Array CGH data analysis Array CGH datasets for 200 Her2 positive inhibitor Carfilzomib breast tumors and control normal Inhibitors,Modulators,Libraries samples were obtained from Gene Expression Omnibus reposi tory in the National Center for Biotechnology Information website. Partek Genomics Suite was used to analyze the data. Raw data were normalized by using the Inhibitors,Modulators,Libraries Robust Multi Array Average method. RMA consists of three steps, a background adjustment, quantile normalization, and final summary. Normalized data were used to calculate the copy number of chromosome 17 in breast tumors. Real time polymerase chain reaction We used real time PCR for measuring copy numbers in genomic DNA. Primers were designed for repeat masked sequences of the human genome by using Mac Vector. We designed pri mers that amplify 100 to 200 bp genomic regions.

Inhibitors,Modulators,Libraries Light Cycler 480 was used for real time PCR. For primer sets of ERBB2, 1, 2, 4, 5, 7, and H19, PCR reactions were carried out in a three step 40 Inhibitors,Modulators,Libraries cycle reaction of 95 C for 30 seconds, 60 C for 3 seconds, and 72 C for 30 seconds by using iQ SYBR Green Supermix. For primer sets of 3, 6, and 8, reac tions were carried out in a two step 40 cycle reaction of 95 C for 15 seconds and 60 C for 60 seconds. We used 5 ng ul of genomic DNA for each reaction. Each sample was run in triplicate and was normalized to the internal con trol of H19 on chromosome 11. The primers used for this analysis are described in Inhibitors,Modulators,Libraries Additional file 1, Table S5. In silico analysis of duplication contents within the complex genomic region A 400 kb region of chromosome 17 was divided into 500 bp segments.

Each segment was scanned for similar regions through out the human genome with BLAT at the UCSC Genome Browser. To exclude the possibility of missing some of the duplicated segments that are located at the boundary of the 500 bp window, we rescanned the region by using a 2,000 bp window. We www.selleckchem.com/products/Paclitaxel(Taxol).html used similar criteria of sequence homology 90%, size 100 bp, to define intraregional duplications, intrachromosomal duplications, and interchromoso mal duplications. For segments that showed similarity within the 400 kb region, a line was drawn for connecting the two fragments. Each line corresponded to a 500 bp region that includes the segment mapping to another 500 bp region within the region. Segments with 90% homology and 100 bp were further separated into subclassifications based on the sequence similarities and sizes. We binned the size of seg ments into seven groups. After separating frag ments into different size bins, we defined the degree of sequence homology for each segment. Deletion polymorphism and PCR genotyping assay In total, 83 structural variants were found in the Database of Genomic Variants over a 350 kb region.