Lo et al. BMC Cancer 2012, 12:235 http://www.biomedcentral.com/1471-2407/12/235 Page 11 of 13 Figure 4 DNA copy number and protein expression level validation in specimens from lung cancer patients. (A) Representative CISH images of ARHGAP19 and ZNF322A genes in paraffin-embedded lung tumor tissue. Images taken from tumor without gene copy number amplification (left) and with gene copy number amplification (right). The enlarged image of one nucleus is shown on the lower right corner. CISH images: 400X magnification. (B) Representative IHC images of PAFAH1B1 protein in tissue array. Patients with protein overexpression are indicated by + symbol. Patients with normal expression are indicated by – symbol. IHC images: 200X magnification. patients. In addition, both qPCR and RT-qPCR con- firmed significant gene amplification and mRNA overex- pression in tumors from Asian but not from Caucasian lung cancer patients (Figure 3A-B). Interestingly, in rela- tion to clinical pathological parameters of Asian lung cancer patients, mRNA overexpression of ARHGAP19 and FRAT2 was significantly associated with lung SCC (Additional file 6: Table S5). ARHGAP19 encodes a Rho GTPase-activating protein that stimulates the intrinsic GTP hydrolysis activity of Rho family proteins [23]. ARHGAP family genes are considered to be cancer- associated genes because their genetic alterations lead to carcinogenesis through the dysregulation of Rho/Rac/ Cdc42-like GTPases [24]. The up-regulation of the FRAT2 gene has been reported in human gastric cancer [25] and has been implicated in carcinogenesis through activation of the Wnt signaling pathway [26]. Our previ- ous study showed that more than 50% of Taiwanese lung cancer patients had alterations in proteins involved in Wnt/β-catenin signaling [27]. It is important to investi- gate the role of ARHGAP19 and FRAT2 alterations in SCC lung tumorigenesis and their correlations with Rho and Wnt signaling pathways. Interestingly, ZNF322A on 6p22.1 showed significant gene amplification and mRNA overexpression in Cauca- sian, and borderline significant in Asian lung cancer patients (Figure 3). The DNA copy number validation for ZNF322A gene was lower than the array CGH result because the BAC may harbor some other genes in addition to ZNF322A. ZNF322A has been reported to be a novel human C2H2 Krüppel-like zinc-finger protein, which regulates transcriptional activation in the MAPK signaling pathways. The Krüppel zinc-finger protein is involved in the regulation of normal cell growth, differ- entiation, embryogenesis, and tumorigenesis [28]. Identi- fication of the role of ZNF322A in lung tumorigenesis is worthy of further study. Note that no common tumor subtype-specific regions for ADC and SCC were found in Asian and Caucasian lung cancer patients when the genomic alteration profiles were compared (Table 2A). Even in the same racial group, ex- treme difference of chromosome alterations could occur between ADC and SCC. These data implicated that distinct etiological mechanism in addition to tobacco and environ- mental exposures are involved in lung cancer of Asian from Caucasian, supporting the epidemiologic observation that lung cancer in Asian shows relatively high percentage of non-smoking female ADC. Notably, Broët et al. [29] identi- fied molecular differences between NSCLCs from East- Asian and Western European patients by using single nucleotide polymorphism microarray platform, and revealed several copy number aberrations significantly associated with ethnicity (gain on 1p36, 16p13, 16p12, and 16p11 in East-Asian; loss on 19p13 in Western European patients), EGFR mutation (gain on 1p36, 1p35, 7p22-21, 7p15-12, 14q31-32, 16p13, and 16p12 in EGFR mutant tumors; loss on 21q21-22 in EGFR wild-type tumors), but not to K-ras or p53 mutations. Correlation of the muta- tional spectrum of EGFR, K-ras, p53, and ALK genes to our array-CGH data warrants further investigations. Conclusions In conclusion, our specialized array-CGH results provide an invaluable database of specific chromosome regions