Whole Genome Sequencing (WGS) to detect repeat expansion disorders including Fragile X Syndrome

Updated: Mar 1

Repeat expansions in the human genome are the most common cause of inherited neurological disorders. They occur when short sequences of DNA are repeated many times over within genes at specific loci (locations on a chromosome). Scientists have recognised that repeat expansions at different loci can cause a single neurological disorder just as different neurological disorders with similar symptoms can manifest from a single locus expansion. This makes it very difficult to identify single genes of interest for genetic testing. Moreover, conventional genetic testing using PCR (polymerase chain reaction) is locus-specific, meaning that only one gene can be tested at a time for presence of repeat expansions. Reaching an accurate diagnosis is thus a challenging, inefficient, and expensive process for clinics, patients, and their families, and up to 70% of individuals with suspected neurological disorders remain genetically undiagnosed.

To address this issue, the Genomics England Research Consortium have for the first time trialled whole genome sequencing (WGS) as a single genetic test to screen thousands of patients for repeated expansions in 13 disorder-associated loci. FMR1 was included as the locus of Fragile X Syndrome (FXS), which remains the leading genetic cause of intellectual disability. Samples from 404 patients suspected of having neurological disorders were acquired from NHS Laboratories and tested using WGS. This automated process correctly identified 215 of 221 expanded and 1316 of 1321 non-expanded sequences, which reflects 97.3% sensitivity (true positive detection) and 99.6% specificity (true negative detection) in WGS. Manual inspection of these initial results allowed for the correction of 4 of 6 false negatives and all 5 false positives, which increased sensitivity and specificity to 99.1% and 100%. To compare diagnostic accuracy of WGS with PCR using samples from the 100 000 Genomes Project, 11631 PCR tested yet undiagnosed patients were screened with WGS. Of the 81 patients identified with repeat expansions, 68 were confirmed to have pathogenic expansions, 11 with non-pathogenic expansions, and 2 with false positive expansions.

Researchers highlighted that it was common for WGS to falsely identify pathogenic FMR1 expansions, and that manual inspection was critical to avoid this. Focused efforts are thus required to optimise specificity of the automated WGS process specifically for the FMR1 locus associated with FXS. As a result of this study, 64 patients received official diagnoses of neurological disorders, 10 of which were that of FXS for individuals under the age of 20. These findings support the use of WGS in standard clinical practice as an accurate, rapid diagnostic test for repeat expansions which underlie neurological disorders, including FXS.

Emma Mather-Pike

Research Information Manager

Fragile X Society

23 February 2022