Multiplex ligation-dependent probe amplification using a completely synthetic probe set

Biotechniques. 2004 Sep;37(3):399-405. doi: 10.2144/04373ST04.


The recent development of multiplex ligation-dependent probe amplification (MLPA) has provided an efficient and reliable assay for dosage screening of multiple loci in a single reaction. However, a drawback to this method is the time-consuming process of generating a probe set by cloning in single-stranded bacteriophage vectors. We have developed a synthetic probe set to screen for deletions in a region spanning 18.5 Mb within chromosome 3q. In a pilot study, we tested 15 synthetic probes on 4 control samples and on 2 patients previously found to possess a heterozygous deletion in the region 3q26-q28. These synthetic probes detected deletions at all previously known deleted loci. Furthermore, using synthetic probes, the variability of results within samples was similar to that reported for commercially available M13-derived probes. Our results demonstrate that this novel approach to MLPA provides a generic solution to the difficulties of probe development by cloning; such synthetically generated probes may be used to screen a large number of loci in a single reaction. We conclude that the use of synthetic probes for MLPA is a rapid, robust, and efficient alternative for research (and potentially diagnostic) deletion and duplication screening of multiple genomic loci.

Publication types

  • Research Support, Non-U.S. Gov't
  • Technical Report

MeSH terms

  • Chromosome Deletion
  • DNA Mutational Analysis / methods*
  • DNA Probes / chemical synthesis*
  • DNA Probes / genetics
  • Gene Dosage*
  • Nucleic Acid Amplification Techniques / methods*


  • DNA Probes