Project description:We reveal three-dimensional patterns of tumour growth by exploiting the unique metastasizing patterns of treatment naïve stage IIIC/IV epithelial ovarian cancer. We performed topographic mapping of structural genomic rearrangements, coding mutations, copy number changes and RNA expression in biopsies derived from 27 primary and metastatic sites across three patients. Based on somatic genomic changes, we performed sample clustering and obtained unique insight in natural tumour growth and spread. Based on extensive multi-level profiling, our data highlight the diverse modes of epithelial ovarian cancer development before applying selective pressure from therapy. We performed SNP array analysis on tumor biopsies from 3 patients (P1, P2, P3) with advanced stage ovarian cancer. This submission includes SNP data for 26 tumor biopsies and 5 normal tissue samples.
Project description:High-grade serous ovarian cancer is the most aggressive histological type of epithelial ovarian cancer, which is characterized by a high frequency of somatic TP53 mutations. To provide a better understanding of the molecular mechanisms involved in the pathogenesis of these cancers and to develop a risk classification system, we conducted profiling of the copy number alterations present in these tumors. Thirty patients who were diagnosed as high-grade serous ovarian cancer were recruited in this study. Affymetrix SNP array were performed according to the manufacturer's directions on DNA extracted from high-grade serous ovarian cancer tissues or peripheral blood samples. The Japanese Serous Ovarian Cancer Study Group
Project description:Little is known about the role of miR-200s in the progression of ovarian cancer. In this study we overexpressed the miR-200c/141 cluster, the miR-200b/200a/429 cluster, or both clusters in two different murine ovarian cancer cell lines (ID8 and 28-2). As co-oeverexpression of both clusters provided the best miR-200 overexpression, we evaluated ID8 and 28-2 cells overexpressing both miR-200 clusters (ID8-200f and 28-2-200f) compared to empty vector control cells (ID8EV and 28-2EV). ID8-200f and 28-2-200f cells showed increased expression of several mesenchymal genes, decreased proliferation, decreased invasion and increased apoptosis compared to their respective controls. RNA sequencing of ID8EV, ID8-200f, 28-2EV and 28-2-200f cells revealed that overexpression of miR-200s primary regulated genes involved in epithelial mesenchymal transition EMT) and gene implicated in migration. Therefore, our work suggests that miR-200s can inhibit characteristics associated ovarian cancer progression (increased proliferation and invasion and promotion of EMT).
Project description:We used NCode Human Long Non-coding RNA microarray to study differential expression of noncoding RNAs in tumor samples from patients with ovarian cancer. Normal ovarian tissue samples were used as controls.
Project description:Data includes all available Affymetrix SNP data from a cohort of Pediatric malignant glioma samples, isolated from Formalin-fixed Paraffin embedded tissue. No clinical data is available. Copy number analysis of Affymetrix 250K Sty SNP arrays was performed for 28 pediatric malignant gliomas. The VN algorithm was used to generate the reference signal based on 48 Mapping 500k HapMap Trio Dataset template.
Project description:250k Sty, 250k Nsp, 250k Hind and 250k Xba Affymetrix SNP arrays for 50 leukemia remission samples used as controls for copy number analysis for GSE9109 and GSE9112. Keywords: Acute leukemia, BCR-ABL1, chronic myeloid leukemia, copy number analysis, loss-of-heterozygosity, genomics *** Due to privacy concerns, the primary SNP array data is no longer available with unrestricted access. Individuals wishing to obtain this data for research purposes may request access using the Web links below. ***