Whole genome sequencing increases the diagnostic rate in Charcot-Marie-Tooth disease

Abstract

Charcot-Marie-Tooth disease (CMT) is one of the most common and genetically heterogeneous inherited neurological diseases, with more than 130 disease-causing genes. Whole genome sequencing (WGS) has improved diagnosis across genetic diseases, but the diagnostic impact in CMT is yet to be fully reported. We present the diagnostic results from a single specialist inherited neuropathy centre, including the impact of WGS diagnostic testing. Patients were assessed at our specialist inherited neuropathy centre from 2009 to 2023. Genetic testing was performed using single gene testing, next-generation sequencing targeted panels, research whole exome sequencing and WGS and, latterly, WGS through the UK National Health Service. Variants were assessed using the American College of Medical Genetics and Genomics and Association for Clinical Genomic Science criteria. Excluding patients with hereditary ATTR amyloidosis, 1515 patients with a clinical diagnosis of CMT and related disorders were recruited. In summary, 621 patients had CMT1 (41.0%), 294 CMT2 (19.4%), 205 intermediate CMT (CMTi, 13.5%), 139 hereditary motor neuropathy (HMN, 9.2%), 93 hereditary sensory neuropathy (HSN, 6.1%), 38 sensory ataxic neuropathy (2.5%), 72 hereditary neuropathy with liability to pressure palsies (HNPP, 4.8%) and 53 'complex' neuropathy (3.5%). Overall, a genetic diagnosis was reached in 76.9% (1165/1515). A diagnosis was most likely in CMT1 (96.8%, 601/621), followed by CMTi (81.0%, 166/205) and then HSN (69.9%, 65/93). Diagnostic rates remained less than 50% in CMT2, HMN and complex neuropathies. The most common genetic diagnosis was PMP22 duplication (CMT1A; 505/1165, 43.3%), then GJB1 (CMTX1; 151/1165, 13.0%), PMP22 deletion (HNPP; 72/1165, 6.2%) and MFN2 (CMT2A; 46/1165, 3.9%). We recruited 233 cases to the UK 100 000 Genomes Project (100KGP), of which 74 (31.8%) achieved a diagnosis; 28 had been otherwise diagnosed since recruitment, leaving a true diagnostic rate of WGS through the 100KGP of 19.7% (46/233). However, almost half of the solved cases (35/74) received a negative report from the study, and the diagnosis was made through our research access to the WGS data. The overall diagnostic uplift of WGS for the entire cohort was 3.5%. Our diagnostic rate is the highest reported from a single centre and has benefitted from the use of WGS, particularly access to the raw data. However, almost one-quarter of all cases remain unsolved, and a new reference genome and novel technologies will be important to narrow the 'diagnostic gap'.

Keywords: CMT; HMSN; WES; WGS; genomics; neurogenetics.

Figure 1

The genetic testing algorithm. CMT1 = Charcot-Marie-Tooth type 1; MDT = multidisciplinary team; MLPA = multiplex ligation-dependent probe amplification; WGS = whole genome sequencing.

Figure 2

Diagnostic breakdown by phenotype. CMT1/2 = Charcot-Marie-Tooth disease type 1/2; CMT(i) = Charcot-Marie-Tooth disease (intermediate); HMN = hereditary motor neuropathy; HSN = hereditary sensory neuropathy; SAN = sensory ataxic neuropathy.

Figure 3

Diagnostic rates and results from the 100 000 genomes project. (A) Solved rate by clinical subtype. (B) Results from patients recruited to 100 000 genomes project; the expanded pie chart to the right denotes how the diagnosis was made. CMT1/2 = Charcot-Marie-Tooth disease type 1/2; CMT(i) = Charcot-Marie-Tooth disease (intermediate); HMN = hereditary motor neuropathy; HSN = hereditary sensory neuropathy; SAN = sensory ataxic neuropathy; 100KGP = 100 000 Genomes Project.

Figure 4

Genetic diagnosis breakdown by phenotype. (A) Charcot-Marie-Tooth disease type 1 (CMT1); (B) CMT2; (C) hereditary motor neuropathy (HMN). (D) How the genetic diagnosis was reached (probands). CMT(i) = Charcot-Marie-Tooth disease (intermediate); HSN = hereditary sensory neuropathy; NGS = next-generation sequencing; PMP22dup = PMP22 duplication; PMP22pm = PMP22 point mutation; SAN = sensory ataxic neuropathy; SGT = single gene test; WES = whole exome sequencing; WGS = whole genome sequencing. Colour scheme in D: blue tones = service laboratory testing, orange tones = research testing; all WGS testing in D is denoted research because only two cases have been diagnosed through the National Health Service WGS.

Figure 5

Illustrative cases. (A) Integrative Genomics Viewer (IGV) showing aligned sequence reads for proband and unaffected mother at the SPG11 locus. An 8.3 kb deletion is carried by the proband and mother, point mutation is carried only by the proband (red circle). (B–D) Clinical images of the proband. (E) Sagittal MRI midline slice showing corpus callosum atrophy. (F) IGV showing loss of read depth in intron 2 of RFC1 (red circle). Reads with red outline (black arrow) indicated an unmatched read-pair suggestive of an expansion. (G and H) Clinical images of the asymptomatic mother easily walking and standing on heels. (I and J) Wasting of distal upper and lower limbs in the proband. (K) IGV showing a variant in ITPR3 present in the proband and mother, but absent in the father (green arrow).