Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Project description:DSP RNA profling using the whole transcriptome atlas kit was performed on a cohort of neuroblastoma tumor samples from pediatric patients.
Project description:Proteomics of 14 tumor tissue samples and 9 paired normal ovarian tissue samples were collected from 14 ovarian carcinosarcoma patients
Project description:The diversity and heterogeneity within high-grade serous ovarian cancer (HGSC) is not well understood. Comprehensive molecular analyses were performed including high-pass whole-genome sequencing, targeted deep DNA sequencing, RNA sequencing, reverse-phase protein arrays, mass spectrometry-based proteomics and phosphoproteomics, and immune profiling on primary and metastatic sites from highly clinically annotated HGSC samples. Samples were obtained pre-treatment based on a laparoscopic triage algorithm from patients who underwent R0 tumor debulking or received neoadjuvant chemotherapy (NACT) with excellent or poor response.
Project description:Neuroblastoma (NB) is a heterogeneous pediatric solid tumor in which minimally invasive biomarkers that reflect tumor biology and treatment response remain limited. Plasma exosomes contain proteins and metabolites that may provide insight into neuroblastoma pathophysiology and enable the identification of mechanistically linked biomarkers. This study employed an integrated proteo-metabolomic approach to identify novel exosomal biomarkers associated with disease status. Plasma samples were obtained from 14 patients with neuroblastoma before tumor resection (on-disease), 15 patients after tumor resection (follow-up), and 20 healthy donors. Plasma exosomes were characterized by transmission electron microscopy, nanoparticle tracking analysis, and immunoblotting. SWATH-targeted proteomic profiling identified 16 significantly altered exosomal proteins, and bioinformatic analysis revealed platelet activation, coagulation cascades, and growth-related signaling, all centralized on exosomal alpha-2-macroglobulin (A2M), which showed the highest level in the on-disease group and declined in the follow-up and healthy control groups.
Project description:Dataset including paired tumor-normal whole-genome deep-sequenced samples from 18 neuroblastoma patients (part1 of a total of 36 patients).
Project description:Dataset including paired tumor-normal whole-genome deep-sequenced samples from 18 neuroblastoma patients (part 2 of a total of 36 patients).
Project description:With the whole genome SNP array information obtained from tumor and matched normal control, we could evaluate the acquired copy number variations (CNVs) and uniparental disomies (UPDs) . Seven MDS patients in a whole genome sequencing project were included in this experiment.
Project description:In this study, mRNA expression profiles of 113 primary untreated human neuroblastoma samples were compared with the aim to identify prognostic exon and gene sets as well as parameters associated with alternative exon use. The primary neuroblastoma specimens were from tumor banks in Cologne or Essen, Germany, Ghent, Belgium and Valencia, Spain. All patients were diagnosed between 1998 and 2007 and treated according to the German Neuroblastoma trials NB97, NB 2004 or the SIOPEN protocol. This submission contains 87 exon array profiles and are used together with exon array data from 26 Samples in GSE21713 (see 'Relation' links below) to predict the outcome of patients with neuroblastoma. The resulting dataset, which is linked below as a supplementary file ('GSE32664_complete_RMA_data.txt'), was used for the subsequent analyses.