New Way of Testing for Fragile X May Be Faster and Cheaper

Using a genetic technique called triplet-primed polymerase chain reaction (TP-PCR) could enable practical and inexpensive diagnosis of fragile X syndrome, a study suggests.

The study, “Repeat expansion and methylation-sensitive triplet-primed polymerase chain reaction for fragile X mental retardation 1 gene screening in institutionalised intellectually disabled individuals,” was published in the Singapore Medical Journal.

Fragile X is caused by a repeat expansion in the FMR1 gene. Essentially, FMR1 has a sequence where the same few nucleotides (the ‘letters’ of DNA) are repeated in the same order a certain number of times. Normally, people have less than 40 repeats, but more than 200 are found in those with this disorder. This repeat expansion causes the gene to become methylated (methyl chemical groups bound to DNA) – in effect, ‘turning it off.’

The gold standard for identifying repeat expansions in FMR1 is Southern blot, where genes of different sizes move differently through a specialized gel when an electric current is applied. However, this technique can be time-consuming.

More recently, tests based on TP-PCR have gained attention as faster and cheaper ways of doing this diagnosis. This approach involves amplifying — that is, making multiple copies — of the repetitive sequence region. Then, the size of the amplified region can be determined based on biochemical assays.

Researchers used TP-PCR in 109 people who were institutionalized at the Centre for Social Rehabilitation of Intellectual Disability Kartini in Temanggung, Indonesia. All had some kind of intellectual disability, but were lacking a definitive diagnosis.

Participants were first tested with the FastFrax FMR1 Identification Kit, a test based on TP-PCR that specifically aims to distinguish expanded from non-expanded FMR1 genes.

Results showed five individuals with such expansions, in comparison to a 53-repeat control.

These five people underwent further testing with the FastFraX FMR1 Sizing Kit and the FastFraX FMR1 Methylation Status Kit tests, which aim to determine the exact size of the FMR1 repeat region and the amount of methylation. This revealed that two of the five had fragile X-causing expansions (over 200 repeats), while the other three did not reach this threshold.

Overall, “[r]epeat expansion and methylation-specific TP-PCR is practical, effective and inexpensive for the diagnosis of FXS [fragile X syndrome], especially in high-risk populations,” the scientists wrote.

“The savings could be greater when such a study is applied in a much larger population with lower prevalence (e.g. newborn screening),” they added.

Three of the study’s seven authors work for Biofactory, which markets the FastFrax kits in Singapore.