Lo et al. BMC Cancer 2012, 12:235 http://www.biomedcentral.com/1471-2407/12/235 2q34-q36.1, 3p11.2-p26.3, 4p15.1-p15.31, 4q33-q34.2, 6p12.3-p21.2, 6p22.1-p22.3, 9q21.1-q21.3, 10q21.3-25.1, 12p12.31-13.33, 12q14-q15, 13q12.3-14.2, 17p12-13.3, 17q24.2-25.3, Xp22.11, Xp22.13-22.31, Xq21.31-21.33, and Xq25-26.1 (see Additional file 2: Table S2). The chromosomal regions examined in the current array-CGH showed a high loss of heterozygosity (LOH) frequency in our previous genome-wide LOH study [13]. To construct this specialized array, genomic segments fully covering these 18 chromosome regions with 3604 BAC genomic clones without gaps were mapped. BAC clones were purified, amp- lified, and arrayed onto glass slides. The homogenous self- self hybridization image of reference DNA shown in the Additional file 3: Figure S1 (upper left panel) indicates the feasibility of our specialized array-CGH. Block-wise normalization was conducted and a Bayes regression approach was used to identify the regions with chromosomal copy number alterations Tumor DNA from 40 Asian NSCLC patients and 20 Caucasian NSCLC patients were labeled with Cy5 (red dye) and co-hybridized with reference DNA (for Asian samples: 28 matched-normal genomic DNA pool; for Caucasian samples: ten male genomic DNA purchased from Promega) labeled with Cy3 (green dye) for array- CGH. Clinical information for the patients is shown in the Additional file 1: Table S1. A “block-wise normalization” method, which normalized the array- CGH data by the log ratio of the self-self hybridization of reference DNA according to the mean and the stand- ard deviations of each array block, was established (lower panel, Additional file 3: Figure S1). The Bayes regression approach was used to determine the chromo- somal breakpoints [17]. A region was assigned +1, 0, or −1 when its gene dosage is higher, uncertain, or lower than those of its neighbors to define the chromosome alteration regions (Additional file 3: Figure S1), respect- ively. Our array-CGH data has been submitted to Gene Expression Omnibus (GEO) database of NCBI with ac- cession number GSE21276. The chromosome regions show high frequency of chromosomal imbalance and significant correlation with specific cancer sub-type in Asian and Caucasian lung cancer patients The chromosome regions with copy number alteration in 40 Asian and 20 Caucasian NSCLC patients were determined. A region with a frequency of gain or loss greater than 50% was defined as a significant chromo- somal imbalance region [18,19]. In samples from Asian lung cancer patients, we have identified eight regions of chromosomal gain and nine regions of chromosomal loss (Table 1A) harboring 476 genes (UCSC Genome browser). In Caucasian lung cancer patients, eleven Page 4 of 13 chromosome regions with frequent gain and nine regions with frequent loss harboring a total of 459 genes were identified (Table 1B). Interestingly, seven common chromosomal imbalance regions harboring 117 genes, included gain on 3p13-14, 6p22.1, 9q21.13, 13q14.1, and 17p13.3; and loss on 3p22.2-22.3 and 13q13.3 (Table 1A-B) were found in both Asian and Caucasian patients. In addition, when tumors were grouped into two major NSCLC tumor subtypes, adenocarcinoma (ADC) and squamous cell carcinoma (SCC), six chromosomal imbal- ance regions showed difference of more than 50% in alter- ation frequency between ADC and SCC in Asian lung cancer patients (Table 2A). In Caucasian lung cancer patients, 14 chromosome regions showed significant differ- ence between ADC and SCC patients (Table 2B). When tumors were grouped based on the tumor stage, three chromosomal imbalance regions with difference of more than 50% in alteration frequency between early stage (stages I and II) and late stage (stages III and IV) in Asian lung cancer patients (Table 3A) were found. In Caucasian lung cancer patients, five chromosome regions showed higher alteration frequency in late stage patients than early stage patients (Table 3B). The significance of altered biological processes in lung cancer We then used Database for Annotation, Visualization and Integrated Discovery (DAVID) bioinformatics resources [20] to identify the difference of significantly altered biological process between Asian and Caucasian lung cancer patients. The results showed that there were seven common altered biological processes of gene ontology between Asian and Caucasian, including cation transport, metal ion transport, cellular chemical homeo- stasis, chromatin assembly or disassembly, protein-DNA complex assembly, nucleosome assembly, and nucleo- some organization (Figure 1A-B, indicated by * symbol). In addition, unique altered biological processes including monovalent inorganic cation transport, protein oligo- merization, Wnt receptor signaling pathway, regulation of membrane potential, and response to estrogen stimu- lus were found in Asian lung cancer patients (Figure 1A). Unique biological processes in Caucasian included cell surface receptor linked signal transduction, G-protein coupled receptor protein signaling pathway, ion homeo- stasis, cellular cation homeostasis, and chemotaxis (Figure 1B). A total of 134 candidate NSCLC-related genes are selected by MetaCore analysis and integration analysis with the expression array database To select potential NSCLC-related genes for further studies, the following strategy of candidate gene decision was performed (Figure 2). First, a total of 818 genes