Detection of FMR1 CGG Repeat Expansions Using Buccal Swab and Blood Samples of Children With Intelectual Disability in A Resource-Limited Country

Abstract

Fragile X Syndrome (FXS), the most common inherited intellectual disability, is caused by CGG-repeat expansions in the FMR1 gene. In resource-limited settings such as Indonesia, the absence of systematic screening programs complicates early detection. This study compared the performance of buccal swab and blood samples in detecting FMR1 repeat expansions to facilitate non-invasive screening. A total of 164 male students with intellectual disabilities in Jakarta provided paired buccal swab and blood samples. Conventional PCR was used for initial screening, followed by Triplet-Primed PCR (TP-PCR) with Melt Curve Analysis (MCA) and sizing confirmation by fluorescent TP-PCR and capillary electrophoresis. Conventional PCR identified 159 normal alleles, three grey zones, and two full mutations, resulting in an FXS prevalence of 1.22 %. A perfect concordance was observed between buccal swab and blood samples (Cohen’s Kappa = 1.000). Additional TP-PCR MCA analysis on 80 selected samples revealed inconsistencies in buccal swab results, with 12 cases classified as indeterminate, suggesting potential DNA quantity and/or quality issues. These findings indicated that buccal swabs are a feasible, non-invasive sampling method to screen FXS via conventional PCR, though further optimization is required for TP-PCR MCA. This study represents the first FXS screening in Jakarta, emphasizing the importance of early detection and scalable genetic testing strategies, particularly in resource-limited settings.