Project description:DNA methylation in colorectal cancer diagnosis. The Illumina GoldenGate Methylation Cancer Panel I was used to select a set of candidates markers informative of colorectal cancer diagnosis from 807 cancer-related genes. In the discovery phase, tumor tissue and paired adjacent normal mucosa from 92 colorectal patients were analyzed.
Project description:We have used Illumina Infinium HumanMethylation450 BeadChip array profiling to profile paediatric high grade gliomas within the HERBY clinical trial. The HERBY trial was a phase-II open-label, randomised, multicentre trial evaluating bevacizumab in patients with newly-diagnosed non-brainstem HGG between the ages of 3-18yrs. The 450K methylation array was used to separate brain tumour samples on the basis of their methylation profiles which represent the cell of origin the time and place in which tumours arise. Methylation arrays provide data for an integrated molecular diagnosis of brain tumours and define specific molecular subgroups and subtypes of high grade gliomas carrying distinct driver mutations and patterns of somatic alterations.
Project description:Proteome characterization of the neoadjuvant clinical trial PROMIX.
https://www.clinicaltrials.gov/ct2/show/NCT00957125
Patients received six rounds of chemotherapy with epirubicin and docetaxel, and if PR or PD after the second course, bevacizumab.
Project description:MITO16/MaNGO-OV2 (NCT01706120) is a multicenter, phase IV, single arm trial for advanced stage IIIB-IV or recurrent, previously untreated, ovarian cancer patients receiving carboplatin, paclitaxel plus bevacizumab for six 3-weekly cycles followed by bevacizumab single agent until progression or unacceptable toxicity up to a maximum of 22 total cycles. The trial that was specifically designed with a translational primary endpoint to explore if selected clinical and biological factors could identify ovarian cancer patients with better prognosis in terms of progression free survival and overall survival after combined first-line treatment with chemotherapy plus Bevacizumab. The translational study, designed together with the clinical trial, the translational study implicated the collection of patients’ tissue (formalin-fixed paraffin-embedded – FFPE) and blood samples. Gene expression profile was among the molecular analyses proposed on FFPE samples.
Project description:EORTC 10994 is a phase III clinical trial comparing FEC with ET in patients with large operable, locally advanced or inflammatory breast cancer (www.eortc.be). Frozen biopsies were taken at randomisation. RNA was extracted from 100um thickness of 14G core needle biopsies. Adjacent sections were tested by H&E to confirm >20% tumour cell content. 100 ng total RNA per chip were amplified using the Affymetrix small sample protocol (IVT then Enzo). 49 tumours were tested on Affymetrix U133A chips. The CEL files were quantile normalised together using rma. Clinical response data are not available yet. Keywords = Apocrine carcinoma Keywords = breast cancer