This poster (#556) will be presented at the ACMG Annual Meeting by Miao Sun, molecular fellow, Friday March 27: 10:30am-noon. Stop by and learn more.
The hereditary ataxias are a group of neurological disorders that demonstrate extreme genetic heterogeneity, involving more than 300 genes and many mutations and mutational mechanisms. The traditional genetic testing approach of sequentially sequencing a large number of candidate genes is slow and expensive. Recent advances in sequencing technology make it possible to investigate the genetic causes of ataxia at the genomic level.
We have developed an exome sequencing-based approach for the molecular diagnosis of ataxia. Exome sequencing was performed using the Agilent SureSelect technology and sequenced on a HiSeq or NextSeq Illumina instrument. An average coverage of > 90% of all coding exons at minimum 30X read depth was obtained. Clinical exome sequencing was performed on 32 patients with ataxia of unknown genetic etiology and in whom prior trinucleotide repeat expansions had either been excluded or not implicated. We focused our analysis on variants identified in 332 carefully reviewed genes reported in isolated or syndromic forms of ataxia and other movement disorders, such as spastic paraplegia, that may have some overlap with ataxia.
Pathogenic and highly likely pathogenic variants were identified in 16 out of 32 patients analyzed, providing a positive molecular diagnostic rate of up to 50%. Pathogenic variants were identified in 14 different genes including: ADCK3, APOB, ATM, CACNA1A, CSTB, DARS2, EIF2B2, ELOVL5, MECP2, NIPA1, SACS, SPG7, SPTBN2, SYNE1. Of the patients with pathogenic variants, approximately 20% were in the SACS gene, which is associated with autosomal recessive spastic ataxia of the Charlevoix Saguenay (ARSACS). Two of the patients had either compound heterozygous or homozygous truncating variants while a third patient had compound heterozygous missense variants determined to be in trans. The patient with the missense variants exhibited a milder phenotype with a very late age of onset atypical for ARSACS and this result potentially broadens the phenotypic spectrum in ARSACS. Highly suspicious missense variants were identified in the SPTBN2 gene, associated with autosomal dominant spinocerebellar ataxia 5, in two patients (12.5%). These patients demonstrated static or slowly progressive ataxia, cerebellar atrophy, dysarthria, hyperreflexia and nystagmus. Parental analysis is being pursued and the determination of these sequence changes in the de novo state will further strengthen their pathogenic nature. Two patients were identified to be carriers of a previously described pathogenic variant in the SH3TC2 gene, associated with recessive Charcot-Marie-Tooth disease type 4C or dominant mild mononeuropathy of the median nerve. These are likely to represent incidental findings, as the phenotype in the patients did not match. Incidental findings should therefore be considered even in cases where a specific gene set is being analyzed, especially when the gene set is large.
Our ataxia exome sequencing strategy of limiting analysis to a set of well-curated ataxia-related genes combines the advantages of panel and exome sequencing. Only genes known to be involved with ataxia are analyzed, limiting the numbers of extraneous variants identified. The process is also dynamic, as newly identified ataxia-related genes can immediately be included. Our strategy results in a high positive molecular diagnostic rate for the genetically heterogeneous group of ataxia disorders and is an important tool for further genotype-phenotype correlation studies.