General information
The SALSA MLPA Probemix P316 Recessive Ataxias is a research use only (RUO) assay for the detection of deletions or duplications in the APTX, SETX, and FXN genes, which are associated with Ataxia with oculomotor apraxia type 1 (AOA1), type 2 (AOA2), and Friedreich ataxia (FRDA).

AOA1 is an autosomal recessive neurodegenerative disorder characterized by a childhood onset of slowly progressive cerebellar ataxia, followed by oculomotor apraxia and a severe primary motor peripheral axonal motor neuropathy. AOA1 has been associated with mutations in the APTX gene. The APTX gene (9 exons) spans ~29 kb of genomic DNA and is located on chromosome 9p13.3, ~33 Mb from the p-telomere. APTX encodes the aprataxin protein, which is involved in single-stranded DNA repair.

AOA2 usually has its onset between the ages of three and 30 years and is characterised by cerebellar atrophy, axonal sensorimotor neuropathy, and oculomotor apraxia. Mutations in the SETX gene have been associated with AOA2 and amyotrophic lateral sclerosis type 4 (ALS4). SETX encodes the senataxin protein, which is suggested to be involved in DNA and RNA processing. The SETX gene (26 exons) spans ~94 kb of genomic DNA and is located on chromosome 9q34.13, ~132 Mb from the p-telomere.

FRDA is characterized by slowly progressive ataxia with mean onset between 10 and 15 years of age. FRDA is caused by mutations in the FXN gene, leading to reduced expression of the mitochondrial protein frataxin. This deficiency causes degeneration of nervous tissue in the spinal cord, which leads to ataxia. The FXN gene (5 exons) spans ~39 kb of genomic DNA and is located on chromosome 9q21.11, ~69 Mb from the p-telomere. Please note that the major cause of Friedreich’s ataxia is an expansion of an intronic trinucleotide repeat, which cannot be detected with this P316-B4 Recessive Ataxias probemix.

More information is available at https://www.ncbi.nlm.nih.gov/books/NBK1456/, https://www.ncbi.nlm.nih.gov/books/NBK1154/, and https://www.ncbi.nlm.nih.gov/books/NBK1281/.

Probemix content
The SALSA MLPA Probemix P316-B4 Recessive Ataxias contains 50 MLPA probes with amplification products between 131 and 481 nucleotides (nt). This includes ten probes for the APTX gene, one probe for each exon and two probes for exon 2, five probes for the FXN gene and 26 probes for the SETX gene, one probe for each exon. In addition, nine reference probes are included that detect autosomal chromosomal locations. Complete probe sequences and the identity of the genes detected by the reference probes are available online (www.mrcholland.com).

This probemix contains nine quality control fragments generating amplification products between 64 and 105 nt: four DNA Quantity fragments (Q-fragments), two DNA Denaturation fragments (D-fragments), one Benchmark fragment, and one chromosome X and one chromosome Y-specific fragment. More information on how to interpret observations on these control fragments can be found in the MLPA General Protocol and online at www.mrcholland.com.