Abstract
BackgroundMultiplex ligation-dependent probe amplification (MLPA) was originally described as an efficient and reliable technique for gene dosage or DNA copy number variation (CNV) analysis. Due to its low cost, reliability, sensitivity, and relative simplicity, MLPA has rapidly gained acceptance in research and diagnostic laboratories, and fills the gap between genome-wide analysis and single gene analysis. A number of new applications have been developed shortly after the introduction of MLPA, including methylation-specific MLPA (MS-MLPA), the use of MLPA in SNP genotyping, copy number analysis in segmentally duplicated regions, etc. However, probe design is time consuming and error prone. Recently software has been developed to help human genomic MLPA probe selection and optimization. For other genomes and MS-MLPA, probe design remains a challenge.FindingsThis paper describes a number of new features added to the previous H-MAPD software, which include: 1) probe selection for MS-MLPA; 2) support of mouse and rat genomes; 3) a set of new stuffer sequences. In addition, a physical-chemical property verification tool was implemented to verify user defined probes.ConclusionsMAPD is a web-based tool which is freely available to non-commercial users. The previous H-MAPD software has been used by about 200 users from more than 30 countries. With the new features, the author hopes MAPD will bring more convenience to the MLPA community.
Highlights
Multiplex ligation-dependent probe amplification (MLPA) was originally described as an efficient and reliable technique for gene dosage or DNA copy number variation (CNV) analysis
The previous H-MAPD software has been used by about 200 users from more than 30 countries
One and only one methylation-sensitive restriction site should be present in the left hybridizing sequence (LHS) and right hybridizing sequence (RHS), otherwise it will be hard to distinguish which site is digested
Summary
MAPD is a web-based tool which is freely available to non-commercial users. The previous H-MAPD software has been used by about 200 users from more than 30 countries. Findings Like the original software [1], MAPD supports both electrophoresis-based and bead-coupled MLPA platforms. Users will specify the desired protocol (electrophoresis-based or bead-coupled) and other experiment parameters (See Additional file 1: MAPD input page). One and only one methylation-sensitive restriction site should be present in the LHS (left hybridizing sequence) and RHS (right hybridizing sequence), otherwise it will be hard to distinguish which site is digested. The union of stuffer/tag/primer sequences to the hybridizing sequences may introduce new recognition sites for the methylation-sensitive restriction enzyme being used.
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