Array-Based FMR1 Sequencing and Deletion Analysis in Patients with a Fragile X Syndrome–Like Phenotype

Abstract

BackgroundFragile X syndrome (FXS) is caused by loss of function mutations in the FMR1 gene. Trinucleotide CGG-repeat expansions, resulting in FMR1 gene silencing, are the most common mutations observed at this locus. Even though the repeat expansion mutation is a functional null mutation, few conventional mutations have been identified at this locus, largely due to the clinical laboratory focus on the repeat tract.Methodology/Principal FindingsTo more thoroughly evaluate the frequency of conventional mutations in FXS-like patients, we used an array-based method to sequence FMR1 in 51 unrelated males exhibiting several features characteristic of FXS but with normal CGG-repeat tracts of FMR1. One patient was identified with a deletion in FMR1, but none of the patients were found to have other conventional mutations.Conclusions/SignificanceThese data suggest that missense mutations in FMR1 are not a common cause of the FXS phenotype in patients who have normal-length CGG-repeat tracts. However, screening for small deletions of FMR1 may be of clinically utility.

C9orf72 hypermethylation protects against repeat expansion-associated pathology in ALS/FTD

“…This would be analogous to Fragile X syndrome where repeat expansion mutations in FMR1 cause dense promoter hypermethylation and transcriptional silencing, resulting in a loss of function [49, 61]. Notably, both nonsense and missense FMR1 mutations are also associated with Fragile X syndrome, supporting the loss of function hypothesis [11, 12, 25, 48]. In contrast, nonsense and missense C9orf72 mutations were not found in a large ALS cohort [29].…”

Recent advances in assays for the fragile X-related disorders

“…For those cases presenting with strong FXS-like symptoms but no evidence of repeat expansion or an FMRP deficit, other sorts of assays like HRM of the FMR1 coding sequence (Handt et al 2014), array-based sequencing (Collins et al 2010b), massively parallel sequencing (Collins et al 2010a) or sequencing of target custom capture libraries (Quartier et al 2017) may be required.…”

Single-tube methylation-specific duplex-PCR assay for rapid and accurate diagnosis ofFragile X Mental Retardation 1–related disorders

“…While array-based methods primarily target FMR1 sequence deletions [32,33], and not CGG-repeat expansion mutation that accounts for more than 99% of FXS cases, latest advancements in parallel sequencing (single-molecule, real-time or SMRT) have enabled sequence characterization of fully expanded FMR1 alleles of up to approximately 750 CGG repeats [34] although the high cost-factor precludes its application in routine clinical setting. Numerous PCR-based assays have been developed in attempts to simplify FXS diagnosis.…”