title: Human MLPA Probe Design (H-MAPD): a probe design tool for both electrophoresis-based and bead-coupled human multiplex ligation-dependent probe amplification assays.
abstract: BACKGROUND
  Multiplex ligation-dependent probe amplification (MLPA) is an efficient and reliable technique for gene dosage analysis. Currently MLPA can be conducted on two platforms: traditional electrophoresis-based, and FlexMAP bead-coupled. Since its introduction in 2002, MLPA has been rapidly adopted in both clinical and research situations. However, MLPA probe design is a time consuming process requiring many steps that address multiple criteria. There exist only one or two commercial software packages for traditional electrophoresis-based MLPA probe design. To our knowledge, no software is yet available that performs bead-coupled MLPA probe design.
  
  
  RESULTS
  We have developed H-MAPD, a web-based tool that automates the generation and selection of probes for human genomic MLPA. The software performs physical-chemical property tests using UNAFold software, and uniqueness tests using the UCSC genome browser. H-MAPD supports both traditional electrophoresis-based assays, as well as FlexMAP bead-coupled MLPA.
  
  
  CONCLUSIONS
  H-MAPD greatly reduces the efforts for human genomic MLPA probe design. The software is written in Perl-CGI, hosted on a Linux server, and is freely available to non-commercial users.
authors.affiliation: Genomics Core Facility, School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA. jzhi@ic.sunysb.edu
authors.forename: Jizu
authors.initials: J
authors.lastname: Zhi
authors.forename: Eli
authors.initials: E
authors.lastname: Hatchwell
mesh_terms: D015342:DNA Probes / Q000138:chemical synthesis / Q000737:chemistry*; D004586:Electrophoresis / Q000379:methods*; D018628:Gene Dosage; D015894:Genome, Human; D006801:Humans; D020407:Internet; D021141:Nucleic Acid Amplification Techniques / Q000379:methods*; D012984:Software
chemical_list: D015342:DNA Probes
references.citation: Genome Res. 2002 Jun;12(6):996-1006
references.pmid: 12045153
references.citation: Genome Res. 2002 Apr;12(4):656-64
references.pmid: 11932250
references.citation: Biotechniques. 2004 Sep;37(3):399-405
references.pmid: 15470894
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W577-81
references.pmid: 15980540
references.citation: Nucleic Acids Res. 2002 Jun 15;30(12):e57
references.pmid: 12060695