Analysis of DNA copy number aberrations by multiple ligation-dependent probe amplification on 50 intestinal type gastric cancers

Abstract Background and Objectives The molecular genetic alterations leading to gastric malignancy are largely unknown. This study aimed to unravel the genomic DNA copy number aberrations (CNAs) profile during gastric tumorigenesis. Methods In this study, we performed genomic profiling in a set of 50 intestinal type gastric carcinomas by a PCR‐based relative quantification method, multiple ligation‐dependent probe amplification (MLPA) with 112 cancer‐related gene loci selected throughout each human chromosome as probes of MLPA assay. Results Numerous chromosomal DNA CNAs, including gains of 3p22, 4q25, 8q24, 11p13, and 20q13, and losses of 1p36 and 9p21, were identified by MLPA assay as recurrent DNA CNAs in gastric cancer. Moreover, we found the median numbers of gains, losses, and total CNAs were significantly higher in lymph node metastasis positive patients than in cases without metastasis. And gain of 11p13 and losses of 9p21.3, 11q13.3, 17q25.3, and 22q11.23 were associated with lymph node metastasis ( P < 0.05). Finally, two major groups, including G1 + 2 with a large number of CNAs and G3 + 4 with a small number of CNAs, can be successfully distinguished by hierarchical cluster analysis. Conclusions Our results proved MLPA is a reliable and efficient method to evaluate DNA copy number changes in gastric cancers. J. Surg. Oncol. 2011; 103:124–132. © 2010 Wiley‐Liss, Inc.