Despite significant advances in the genetic diagnosis of neurological disorders, a significant number of patients remains genetically undiagnosed. Even extensive whole-exome sequencing studies appear to have a diagnostic yield of 50%.
Repeat expansion disorders are an important cause of neurogenetic disorders but their diagnosis is often challenging due to their phenotypic heterogeneity and time-consuming molecular assessment. Therefore, new methods are needed to interrogate repeat expansions simultaneously and fully take advantage of the developments in the field of next-generation sequencing.
In a recently published study on Lancet Neurology (PMID 35182509), Ibañez et al. assessed the utility of a whole genome sequencing (WGS) approach to detect repeat expansions in patients recruited from the 100 000 Genomes Project and the Genomic Laboratory based at Cambridge University Hospitals. Diagnostic accuracy was retrospectively evaluated using data from patients who had previously been tested by PCR for repeat expansions known to cause neurological disease. Clinical accuracy to detect repeat expansions was evaluated in previously genetically tested and undiagnosed patients recruited to the 100 000 Genomes Project, who were suspected of having a genetic neurological disorder.
Diagnostic accuracy evaluation for the 13 neurogenetic disease-associated loci studied (AR, ATN1, ATXN1, ATXN2, ATXN3, ATXN7, C9orf72, CACNA1A, DMPK, FMR1, FXN, HTT, and TBP) revealed a minimum of 97·3% sensitivity and 99·6% specificity when compared with PCR testing, which could be further improved by visual inspection to detect false positive and reclassify false negative alleles in samples with biallelic expansions. This was particularly important in the FMR1 gene, in which false positives were common. There was also high concordance between WGS and PCR for repeat size estimates when the allele was shorter than the sequencing read length (150 bp).
Regarding clinical accuracy, WGS identified 81 repeat expansions in samples from 11 631 patients, of which 68 were confirmed by PCR as repeat expansions in the full pathogenic range (16% false discovery rate, predominantly due to FMR1 alleles).
The authors discuss the algorithm designed and used in this study, considering that it can reliably assess the most common disease-causing repeat expansions, and its limitations, mainly due to the underestimation of the size of large expansions and the false positives in the FMR1 alleles. They also present a clinical diagnostic workflow for WGS, proposing visual inspection for all calls classified as expanded to detect false positives, and for biallelic expansions for which only one expanded allele has been detected.
This study further supports implementation of WGS in clinical laboratories and its transition as a possible first-line diagnostic test in patients in which a neurogenetic disorder is suspected. This is particularly important since progresses made in emerging therapies for neurogenetic disorders will lead to an even greater need of early detection.
- WGS showed high sensitivity and specificity when compared with the gold standard to detect repeat expansions.
- The method used was able to identify repeat expansions in patients with a suspected but still undiagnosed neurogenetic disorder, with a 16% false discovery rate.
- Visual inspection is still essential for all calls classified as expanded to detect false positives and for biallelic expansions for which only one expanded allele has been detected.
- This study supports a role for WGS in the diagnosis of repeat expansion disorders, further expanding its importance as a tool in undiagnosed rare neurological disease
Ibañez K, Polke J, Hagelstrom RT, et al. Whole genome sequencing for the diagnosis of neurological repeat expansion disorders in the UK: a retrospective diagnostic accuracy and prospective clinical validation study. Lancet Neurol. 2022;21(3):234-245. doi:10.1016/S1474-4422(21)00462-2 https://pubmed.ncbi.nlm.nih.gov/35182509/
Ngo KJ, Rexach JE, Lee H, et al. A diagnostic ceiling for exome sequencing in cerebellar ataxia and related neurological disorders. Hum Mutat. 2020;41(2):487-501. doi:10.1002/humu.23946 https://pubmed.ncbi.nlm.nih.gov/31692161/