Abstract
Multiplex ligation-dependent probe amplification (MLPA) is a multiplex copy number analysis method that is routinely used to identify large mutations in many clinical and research labs. One of the most important drawbacks of the standard MLPA setup is a complicated, and therefore expensive, procedure of generating long MLPA probes. This drawback substantially limits the applicability of MLPA to those genomic regions for which ready-to-use commercial kits are available. Here we present a simple protocol for designing MLPA probe sets that are composed entirely of short oligonucleotide half-probes generated through chemical synthesis. As an example, we present the design and generation of an MLPA assay for parallel copy number and small-mutation analysis of the EGFR gene.
Highlights
Copy number variation (CNV) in the human genome has become well recognized in recent years
Genomic deletion mutations occurring in genes that cause Mendelian disorders are a special subcategory of germline CNVs, and account for up to 70% of all mutations seen in some genes (e.g., BRCA1, DMD, TSC2, STK11)[3,4,5,6,7]
Multiplex ligation-dependent probe amplification (MLPA) was designed as a copy number analysis tool, and it has been successfully used in the testing and identification of hundreds of large mutations in numerous disease-related genes, including DMD, BRCA1, NF1, STK11, and TSC2
Summary
Copy number variation (CNV) in the human genome has become well recognized in recent years. MLPA was designed as a copy number analysis tool, and it has been successfully used in the testing and identification of hundreds of large mutations in numerous disease-related genes, including DMD, BRCA1, NF1, STK11, and TSC2. The main disadvantage of the standard MLPA setup is a complicated and time-consuming (and expensive) process of probe design and generation This is due to the necessity for creating long 3’ half-probes (~100–400 nt). This is done by cloning 3’ half-probes in specially prepared M13 vectors, enabling insertion of arbitrary numbers of nucleotides into those probes[16] This disadvantage seriously limits the applicability of MLPA to novel genes or sets of genes for which readyto-use commercial kits are not available. We present here the design of an MLPA probe set (assay) for the combined copy number and small-mutation analysis of the EGFR gene. Capillary electrophoresis: CE analysis can be performed on any standard multicapillary DNA analyzer (e.g., ABI-Prism 3130XL, 3100, 1700 [Applied Biosystems], CEQ-2000, 8000, 8800 [Beckman])
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