Project description:<p>This study was the first-known effort to complete the complete genome sequencing of primary colorectal adenocarcinomas and the matched germline genome. Nine colorectal adenocarcinomas selected on the basis of having chromosomal instability were subjected to 'shotgun' Illumina sequencing with 101-bp paired end reads to an approximate goal of 30x coverage of tumor and of normal. From these sequences, we used various computational techniques to identify somatic point mutations, insertion/deletions and structural rearrangements in these tumors. From these data, we identified new insights into the rates of background mutations in these cancers, new spectrums of structural alterations including the identification of a novel in-frame fusion gene.</p>
Project description:We showed that some microRNAs could be characteristic of the progression from adenoma to adenocarcinoma in colorectal cancer. 48 colorectal biopsy samples (28 adenomas, 15 adenocarcinomas and 5 normal mucosae) were analyzed. We generated three comparisons: adenomas versus. normal mucosae, adenocarcinomas versus. normal mucosae, and adenocarcinomas versus. adenomas.
Project description:Five colorectal adenocarcinomas and matched normal colonic tissues were analyzed with Affymetrix HG-U133-Plus-2.0 microarrays. Two labs independently generated microarray data with the same array platform on the same biological samples.
Project description:We showed that a lot of genes were deregulated in colorectal adenocarcinomas in comparison with colorectal adenomas. 37 colorectal adenoma and 9 colorectal adenocarcinoma samples were analyzed. We generated a comparison between adenocarcinomas and adenomas.
Project description:Serrated adenocarcinomas are morphologically different from conventional adenocarcinomas. The serrated pathway has recently been proposed to represent a novel mechanism of colorectal cancer (CRC) formation. However, whether they are biologically different and truly form a distinct subclass of CRC, is not known. This study shows that the gene expression profile of serrated and conventional CRCs differs from each others and that serrated CRCs are not only morphologically novel, but also biologically distinct subclass of CRC. Experiment Overall Design: Total RNA was extracted from fresh frozen tumors with Trizol (GibcoBRL) and purified using RNeasy spin columns (Qiagen). The RNA quality was analyzed using a spectrophotometer and a Agilent 2100 Bioanalyzer (Agilent Technologies). Biotin labeled and fragmented cRNA was prepared from 8 micrograms of total RNA with procedures recommended for the HG-U133 GeneChip expression analysis (Affymetrix). The HG-U133A chips were hybridized, scanned and analyzed with Microarray Suite 5.0 software according to the manufacturerâ??s instructions (Affymetrix).