Applying microsatellite multiplex PCR analysis (MMPA) for determining allele copy-number status and percentage of normal cells within tumors

Carles Garcia-Linares; Jaume Mercadé; Bernat Gel; Josep Biayna; Ernest Terribas; Conxi Lázaro; Eduard Serra

doi:10.1371/journal.pone.0042682

Applying microsatellite multiplex PCR analysis (MMPA) for determining allele copy-number status and percentage of normal cells within tumors

PLoS One. 2012;7(8):e42682. doi: 10.1371/journal.pone.0042682. Epub 2012 Aug 15.

Authors

Carles Garcia-Linares¹, Jaume Mercadé, Bernat Gel, Josep Biayna, Ernest Terribas, Conxi Lázaro, Eduard Serra

Affiliation

¹ Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona, Barcelona, Spain.

Abstract

The study of somatic genetic alterations in tumors contributes to the understanding and management of cancer. Genetic alterations, such us copy number or copy neutral changes, generate allelic imbalances (AIs) that can be determined using polymorphic markers. Here we report the development of a simple set of calculations for analyzing microsatellite multiplex PCR data from control-tumor pairs that allows us to obtain accurate information not only regarding the AI status of tumors, but also the percentage of tumor-infiltrating normal cells, the locus copy-number status and the mechanism involved in AI. We validated this new approach by re-analyzing a set of Neurofibromatosis type 1-associated dermal neurofibromas and comparing newly generated data with results obtained for the same tumors in a previous study using MLPA, Paralog Ratio Analysis and SNP-array techniques.Microsatellite multiplex PCR analysis (MMPA) should be particularly useful for analyzing specific regions of the genome containing tumor suppressor genes and also for determining the percentage of infiltrating normal cells within tumors allowing them to be sorted before they are analyzed by more expensive techniques.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Alleles*
Gene Dosage*
Humans
Microsatellite Repeats / genetics*
Multiplex Polymerase Chain Reaction / methods*
Neoplasms / genetics*
Neoplasms / pathology

Grants and funding

This work was supported by grants from the Spanish Health Research Foundation: Instituto de Salud Carlos III (PI051155, PI081871, PI10/01422 and ISCIII-RTICC RD06/0020/1050; RD06/0020/1051); the Government of Catalonia (2009SGR290); the Asociación Española Contra el Cáncer (AECC) that recognizes and supports our group as a Grupo Estable de Investigación Oncológica 2010. The authors would like to especially acknowledge the Asociación Española de Afectados de Neurofibromatosis for their constant support to our research. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.