Efficacy of Exome-Targeted Capture Sequencing to Detect Mutations in Known Cerebellar Ataxia Genes

Abstract

Importance: Molecular diagnosis is difficult to achieve in disease groups with a highly heterogeneous genetic background, such as cerebellar ataxia (CA). In many patients, candidate gene sequencing or focused resequencing arrays do not allow investigators to reach a genetic conclusion.

Objectives: To assess the efficacy of exome-targeted capture sequencing to detect mutations in genes broadly linked to CA in a large cohort of undiagnosed patients and to investigate their prevalence.

Design, setting, and participants: Three hundred nineteen index patients with CA and without a history of dominant transmission were included in the this cohort study by the Spastic Paraplegia and Ataxia Network. Centralized storage was in the DNA and cell bank of the Brain and Spine Institute, Salpetriere Hospital, Paris, France. Patients were classified into 6 clinical groups, with the largest being those with spastic ataxia (ie, CA with pyramidal signs [n = 100]). Sequencing was performed from January 1, 2014, through December 31, 2016. Detected variants were classified as very probably or definitely causative, possibly causative, or of unknown significance based on genetic evidence and genotype-phenotype considerations.

Main outcomes and measures: Identification of variants in genes broadly linked to CA, classified in pathogenicity groups.

Results: The 319 included patients had equal sex distribution (160 female [50.2%] and 159 male patients [49.8%]; mean [SD] age at onset, 27.9 [18.6] years). The age at onset was younger than 25 years for 131 of 298 patients (44.0%) with complete clinical information. Consanguinity was present in 101 of 298 (33.9%). Very probable or definite diagnoses were achieved for 72 patients (22.6%), with an additional 19 (6.0%) harboring possibly pathogenic variants. The most frequently mutated genes were SPG7 (n = 14), SACS (n = 8), SETX (n = 7), SYNE1 (n = 6), and CACNA1A (n = 6). The highest diagnostic rate was obtained for patients with an autosomal recessive CA with oculomotor apraxia-like phenotype (6 of 17 [35.3%]) or spastic ataxia (35 of 100 [35.0%]) and patients with onset before 25 years of age (41 of 131 [31.3%]). Peculiar phenotypes were reported for patients carrying KCND3 or ERCC5 variants.

Conclusions and relevance: Exome capture followed by targeted analysis allows the molecular diagnosis in patients with highly heterogeneous mendelian disorders, such as CA, without prior assumption of the inheritance mode or causative gene. Being commonly available without specific design need, this procedure allows testing of a broader range of genes, consequently describing less classic phenotype-genotype correlations, and post hoc reanalysis of data as new genes are implicated in the disease.

Figure 1.. General Study Results

Variants were sorted based on classic criteria (detailed in the Variant Analysis subsection of the Results section), then analyzed assuming an autosomal recessive (AR) transmission mode (including homozygous and heterozygous compound variants), which allowed identifying possibly to definitely causative variants in 74 patients (23.2%). Combining this analysis with one based on presumed autosomal dominant (AD) transmission (including heterozygous varients and a frequency ≤0.1%) improved this number to 91 patients (28.5%) for AD and AR inheritance modes, with 10 additional patients carrying very probable to definite pathogenic mutations. VUS indicates variant of unknown significance.

Figure 2.. Number of Possible to Definite Diagnoses per Gene and Disease Group

The left part of the Figure plots the number of patients identified with possible to definite mutations for each gene listed. The right part shows the repartition of these patients among the 6 disease subgroups. Disease groups are described in the Patient Recruitment and Clinical Evaluation subsection of the Methods section. AD indicates autosomal dominant; AR, autosomal recessive; AOA, cerebellar ataxia with oculomotor apraxia.

Figure 3.. Magnetic Resonance Image of the Brain in a Patient

A woman in her 40s harbored homozygous nonsense mutations in ERCC5 (p. Q1002X). After 22 years of disease evolution, the sagittal section of a T1-weighted image (A) showed mild atrophy of the upper cerebellar vermis (white arrowhead), and the axial fluid-attenuated inversion recovery section (B) showed slight white matter blurring (black arrowheads).