Application of whole‐exome sequencing for detecting copy number variants in CMT1A/HNPP

Abstract

Large insertions and deletions (indels), including copy number variations (CNVs), are commonly seen in many diseases. Standard approaches for indel detection rely on well-established methods such as qPCR or short tandem repeat (STR) markers. Recently, a number of tools for CNV detection based on next-generation sequencing (NGS) data have also been developed; however, use of these methods is limited. Here, we used whole-exome sequencing (WES) in patients previously diagnosed with CMT1A or HNPP using STR markers to evaluate the ability of WES to improve the clinical diagnosis. Patients were evaluated utilizing three CNV detection tools including CONIFER, ExomeCNV and CEQer, and array comparative genomic hybridization (aCGH). We identified a breakpoint region at 17p11.2-p12 in patients with CMT1A and HNPP. CNV detection levels were similar in both 6 Gb (mean read depth = 80×) and 17 Gb (mean read depth = 190×) data. Taken together, these data suggest that 6 Gb WES data are sufficient to reveal the genetic causes of various diseases and can be used to estimate single mutations, indels, and CNVs simultaneously. Furthermore, our data strongly indicate that CNV detection by NGS is a rapid and cost-effective method for clinical diagnosis of genetically heterogeneous disorders such as CMT neuropathy. Conflict of interestThe authors report no conflict of interest. Structural variants including copy number variation (CNV) and insertions and deletions (indel) have been highlighted as the causes of genetic disorders. Recently, it has been reported that CNVs significantly contribute to various diseases such as neurodevelopmental disorders, intellectual disabilities and numerous cancers

Identification of genomic deletions causing inherited retinal degenerations by coverage analysis of whole exome sequencing data

“…Recent studies used different analysis tools of WES data aiming to obtain some initial information regarding the possibility of CNV occurrence at multiple known loci 28 29. The analyses are based on coverage data of specific genomic regions, which need to be at a minimal quality to ensure reliability.…”

“…A few WES-based approaches have been developed for CNV detection including ExomeCNV,30 CONIFER31 and CEQer 32. Although developed for detecting CNVs at a genomic view, these tools were reported to be applicable mainly in targeted analysis of a specific genomic locus and were reported to indeed yield reliable results 29. The most challenging task of these tools is to effectively filter out false-positive CNVs when analysing a large set of data with no previous knowledge of the deletion location.…”

The Role of Copy Number Variants in Disorders of Sex Development

“…The technique has the potential to detect CNVs in the coding regions of genes at an exon level resolution, which is not always feasible when using traditional CGH and MLPA approaches [Gambin et al, 2016]. Only within the last year has WES successfully been able to detect CNVs in other human disease studies with acceptable reliability [Gambin et al, 2016;Jo et al, 2016], although the precision of the data analysis pipelines is currently less than 80% when comparing large cohorts [Gambin et al, 2016]. Recently a study using WES to screen 2,603 patients with a range of genetic disorders, including 38 DSD patients, showed that on average each patient had 6 CNVs throughout their genome [Pfundt et al, 2017].…”

Recent advances in the genetic neuropathies

“…To date, diagnostic algorithms for CMT1 have proposed using multiplex ligation probe amplification (MLPA) for the detection of duplications and deletions of the short arm of chromosome 17 before proceeding to disease-specific panels or WES [2]. In a small sample of three patients with CMT1A, Jo and colleagues were able to identify both duplications and deletions in chromosome 17p using WES suggesting that NGS may eventually supersede the need for MLPA for diagnosing CMT1A [6]. …”