Targeted sequencing with expanded gene profile enables high diagnostic yield in non-5q-spinal muscular atrophies

Abstract

Spinal muscular atrophies (SMAs) are a heterogeneous group of disorders characterized by muscular atrophy, weakness, and hypotonia due to suspected lower motor neuron degeneration (LMND). In a large cohort of 3,465 individuals suspected with SMA submitted for SMN1 testing to our routine diagnostic laboratory, 48.8% carried a homozygous SMN1 deletion, 2.8% a subtle mutation, and an SMN1 deletion, whereas 48.4% remained undiagnosed. Recently, several other genes implicated in SMA/LMND have been reported. Despite several efforts to establish a diagnostic algorithm for non-5q-SMA (SMA without deletion or point mutations in SMN1 [5q13.2]), data from large-scale studies are not available. We tested the clinical utility of targeted sequencing in non-5q-SMA by developing two different gene panels. We first analyzed 30 individuals with a small panel including 62 genes associated with LMND using IonTorrent-AmpliSeq target enrichment. Then, additional 65 individuals were tested with a broader panel encompassing up to 479 genes implicated in neuromuscular diseases (NMDs) with Agilent-SureSelect target enrichment. The NMD panel provided a higher diagnostic yield (33%) than the restricted LMND panel (13%). Nondiagnosed cases were further subjected to exome or genome sequencing. Our experience supports the use of gene panels covering a broad disease spectrum for diseases that are highly heterogeneous and clinically difficult to differentiate.

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.…”

“…Diagnostic success was negatively correlated with PAR. Other cohorts have displayed enrichment of diagnoses in patients <18 years . The higher diagnostic success in patients <18 years, especially infants in intensive care, suggests that later‐onset diseases may be more likely to have a polygenic and/or nongenetic etiology (e.g., diabetes causing a peripheral neuropathy) …”

“…Other cohorts have displayed enrichment of diagnoses in patients <18 years. 31,34,35 The higher diagnostic success in patients <18 years, especially infants in intensive care, Table 4. Clinical correlation percentage in genes with 5+ reports issued.…”

Biallelic variant in AGTPBP1 causes infantile lower motor neuron degeneration and cerebellar atrophy

“…For data analysis, we used a new version of our Varbank analysis tool (Varbank 2.0) (https://varbank.ccg.uni-koeln.de/varbank2/), which refers to the GRCh38/hg38 reference human genome and provides a number of new features at the on‐line graphical user interface. Our variant filtering strategy was as described previously (Karakaya et al, ).…”

“…The implementation of high‐throughput sequencing into clinical practice has unveiled a number of clinical conditions designated as infantile LMND, or non‐5q spinal muscular atrophy (non‐5q‐SMA) resembling spinal muscular atrophy (SMA) but without deletions or point mutations in SMN1 (Peeters, Chamova, & Jordanova, ). According to our previous work, 48.4% of the individuals failed to show a deletion/mutation in SMN1 in the routine SMN1 deletion/point mutation analysis of 3,465 suspected SMA individuals (Karakaya et al, ). These non‐5q‐SMA phenotypes may also exhibit additional neurologic and multisystemic features (Teoh et al, ).…”