Cells then were stained with 500 ul of propidium iodide (PI) staining solution (50 ug/ml PI, 0.1%Triton X-100, 200 mg/ml DNase-free RNase in PBS) for 30 min at room temperature in the dark. Ten thousand events per sample were acquired using a LSR-II flow cytometer (Becton-Dickinson, San Jose, CA, USA), ICG-001 cell line and the percentage of cells in G0/G1, S, G2/M and Sub-G2/M phases of the cell cycle were determined using FACS DIVA software (Becton-Dickinson). Annexin V and propidium iodide (Annexin V–PI) staining https://www.selleckchem.com/products/Tipifarnib(R115777).html apoptosis test 4 × 105 cells were seeded into each well of a 6-well plate for 48 h. The staining was carried out according to the instructions

provided by the manufacturer of PE Annexin V Apoptosis Detection Kit I, BD Pharmingen (BD Biosciences, USA). Briefly, cells were washed with PBS, suspended in 1X binding buffer and then added Fer-1 cell line with annexin-V APC and propidium iodide (PI) for 15 min. The samples were then analyzed by LSR-II flow cytometer (Becton-Dickinson, San Jose, CA, USA). Results Whole genomic copy number analysis using high resolution SNP-Chips in NSCLC samples and cell lines Initially, genomic alterations were examined in a small sample set of Asians with NSCLC with EGFR mutations. Nine clinical NSCLC samples with EGFR mutation were analyzed for copy number aberrations (CNA) using a high-resolution SNP-Chip microarray platform (Affymetrix). The alterations of the CNA in these mutant EGFR samples were compared

to 56 NSCLC samples from The Cancer Genome Atlas (TCGA) data base. The mutational status of EGFR in these 56 NSCLC samples is not available; but because most of the patients are Caucasians from the USA, the EGFR in the NSCLC probably is mutated in less than 7% of these cases [14]. The overall genomic profiles of NSCLC were highly similar when Interleukin-3 receptor comparing our samples having a mutant EGFR and the samples in the TCGA data base (Figure 1A; Table 1). This is consistent with our earlier study where we reported this observation across a

larger cohort [15]. For example, 78% (7/9) and 75% (42/56) of samples of both cohorts had gain at 5p13.2, and 67% (6/9) and 73% (41/56) of samples had gain at 8q24.12-24.3, respectively. Nevertheless, several CNAs were associated with the EGFR mutation-positive NSCLC samples (Table 2). For example, 89% (8/9) of our EGFR mutant tumors versus 27% (15/56) of the TCGA samples had CN gain at 1p36.31-36.32; also, 56% (5/9) of our EGFR mutant samples versus 11% (6/56) of the TCGA samples had gain at 19q12. Clearly, too few EGFR mutant samples were analyzed to perform statistical analysis. We also did SNP analysis on 8 EGFR mutant NSCLC cell lines. These cell lines frequently had CN gain throughout much of each chromosome (Figure 1B). Loss of CN in the NSCLC samples and cell lines was infrequent, occurring slightly more often at 6q22.3-27, 8p, and 9p21.3 (Figure 1A, B; Tables 1, 2). Figure 1 Whole genome copy number analysis using high resolution SNP-Chips .