Murdoch Children’s Research Institute (MCRI) in collaboration with Lineagen, a Utah-based diagnostic genetic testing and clinical information services company, has developed a new test, called Methylation Specific Quantitative Melt Analysis, for the more accurate and timely diagnosis of Fragile X syndrome.
Fragile X syndrome is a common genetic cause of intellectual disability and autism spectrum disorder.
This syndrome impacts about one in 4,000 children. Approximately 90,000 Australians and over one million Americans are impacted in some way by this syndrome.
A large section of these are women who may not be affected with Fragile X, but carry a DNA ‘premutation’ in their FMR1 gene, which then impacts their children.
One major problem with Fragile X is that this syndrome is not clinically identifiable at a young age. An average age of diagnosis in Australia is about five years, while in the US, it is over three years, according to the Centers for Disease Control and Prevention.
Due to delayed diagnosis, impacted children often do not receive the medical care they need in time.
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MCRI’s associate professor and lead researcher of this international study David Godler said: “The impact of delayed diagnosis is significant and potentially preventable not only to the families but also for our health system. This is why we developed our new test, called Methylation Specific Quantitative Melt Analysis (MS-QMA). This is a one step process, to assist in more accurate and timely diagnosis of Fragile X in affected children referred for genetic testing.”
This one-step process looks at the number of chemical modifications or “marks”, called methylation, added to a FMR1 gene in patients with Fragile X syndrome. Such marks are not usually found in children without the syndrome.
An increase in these marks cut down the production of a protein called FMRP, which is needed for healthy brain development and function.
For the first time, this study shows that the number of these marks get increased, even in people without the usual genetic changes seen in Fragile X syndrome (called CGG repeats).
Previously, this was not known, partly because the regular testing does not look at these marks as part of the initial CGG screen.
The existing testing examines these marks through a second separate test, and only on the restricted number of patients suspected with the typical genetic change (CGG repeats) linked with Fragile X, called full mutation, and ‘large’ permutation alleles. A reason for this is because the second methylation test is expensive.
For this trial, Lineagen and MCRI compared DNA test results of over 300 patients from pediatric clinics in the US and Australia.
As per the standard testing, these patients either had Fragile X mutations or did not have mutations.
Although the second group of patients had no Fragile X mutations diagnosed by standard CGG repeat testing, doctors considered these patients to have some kind of intellectual disability, with or without autism.
The genetic testing was performed in associate professor Godler’s laboratory at MCRI. This testing was done using MS-QMA on male and female samples blinded by Lineagen.
With the lifting of the blind, all male and female patients with Fragile X diagnosis received the exact diagnosis using MS-QMA.
Godler said: “We also identified, for the first time, smaller more common FMR1 alleles that are not usually tested for methylation (a tell-tale sign of Fragile X), that had abnormal methylation signatures in a significant number of affected patients.
“These abnormal signatures were confirmed to be present by the current standard confirmatory methylation test performed by Lineagen. These signatures may compromise function of the FMR1 gene, and potentially lead to Fragile X like clinical features, and is an active area of research for my group.”
Contribution to the findings also came from researchers of the University of Melbourne, Victorian Clinical Genetics Services, Genetics of Learning Disability in Newcastle, and The Royal Children’s Hospital.