Targeted exome analysis identifies the genetic basis of disease in over 50% of patients with a wide range of ataxia-related phenotypes

Abstract

Purpose: To examine the impact of a targeted exome approach for the molecular diagnosis of patients nationwide with a wide range of ataxia-related phenotypes.

Methods: One hundred and seventy patients with ataxia of unknown etiology referred from clinics throughout the United States and Canada were studied using a targeted exome approach. Patients ranged in age from 2 to 88 years. Analysis was focused on 441 curated genes associated with ataxia and ataxia-like conditions.

Results: Pathogenic and suspected diagnostic variants were identified in 88 of the 170 patients, providing a positive molecular diagnostic rate of 52%. Forty-six different genes were implicated, with the six most commonly mutated genes being SPG7, SYNE1, ADCK3, CACNA1A, ATP1A3, and SPTBN2, which accounted for >40% of the positive cases. In many cases a diagnosis was provided for conditions that were not suspected and resulted in the broadening of the clinical spectrum of several conditions.

Conclusion: Exome sequencing with targeted analysis provides a high-yield approach for the genetic diagnosis of ataxia-related conditions. This is the largest targeted exome study performed to date in patients with ataxia and ataxia-like conditions and represents patients with a wide range of ataxia phenotypes typically encountered in neurology and genetics clinics.

Keywords: ataxia; clinical; diagnosis; exome sequencing; molecular genetics.

Figure 1:

RT-PCR analysis in patient 059. RT-PCR analysis across exons 11 through 16 of the SPG7 gene demonstrated the presence of a single allele containing c.1529T in exon 11 in patient 059. The two siblings who are heterozygous for c.1529C>T (p.Ala510Val) and do not carry the c.2181+5G>A intron 16 variant, demonstrated the presence of two alleles at position c.1529 (c.1529C and c.1529T). The normal control demonstrated c.1529C at this position. This result is indicative of the c.1529C>T and c.2181+5G>A variants being in trans in patient 059 with the c.2181+5G>A allele not being amplified.

Figure 2:

RT-PCR analysis in patient 078. RT-PCR analysis across exons 83 and 84 of SYNE1 demonstrated aberrant splicing with the c.16024–13C>G variant being used as a cryptic splice acceptor site. Both the normal and aberrant splice product was observed in patient 078 compared to only a normal splice product in the normal control sample. Aberrant splicing at the c.16024–13C>G site results in the creation of a truncating TGA stop codon immediately after the splice site.