to be detected.…”

New mutations found by Next-Generation Sequencing screening of Spanish patients with Nemaline Myopathy

“…Samples from patients 2 and 3 were analysed on a custom comparative genomic hybridization array targeting the known NM genes and 175 other genes related to neuromuscular disorders [12]. Moreover, a SNP array, CytoScan HD (Affymetrix), was used in patient 3.…”

Nebulin: big protein with big responsibilities

“…A definite diagnosis of NEB related disease was most often achieved by a combination of denaturing high-performance liquid chromatography and Sanger sequencing (Lehtokari et al 2006). Later, next generation sequencing and microarray analysis became available and resulted in a large improvement in the diagnosis of diseases caused by mutations in NEB and other large genes, such as TTN (Böhm et al 2013;Kiiski et al 2016;Sagath et al 2018;Scoto et al 2013;Vasli and Laporte 2013;Zenagui et al 2018). These techniques were further developed in recent years to improve the capture and coverage of difficult areas, such as repeat regions in NEB, and the detection of insertions/deletions as well as copy number variations in TTN and NEB (Kiiski et al 2016;Sagath et al 2018;Zenagui et al 2018).…”