Project description:Transcriptomic profiling of cancer patients from tumor tissue and organ-matched normal tissue as reference which were taken as part of the WINTHER clinical trial. The organ-matched normal tissues were used in order to eliminate host gene expression variability while discarding most genetic variability between individuals. The goal was to develop an algorithm, Digital Display Precision Predictor (DDPP), which aims to identify transcriptomic predictors of treatment outcome, which were recorded in the trial.
Project description:Expression profiling studies on colon cancer comparing tumoral and normal biopsies from a series of patients in order to identify molecular biomarkers.
Project description:Cross-platform target gene screening in colorectal cancer (CRC): we have compared 25 tumoural CRC biopsies against their normal counterpart in 30 hybridizations with a home-made cDNA array (CNIO oncochip) and 16 hybridisations with a custom oligoarray (Agilent Technologies).
Project description:The challenge of preventing colorectal cancer (CRC) is the early identification of individuals whose apparently normal colorectal mucosa will develop cancer, because of inherited trait or environmental exposure. We sought to use genome-wide expression profiling of endoscopic biopsies to detect a signature of propensity for cancer. We performed oligonucleotide microarray analysis of normal appearing mucosa of the following cases: healthy individuals (NOR), disease-free carriers predisposed to HNPCC (hereditary non-polyposis CRC), disease-free patients who underwent curative large bowel resection for CRC 1 to 15 years earlier and patients with CRC (MCRC) (GSE23011). As test set we run on affymetrix arrays an independent set of mucosal biopsies of MCRC and NOR samples.
Project description:DM1 and DM2 biopsies from patients were compared to Normal adult individuals Keywords: 3 groups of samples 10 DM1 biopsies, 20 DM2 biopsies, and 6 Normal individuals biopsies
Project description:Transcriptional profiling of colon epithelial biopsies from ulcerative colitis patients and healthy control donors. Study aims to survey and analyze variation from disease in different GI regions. Keywords: disease state analysis Biopsies from a variety of anatomic locations, from patients of various treatment status or healthy controls.
Project description:Histologic findings on 1-year biopsies such as inflammation with fibrosis and transplant glomerulopathy predict renal allograft loss by 5 years. However, almost half of the patients with graft loss have a 1-year biopsy that is either normal or has only interstitial fibrosis. The goal of this study was to determine if there was a gene expression profile in these relatively normal 1-year biopsies that predicted subsequent decline in renal function. Using transcriptome microarrays we measured intragraft mRNA levels in a retrospective Discovery cohort (170 patients with a normal/minimal fibrosis 1-year biopsy, 54 with progressive decline in function/graft loss and 116 with stable function) and developed a nested 10-fold cross-validated gene classifier that predicted progressive decline in renal function (positive predictive value=38±34%%; negative predictive value=73±30%, c-statistic=0.59). In a prospective, multicenter Validation cohort (270 patients with Normal/Interstitial Fibrosis [IF]), the classifier had a 20% positive predictive value, 85% negative predictive value and 0.58 c-statistic. Importantly, the majority of patients with graft loss in the prospective study had 1-year biopsies scored as Normal or IF. We conclude predicting graft loss in many renal allograft recipients (i.e. those with a relatively normal 1-year biopsy and eGFR >40) remains difficult.
Project description:Comparison of miRNA expression profiles in a small set of prostate needle core biopsies or fine needle aspirates. Keywords: Expression profiling of prostate needle core biopsies MicroRNA expression was compared between a pooled normal sample consisting of 10 separate normal adjacent to tumor prostate needle core biopsies, two prostate tumor cell lines (PC3 and LNCaP), two needle core biopsies, and a fine needle aspirate of a prostate tumor metastasis to the supraclavicular lymph node. MicroRNA was isolated from fresh frozen tissue sections of the needle core biopsies using the mirVana miRNA Isolation kit from Ambion per the manufacturer's instructions. MicroRNA was amplified using 10 ng input and 750 ng of amplified material was subsequently labeled for hybridization. All samples were normalized to the same normal prostate control.