Rare Cancer Tumors Project
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA241050 | ENA |
REPOSITORIES: ENA
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Project description:<p>A large proportion of common cancers affecting patients around the world have been selected for comprehensive cancer genome studies. Further efforts will be needed to tackle the remaining tumor types, including the rare forms of cancers. Although rare, these cancers tend to be more aggressive and fast growing with an early recurrence following initial chemotherapy and poor prognosis. Besides, patients diagnosed with rare cancers may have difficulty finding a physician knowledgeable in treating their type of cancer. While sample collection is a major challenge, the integrated genomic analyses would identify novel causative genes in these rare cancers, shed new light on the biology of the rare cancers, as well as guide novel targeted cancer therapies. Through efficient collaboration, the Human Genome Sequencing Center (HGSC) at Baylor College of Medicine (BCM) has collected/is expected to collect 20 different types of rare cancers, 15-30 cases each. Whole-exome sequencing and high-resolution SNP array analysis were/will be performed for all cases and whole-genome sequencing was designed for a selected subset of the cases.</p> <p><b>The Rare Cancer Tumors Cohort is utilized in the following dbGaP sub-studies.</b> To view genotypes, other molecular data, and derived variables collected in this sub-study, please click on the following sub-study below or in the "Sub-studies" box located on the right hand side of this top-level study page <a href="./study.cgi?study_id=phs000725">phs000725</a> Rare Cancer Tumors Cohort. <ul> <li><a href="./study.cgi?study_id=phs000754">phs000754</a> Intracranial Germ Cell Tumors</li> <li><a href="./study.cgi?study_id=phs000861">phs000861</a> Craniopharyngioma Tumors</li> <li><a href="./study.cgi?study_id=phs000859">phs000859</a> Sezary Syndrome Genomic Analysis</li> </ul> </p>
| phs000725 | dbGaP
Project description:The project analyzed 88 breast cancer clinical samples, including lymph node negative and positive primary tumors, lymph node metastases, and healthy tissue as control. All samples were combined with a super-SILAC mix that served as an internal standard for quantification.
2016-06-16 | MSV000079830 | MassIVE
Project description:Generating a new mouse model for breast cancer heterogenaity. We use lentiviral infection to integrate the sporatically transforming EF1α-PyMT10C or Muc-PyMT10C into mouse mammary epithelial cell genomes. We then transplant those cells into cleared mammary fat pads of recipient mice, allowing tumors to develop from luminal , myoepithelial, stem and progenitor cell lineages. We developed a wide variety of tumors including rare histologies such as squamous, tubular, spindloid and lipid rich. We used microarray analysis to compare our mouse model with a microarray analysis of 9 established mouse models (Herschkowitz, J.I. et al. Genome Biology, 2007). Heirarchal clustering was used to establish the molecular subtype of tumors developed through the lentiviral-PyMT mouse model. In addition, micrarray analysis was used in conjunction with GeneSifter and GO ontology to identify unique pathways for each of the rare tumor types 43 total microarrays were generated from lentiviral-PyMT tumors, MMTV-PyMT transgenic tumors, and embryonic samples . Nine samples were two color arrays run at UNC microarray facility, while 34 were one color arrays run at Huntsman Cancer Instutite. The two color arrays were treated as one color arrays, we used the Cy3 intensity data for analysis. These data were merged and normalized (quantile and combat) with previously published arrays from UNC. Data were filtered on an intrinsic gene set developed in 2007 (Herschkowitz, J.I. et al. Genome Biology, 2007) and clustered using euclidian distance metrics This GEO submission consists of the 34 one color arrays run at Huntsman Cancer Instutite. The nine two color arrays run at UNC microarray facility are not included.
2012-08-09 | E-GEOD-40001 | biostudies-arrayexpress
Project description:This series represents the Cancer Genome Anatomy Project SAGE library collection. Libraries contained herein were either produced through CGAP funding, or donated to CGAP. The Cancer Genome Anatomy Project (CGAP: http://cgap.nci.nih.gov) is an interdisciplinary program established and administered by the National Cancer Institute (NCI: http://www.nci.nih.gov) to generate the information and technological tools needed to decipher the molecular anatomy of the cancer cell. SAGE libraries are named according to the following convention: * SAGE_Organ_histology_code_unique identifier, e.g., SAGE_Colon_adenocarcinoma_CL_Caco2 * Codes: B = bulk; CL = cell line; CS = short-term cell culture; MD = micro-dissected; AP = antibody purified.
2009-03-20 | GSE15312 | GEO
Project description:This series represents the Cancer Genome Anatomy Project SAGE library collection. Libraries contained herein were either produced through CGAP funding, or donated to CGAP. The Cancer Genome Anatomy Project (CGAP: http://cgap.nci.nih.gov) is an interdisciplinary program established and administered by the National Cancer Institute (NCI: http://www.nci.nih.gov) to generate the information and technological tools needed to decipher the molecular anatomy of the cancer cell. SAGE libraries are named according to the following convention: * SAGE_Organ_histology_code_unique identifier, e.g., SAGE_Colon_adenocarcinoma_CL_Caco2 * Codes: B = bulk; CL = cell line; CS = short-term cell culture; MD = micro-dissected; AP = antibody purified.
2004-10-28 | GSE1902 | GEO
Project description:This series represents the Cancer Genome Anatomy Project SAGE library collection. Libraries contained herein were either produced through CGAP funding, or donated to CGAP. The Cancer Genome Anatomy Project (CGAP: http://cgap.nci.nih.gov) is an interdisciplinary program established and administered by the National Cancer Institute (NCI: http://www.nci.nih.gov) to generate the information and technological tools needed to decipher the molecular anatomy of the cancer cell. SAGE libraries are named according to the following convention: * SAGE_Organ_histology_code_unique identifier, e.g., SAGE_Colon_adenocarcinoma_CL_Caco2 * Codes: B = bulk; CL = cell line; CS = short-term cell culture; MD = micro-dissected; AP = antibody purified.
2009-03-20 | GSE15309 | GEO
Project description:This series represents the Cancer Genome Anatomy Project SAGE library collection. Libraries contained herein were either produced through CGAP funding, or donated to CGAP. The Cancer Genome Anatomy Project (CGAP: http://cgap.nci.nih.gov) is an interdisciplinary program established and administered by the National Cancer Institute (NCI: http://www.nci.nih.gov) to generate the information and technological tools needed to decipher the molecular anatomy of the cancer cell. SAGE libraries are named according to the following convention: * SAGE_Organ_histology_code_unique identifier, e.g., SAGE_Colon_adenocarcinoma_CL_Caco2 * Codes: B = bulk; CL = cell line; CS = short-term cell culture; MD = micro-dissected; AP = antibody purified.
2009-03-20 | GSE15311 | GEO
Project description:This phase II trial studies how well cobimetinib and atezolizumab work in treating participants with rare tumors that have spread to other places in the body (advanced) or that does not respond to treatment (refractory). Cobimetinib may stop the growth of tumor cells by blocking some of the enzymes needed for cell growth. Immunotherapy with monoclonal antibodies, such as atezolizumab, may help the body’s immune system attack the cancer, and may interfere with the ability of tumor cells to grow and spread. Giving cobimetinib and atezolizumab may work better in treating participants with advanced or refractory rare tumors.
| 2240921 | ecrin-mdr-crc
Project description:The project analyzed 88 breast cancer clinical samples, including lymph node negative and positive primary tumors, lymph node metastases, and healthy tissue as control. All samples were combined with a super-SILAC mix that served as an internal standard for quantification.
2016-01-25 | PXD000815 | Pride