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ME029 FMR1-AFF2

SALSA MLPA Probemix ME029 FMR1-AFF2 detects copy number variations and methylation status of the genes FMR1 and AFF2.

Specifications

Contents: 48 MLPA probes, including 20 probes for FMR1 and 14 probes for AFF2. Of these, 6 provide information on the methylation status of FMR1 exon 1 and 3 of APP2 exon 1.

Tissue: human genomic DNA.

Application: research on fragile X syndrome (FXS), fragile X-associated tremor/ataxia syndrome (FXTAS), fragile X-associated primary ovarian insufficiency (FXPOI), fragile XE syndrome (FRAXE).

For research use only (RUO). Not for use in diagnostics.

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List Prices Documentation

General information

The SALSA MS-MLPA Probemix ME029 FMR1-AFF2 is a research use only (RUO) assay for the detection of aberrant methylation of one or more sequences of the FMR1 and AFF2 genes. This probemix can also be used to detect deletions/duplications in the aforementioned genes.

The FMR1 (FRAXA) gene (17 exons) spans ~39 kb on Xq27.3. The AFF2 (FMR2 , FRAXE) gene (21 exons) spans ~500 kb of genomic DNA and is located in Xq28, at a distance of ~600 kb telomeric of FMR1. The most common defect in these two genes is an expansion of a trinucleotide repeat sequence in exon 1.

For the FMR1 gene, the trinucleotide repeat motif is CGG, where alleles are classified as normal (unmethylated alleles; 5-44 repeats), intermediate (45-54 repeats), premutation (55-200 repeats) and full-mutation (>200 repeats) (Jorge et al. 2013). Hyper-expansion of FMR1 CGG repeats to >200 is accompanied by hypermethylation of the promoter and gene silencing, which results in Fragile X syndrome (FXS) due to a reduced or absent FMR1 protein (FMRP) (Liu et al. 2021). FXS has an X-linked dominant inheritance pattern and is the most common inherited form of intellectual disability and autism spectrum disorders (Pugin et al. 2017) with a population prevalence of about 1/4000–9000 males and 1/7000–15,000 females (Rzonka et al. 2016). Individuals with a repeat range of 55 to 200 repeats are said to be carriers of a premutation, which does not affect the promoter methylation. However, it can lead to fragile X-associated tremor/ataxia syndrome (FXTAS) affecting primarily men which is characterised by late-onset (>50 years), progressive cerebellar ataxia and intention tremor followed by cognitive impairment. Premutations can also lead to fragile X-associated primary ovarian insufficiency (FXPOI) in females, which manifests as cessation of menstrual periods before reaching the age of 40 (Pugin et al. 2017).

In the AFF2 gene a CCG expansion can occur. In the normal population, the number of repeats varies between 6 and 35 and is increased to >200 in the Fragile XE Syndrome (FRAXE). To what extent the alleles with CCG repeats in the range between 36 and 199 may exhibit a pathogenic role remains elusive. FRAXE is the most prevalent form of non-syndromic X-linked intellectual disability with a milder to borderline phenotype as compared to FXS. It has also been described that microdeletions in AFF2 may be a significant cause of premature ovarian failure (Murray et al. 1999). However, in contrast to FXS, reports of AFF2 full expansions are very rare and the dynamics of this repeat is not as clearly characterized as that of FMR1 leading to poorly defined phenotypes (Jorge et al. 2013).

Results obtained with this SALSA MLPA Probemix ME029 FMR1-AFF2 have shown that FMR1 promoter methylation can be easily detected in DNA samples from males with a FMR1 full mutation (>200 repeats). However, a distinction between premutation alleles and normal alleles cannot be made. For female DNA samples, the presence of an imprinted X-chromosome complicates analysis and can easily result in false positive results. In our studies, the variation in results was too high to reliably detect all full mutation female samples. For methylation quantification, this product can be used for the analysis of the methylation status of the promoters of FMR1 and AFF2 in male samples only. Thus, even if it is not possible to measure the length of the repeat by MLPA, the methylation at certain CpG sequences in the promoter region of these genes can still be quantified by MS-MLPA.

More information is available at https://www.ncbi.nlm.nih.gov/books/NBK1384/(FMR1-Related Disorders)

Regulatory status

SALSA MLPA Probemix ME029 FMR1-AFF2 is for research use only (RUO) in all territories.

Product documentation

Version C1

Other versions

Contact us for earlier versions.

List prices

Product

Item no.
Description
Technology
Price
ME029-025R
SALSA MLPA Probemix ME029 FMR1-AFF2 – 25 rxn
MS-MLPA
€ 296.00
ME029-050R
SALSA MLPA Probemix ME029 FMR1-AFF2 – 50 rxn
MS-MLPA
€ 580.00
ME029-100R
SALSA MLPA Probemix ME029 FMR1-AFF2 – 100 rxn
MS-MLPA
€ 1135.00

Required reagents

A general SALSA MLPA Reagent Kit and SALSA HhaI are required for MS-MLPA experiments (to be ordered separately).

Item no.
Description
Technology
Price
EK1-FAM
SALSA MLPA Reagent Kit – 100 rxn – FAM (6 vials)
MLPA MS-MLPA
€ 361.00
EK1-CY5
SALSA MLPA Reagent Kit – 100 rxn – Cy5 (6 vials)
MLPA MS-MLPA
€ 361.00
EK5-FAM
SALSA MLPA Reagent Kit – 500 rxn – FAM (5×6 vials)
MLPA MS-MLPA
€ 1658.00
EK5-CY5
SALSA MLPA Reagent Kit – 500 rxn – Cy5 (5×6 vials)
MLPA MS-MLPA
€ 1658.00
EK20-FAM
SALSA MLPA Reagent Kit – 2000 rxn – FAM (5×6 vials)
MLPA MS-MLPA
€ 6373.00
SMR50
SALSA HhaI – 115 μl
MS-MLPA
€ 48.00

Price details & ordering

The prices above are list prices for direct orders from MRC Holland. Contact us for a quote that takes discounts and additional costs (such as shipping costs) into account. Different prices apply for orders through one of our sales partners; contact your local supplier for a quote.

More information about ordering & prices

Positive samples

Inclusion of a positive sample is usually not required, but can be useful for the analysis of your experiments. MRC Holland has very limited access to positive samples and cannot supply such samples. We recommend using positive samples from your own collection. Alternatively, you can use positive samples from an online biorepository, such as the Coriell Institute.

See this support article for commercially available positive samples that can be used with this product.

Resources

General MLPA resources

MLPA education

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