Comparing targeted exome and whole exome approaches for genetic diagnosis of neuromuscular disorders

Abstract

Massively parallel sequencing is rapidly becoming a widely used method in genetic diagnostics. However, there is still no clear consensus as to which approach can most efficiently identify the pathogenic mutations carried by a given patient, while avoiding false negative and false positive results. We developed a targeted exome approach (MyoPanel2) in order to optimize genetic diagnosis of neuromuscular disorders. Using this approach, we were able to analyse 306 genes known to be mutated in myopathies as well as in related disorders, obtaining 98.8% target sequence coverage at 20 ×. Moreover, MyoPanel2 was able to detect 99.7% of 11,467 known mutations responsible for neuromuscular disorders. We have then used several quality control parameters to compare performance of the targeted exome approach with that of whole exome sequencing. The results of this pilot study of 140 DNA samples suggest that targeted exome sequencing approach is an efficient genetic diagnostic test for most neuromuscular diseases.

Genetic Characterization of a French Cohort of GNE‐mutation negative inclusion body myopathy patients with exome sequencing

“…Our initial analysis strategy focused on 306 genes that had previously been reported to cause neuromuscular disorders, selected from the Gene Table of Neuromuscular Disorders (including groups 1 to 5 and the main differential diagnosis genes), as previously described . A mean overall sequencing depth of 106X and a mean coverage of the coding exons of 95% (at 20X depth) and 91% (at 30X depth) was obtained for these 306 genes.…”

Novel CAPN3 variant associated with an autosomal dominant calpainopathy

“…Targeted NGS analysis used different genes panels, depending on the genetic laboratory, but covered at least the initial 'Limb Girdle Muscular Dystrophies' clinical entry-diagnosis group defined by the FILNEMUS network guidelines, with the exception of a few newly involved genes added very recently to the corresponding genes list [13]. Therefore, targeted NGS sequencing was performed for 306 genes [15], 135 genes [16] or 38 genes associated to neuromuscular disorder [17], depending on the genetic laboratory, respectively for index cases from family 2 (2/ III.1) and family 3 (3/II.6) as well as for a symptomatic patient from family 4 (4/II.1). See Supporting Information for detailed genes panels and genes lists (Appendix S1).…”

Genotype‐guided diagnostic reassessment after exome sequencing in neuromuscular disorders: experiences with a two‐step approach

“…With the advent of next-generation sequencing (NGS) approaches such as gene panels, exome sequencing (ES) or genome sequencing, a growing number of causative variants can be identified [1][2][3]. Even so, the majority of patients with NMDs still remain undiagnosed with variable success rates, mainly depending on the selected patient population and the applied method [4][5][6][7][8][9][10][11][12]. It is therefore a major challenge facing clinicians and geneticists to further enhance the application of NGS techniques.…”