Synthetic probe design
Although MRC-Holland offers an ever-growing range of MLPA probemixes, your application of interest may be too rare or not yet sufficiently investigated to warrant the development of a new SALSA MLPA probemix. Alternatively, you may have purchased an SALSA MLPA kit and would like to add some probes of your own. In both cases, the solution is to design your own synthetic MLPA probes.

About 11 probes can be included in a synthetic probemix. Designing synthetic probes consists of the following steps:
  1. Determining the genes or genomic region of interest
  2. Obtaining genomic sequences from NCBI website
  3. Determining exon boundaries and SNPs using NCBI Blast and UCSC BLAT
  4. Designing your probes based on the mRNA sequence obtained
  5. Order probes from synthetic oligo supplier and a SALSA MLPA kit from MRC-Holland
Detailed guidelines on how to design synthetic MLPA probes and the necessary RAW program can be found below. Unfortunately, we cannot offer additional support on probe design. Please read our synthetic probe design protocol very carefully before you start designing. To facilitate data analysis we have developed SALSA MLPA kits P200/P300 Reference. These kits contain control fragments, reference probes and space to include your own synthetic probes.
References for MLPA synthetic probe design
  • Roelfsema JH, et al. (2005) Genetic Heterogeneity in Rubinstein-Taybi Syndrome: Mutations in Both the CBP and EP300 Genes Cause Disease Am J Hum Genet 76, 4:572-80.
  • White SJ, et al. (2004). Two-color multiplex ligation-dependent probe amplification: detecting genomic rearrangements in hereditary multiple exostoses Hum Mutat 24, 1:86-92.
  • Stern RF, et al. (2004). Multiplex ligation-dependent probe amplification using a completely synthetic probe set Biotechniques 37, 3:399-405.
  • Vink GR, et al. Mutation screening of EXT1 and EXT2 by direct sequence analysis and MLPA in patients with multiple osteochondromas: splice site mutations and exonic deletions account for more than half of the mutations Eur J Hum Genet 13, 4:470-4.
  • Langerak P, et al. (2005). Rapid and quantitative detection of homologous and non-homologous recombination events using three oligonucleotide MLPA. Nucleic Acids Res 9;33(22):e188.
  • Harteveld CL, et al. (2005). Nine unknown rearrangements in 16p13.3 and 11p15.4 causing {alpha}- and {beta}-thalassemia characterised by high resolution multiplex ligation-dependent probe amplification. J Med Genet 13.
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