Prior Knowledge Transfer Across Transcriptional Datasets Using Compositional Statistics [Tumor]
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE73551 | GEO | 2016/11/08
SECONDARY ACCESSION(S): PRJNA297280
REPOSITORIES: GEO
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Project description:Compositional statistics and random gene-sets were used to assign the tumor site of origin and histopathology of 18 epithelial ovarian cancer cell lines
2016-11-08 | GSE73637 | GEO
Project description:Prior Knowledge Transfer Across Transcriptional Datasets Using Compositional Statistics
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2016-11-08 | GSE73638 | GEO
Project description:Within a project aim to define the genomic aberration of thymic epithelial tumors, we performed array CGH in 65 thymic epithelial tumors. Tumor samples were collected during surgery or by image-guided biopsies and immediately frozen. Section from frozen material were cut and stained with Haematoxylin and Eosin. A pathologist reviewed the slides and selected only cases with >80% of cancer cells.
2014-06-21 | GSE55852 | GEO
Project description:The purpose of this study was to identify de-regulated miRNAs in human papillary thyroid carcinoma (PTC). To this aim miRNA expression profiles of PTCs and normal thyroid samples were compared. Tissue specimens were selected by an expert pathologist. Details about the histological type of tumor samples are provided.
2016-11-01 | GSE73182 | GEO
Project description:Tumor specimens were collected from women with ovarian tumors at primary surgery in a study covering most of Denmark called the MALOVA-study (MALignant OVArian cancer study). This multidisciplinary study on ovarian cancer covers epidemiology (life style factors), biochemistry, and molecular biology with the purpose of identifying risk factors and prognostic factors for EOC. The study has been approved by the Scientific Ethic Committees in the study area (KF01-384/95). Sample collection went on from 1994 to 1999, and the study is described in details in other articles(20;21;24;30). Histopathological classification of the ovarian tumors was based on the typing criteria of the WHO. Pathology reports and tissue were collected from the participating hospitals. One pathologist specialized in ovarian tumors, reviewed the tissue specimens without knowledge of the primary diagnoses. Subsequently, the reviewed diagnosis was compared to the original diagnosis and agreement on invasiveness was present in 98 % of the cases. The histopathological type was refined in 14% of the cases. FIGO stages were obtained from clinical records and were reviewed by two gynecologists, both specialized in OC. Reviewed data were used for further analysis. Furthermore all other relevant hospital files were collected, and data concerning, debulking status, CA-125 level prior to operation, amount and type of chemotherapy and cause of death (if dead) were registered. Patients were scored as Âradical (optimally debulked) if no macroscopic residual tumor nodules were left, and as Ânon-radical (sub-optimally debulked) if macroscopic nodules were left. All fresh tumor samples included in this study were intended to be snap frozen within 20 minutes after the tumor was removed, but exact transportation time is not known. All samples have been stored at -80ºC. We selected samples from the largest and most common histological subtype, the serous ovarian cancers, all stages. The tumor sample material consisted of 70 stage III/IV tumors and 19 stage I/II tumors. Further patient information can be obtained from the submitters on request.
2007-10-01 | E-MEXP-1085 | biostudies-arrayexpress
Project description:Within a project aim to define the genomic aberration of thymic epithelial tumors, we performed array CGH in 65 thymic epithelial tumors. Tumor samples were collected during surgery or by image-guided biopsies and immediately frozen. Section from frozen material were cut and stained with Haematoxylin and Eosin. A pathologist reviewed the slides and selected only cases with >80% of cancer cells. Copy number aberrations of a series of 65 thymic epithelial tumors were evaluated using array CGH. Differences in copy number aberrations between different histotypes were evaluated. Significant regions of CN aberrations were defined using GISTIC algorithms.
2014-06-21 | E-GEOD-55852 | biostudies-arrayexpress
Project description:<p>The case-control data provided to dbGaP were collected under NCI grant number CA54419 which had 3 enrollment phases: I (1992-1997), II (1998-2002) and III (2003-2008). Altogether, CA54419 funded 15 years of data and specimen collection, resulting in one of the longest running population based case-control studies of ovarian cancer. The study goal was to examine reproductive factors, lifestyle exposures, and genetic background in relation to ovarian cancer risk. The project recruited cases from Eastern Massachusetts and New Hampshire, and became known as the New England-based Case-Control study (NECC) of ovarian cancer. </p> <p>3957 ovarian cancer cases diagnosed at ages 18-80 and residing in Eastern Massachusetts and New Hampshire were identified through tumor boards and registries. Of these, 3083 (78%) were eligible and among those eligible, 2203 (71%) were enrolled. After excluding 127 non-epithelial and 35 mixed mesodermal tumors, 2041 cases with epithelial tumors of ovarian, primary peritoneal, and fallopian tube origin, including borderline malignancies were included. On average, cases were interviewed 10 months after their diagnosis. A pathologist reviewed pathology reports and recorded histologic subtype, grade, and stage. Mixed ovarian cancers described as predominantly one type were classified as that type. Undifferentiated, transitional cell tumors, or mixed serous/transitional cell tumors were counted as serous. Other mixed epithelial, malignant Brenner, and unspecified epithelial tumors were classified as other. </p> <p>2100 controls were identified through random digit dialing (RDD), driver-license lists, and town-resident lists. During the first funding phase from 1992 to 1997, 420 (72%) controls identified through RDD and 102 (51%) through town-resident lists agreed to participate. From 1998 to 2008, only town-resident lists were used to identify potential controls. 4366 controls were identified, of whom 1426 (33%) were ineligible if they had died, moved, or were seriously ill or if they did not have a working telephone, speak English, or have at least one ovary. Of eligible controls, 1362 (46%) declined to participate by phone or via 'opt-out' postcard and 1578 (54%) were enrolled. Controls were frequency matched to cases by 5-year age groups and region of residence.</p> <p>In all phases, after written informed consent, demographic information, reproductive and medical history, and habits were assessed by in-person or telephone interview (in a few instances). All of the questions were framed with respect to a reference date defined as 1 year before the diagnosis date for women in the case group and the date of interview for those in the control group. This study was approved by institutional review boards at Dana Farber Harvard Cancer Center and Dartmouth Medical Center.</p>
| phs001034 | dbGaP
Project description:Prior Knowledge Transfer Across Transcriptional Datasets Using Compositional Statistics [Tumor]
| PRJNA297280 | ENA
Project description:The main goal of this study is to explore the proteomic expression in prophylactic salpingooophorectomy specimens, obtained from highly selected cohort of patients at risk of developing a high-grade serous ovarian carcinoma (HGSOC), because of a hereditary (BRCA 1 or 2 mutation) or a documented familial context. Pathological aspects of fallopian tube specimens, at the origin of most HGSOC in this selected feminine population, are extracted from slides annotated by the pathologist, then submitted to a proteomic analysis. We carried out an in-depth proteomics analysis of these epithelial lesions (p53 signature, serous tubal intraepithelial carcinoma-STIC and serous tubal intraepithelial lesions-STIL) based on spatially resolved proteomic guided by IHC technique.
2023-10-24 | PXD020024 | Pride