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TheScientificWorldJOURNAL
Volume 10 (2010), Pages 2003-2018
http://dx.doi.org/10.1100/tsw.2010.195
Peer-Reviewed Protocol

Design and Generation of MLPA Probe Sets for Combined Copy Number and Small-Mutation Analysis of Human Genes: EGFR as an Example

1Laboratory of Cancer Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
2Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
3Ludwig Center at Dana-Farber/Harvard Cancer Center, Boston, MA, USA
4Division of Translational Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA

Received 26 July 2010; Revised 6 September 2010; Accepted 23 September 2010

Academic Editor: Steve Brown

Copyright © 2010 Malgorzata Marcinkowska et al.

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.