ProSeeK: A web server for MLPA probe design

Lorena Pantano, Lluís Armengol, Sergi Villatoro, Xavier P. Estivill

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

Background: The technological evolution of platforms for detecting genome-wide copy number imbalances has allowed the discovery of an unexpected amount of human sequence that is variable in copy number among individuals. This type of human variation can make an important contribution to human diversity and disease susceptibility. Multiplex Ligation-dependent Probe Amplification (MLPA) is a targeted method to assess copy number differences for up to 40 genomic loci in one single experiment. Although specific MLPA assays can be ordered from MRC-Holland (the proprietary company of the MLPA technology), custom designs are also developed in many laboratories worldwide. After our own experience, an important drawback of custom MLPA assays is the time spent during the design of the specific oligonucleotides that are used as probes. Due to the large number of probes included in a single assay, a number of restrictions need to be met in order to maximize specificity and to increase success likelihood. Results: We have developed a web tool for facilitating and optimising custom probe design for MLPA experiments. The algorithm only requires the target sequence in FASTA format and a set of parameters, that are provided by the user according to each specific MLPA assay, to identify the best probes inside the given region. Conclusion: To our knowledge, this is the first available tool for optimizing custom probe design of MLPA assays. The ease-of-use and speed of the algorithm dramatically reduces the turn around time of probe design. ProSeeK will become a useful tool for all laboratories that are currently using MLPA in their research projects for CNV studies.

Original languageEnglish
Article number573
JournalBMC Genomics
Volume9
DOIs
Publication statusPublished - 28 Nov 2008
Externally publishedYes

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Multiplex Polymerase Chain Reaction
Disease Susceptibility
Oligonucleotides
Netherlands
Genome
Technology
Research

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

ProSeeK : A web server for MLPA probe design. / Pantano, Lorena; Armengol, Lluís; Villatoro, Sergi; Estivill, Xavier P.

In: BMC Genomics, Vol. 9, 573, 28.11.2008.

Research output: Contribution to journalArticle

Pantano, Lorena ; Armengol, Lluís ; Villatoro, Sergi ; Estivill, Xavier P. / ProSeeK : A web server for MLPA probe design. In: BMC Genomics. 2008 ; Vol. 9.
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