Target-enrichment sequencing and copy number evaluation in inherited polyneuropathy

Abstract

Objective: To assess the efficiency of target-enrichment next-generation sequencing (NGS) with copy number assessment in inherited neuropathy diagnosis.Methods: A 197 polyneuropathy gene panel was designed to assess for mutations in 93 patients with inherited or idiopathic neuropathy without known genetic cause. We applied our novel copy number variation algorithm on NGS data, and validated the identified copy number mutations using CytoScan (Affymetrix). Cost and efficacy of this targeted NGS approach was compared to earlier evaluations.Results: Average coverage depth was ;7603 (median 5 600, 99.4% . 1003). Among 93 patients, 18 mutations were identified in 17 cases (18%), including 3 copy number mutations: 2 PMP22 duplications and 1 MPZ duplication. The 2 patients with PMP22 duplication presented with bulbar and respiratory involvement and had absent extremity nerve conductions, leading to axonal diagnosis. Average onset age of these 17 patients was 25 years (2-61 years), vs 45 years for those without genetic discovery. Among those with onset age less than 40 years, the diagnostic yield of targeted NGS approach is high (27%) and cost savings is significant (;20%). However, the cost savings for patients with late onset age and without family history is not demonstrated. Conclusions:Incorporating copy number analysis in target-enrichment NGS approach improved the efficiency of mutation discovery for chronic, inherited, progressive length-dependent polyneuropathy diagnosis. The new technology is facilitating a simplified genetic diagnostic algorithm utilizing targeted NGS, clinical phenotypes, age at onset, and family history to improve diagnosis efficiency. Our findings prompt a need for updating the current practice parameters and payer guidelines. Neurology ® 2016;86:1762-1771 GLOSSARY CIAP 5 chronic idiopathic axonal polyneuropathy; CMT 5 Charcot-Marie-Tooth; CNV 5 copy number variation; DGV 5 Database of Genomic Variants; HMSN 5 hereditary motor and sensory polyneuropathy; MAF 5 minor allele frequency; NGS 5 next-generation sequencing; VUS 5 variants of unclear significance; WES 5 whole exome sequencing.Polyneuropathies are common, with overall prevalence of 1.7%, and 6.6% among persons over 60 years old.1 The high prevalence, multiple impairments, and complicated diagnostic procedures lead to high health care cost.1,2 Separating inherited from acquired causes is often difficult for insidious adult-onset cases, due to overlapping phenotypes.3,4 Furthermore, inherited and acquired polyneuropathies may coexist, resulting in worse severity. [5][6][7][8] One large prospective study indicated that as many as 42% of patients with previously undiagnosed polyneuropathy coming to tertiary care referral had familial occurrence. 9Pragmatic diagnostic strategies have long been sought to improve testing effectiveness and reduce costs in neuropathy diagnosis. [10][11][12] In Charcot-Marie-Tooth clinics, algorithms have been developed for selecting candidate genes.13 This approach is helpful for patients who have c...

Copy number analysis reveals a novel multiexon deletion of the COLQ gene in congenital myasthenia

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“…Sequencing reads were aligned to a human reference (hg19) using in-house pipeline GenomeGPS as previously described. 11 Variant-detections were conducted on exons and flanking 50 base pairs of intronic sequence. Variant data for each case was summarized in variant call format (VCF).…”

Next-generation sequencing in neuromuscular diseases

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