UCSF Adult Glioma Study
Ontology highlight
ABSTRACT: The UCSF Adult Glioma Study is a case-control study conducted at the University of California, San Francisco. The goals of the study were to discover inherited (genetic), developmental, immunologic and other risk factors for glioma and to determine molecular level tumor markers that would be helpful in classifying glioma into more homogeneous groups.
SECONDARY ACCESSION(S): PRJNA421233PRJNA421232
REPOSITORIES: dbGaP
Dataset's files
Items per page: 5 1 - 5 of 32 |
Similar Datasets
Project description:<p>The main goals of the GICC Study were: 1) to identify novel genetic risk variants for glioma, as well as validate variants implicated by previous genome-wide association studies of glioma; and 2) to explore biologically relevant gene-gene and gene-environment interactions in glioma susceptibility. The GICC Study includes participants from the following centers: Brigham and Women's Hospital (Boston, Massachusetts), Case Western Reserve University (Cleveland, Ohio), Columbia University (New York, New York), the Danish Cancer Society Research Centre (Copenhagen, Denmark), Duke University (Durham, North Carolina), the University of Texas MD Anderson Cancer Center (Houston, Texas), Memorial Sloan Kettering Cancer Center (New York, New York), the Mayo Clinic (Rochester, Minnesota), NorthShore HealthSystem (Chicago, Illinois), Umea University (Umea, Sweden), the University of California, San Francisco (San Francisco, California), the University of Southern California (Los Angeles, California), and the Institute of Cancer Research (London, United Kingdom).</p>
| phs001319 | dbGaP
Project description:Please Note, if a password is required, please try "a", the generic password for Massive.
These data are in support of the manuscript:
Post-translational Modifications of Endogenous Tau in Wildtype and Human Amyloid Precursor Protein Transgenic Mice
Meaghan Morris*a,b, Giselle M. Knudsen*c, Sumihiro Maedaa,d, Jonathan C. Trinidadc, Alexandra Ianoviciuc, Alma L. Burlingamec, Lennart Muckea,d
aGladstone Institute of Neurological Disease, San Francisco, California 94158, USA
bBiochemistry, Cellular and Molecular Biology Graduate Program, Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
cMass Spectrometry Facility, Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, USA
dDepartment of Neurology, University of California, San Francisco, California 94158, USA
*These authors contributed equally to this work
2014-07-30 | MSV000078796 | MassIVE
Project description:Endovascular biopsy and fluorescence activated cell sorting was used to enrich for viable endothelial cells (ECs) from a vertebrobasilar aneurysm and the femoral artery. scRNAseq was then performed on 24 aneurysmal endothelial cells and 23 patient-matched non-aneurysmal femoral artery endothelial cells. cDNA libraries were prepared using the Smart-seq2 protocol on a Fluidigm C1 system (Fluidigm, South San Francisco, California) and sequenced on a HiSeq2500 machine (Illumina, San Diego, California).
2021-07-01 | E-MTAB-10681 | biostudies-arrayexpress
Project description:Participants were recruited from the California Lupus Epidemiology Study (CLUES). CLUES was approved by the Institutional Review Board of the University of California, San Francisco. Peripheral blood mononuclear cells were isolated from patient donors. Cells were isolated from peripheral blood utilizing magnetic beads (CD14+monocytes, B cells, CD4+T cells and NK cells) using EasySep protocol from STEM cell technologies on 120 patients. RNA and DNA were extracted using Qiagen column and quality was assessed on Agilent bioanalyzer. 1ng - 5ng of RNA was used with SmartSeqv2 protocol to get cDNA, followed by Illumina Nextera XT DNA library prep with input of 0.8ng cDNA and 15 cycles of PCR amplification. Both cDNA and DNA libraries qualities were controlled on Agilent bioanalyzer. Libraries were sequenced on HiSeq4000 PE150.
2021-03-04 | GSE164457 | GEO
Project description:This is a audio based mindfulness meditation intervention for colorectal cancer patients and caregivers. A 8-week single arm study will be conducted among University of California, San Francisco (UCSF) patients with metastatic colorectal cancer undergoing chemotherapy and caregivers of these patients (44 participants total).
| 2188452 | ecrin-mdr-crc
Project description:We applied DNA content based flow cytometry methods to interrogate the genomes of clinical samples from 8 patients with ovarian cancer. These included 6 high grade serous ovarian carcinomas, a low grade serous carcinoma, and an endometriod carcinoma. Archived samples obtained from surgical resections from a University of California San Francisco (UCSF) tissue bank. Notably for this study we distinguished and sorted diploid and aneuploid tumors. We then profiled the the whole genome copy number for each sample. These data were used to provide standards for single cell analyses of the same tissues including FFPE samples.
2024-09-24 | GSE268921 | GEO
Project description:Astrocytoma, oligodendroglioma, oligoastrocytoma, and ependymoma are the main histologic subtypes of glioma. The molecular character of these subtypes has profound implications for understanding their causes and treatment. We describe the epigenetic landscape of these tumor types using novel DNA methylation profiling tools. There is a robust association of methylation profile with tumor histology and IDH1 mutation status. Furthermore, tumors with IDH1 mutation independently predict a tumor hypermethylator phenotype, histology, TP53 mutation status, patient age, and survival. Integrating tumor epigenetic and genetic alterations, this work provides a critical step toward better defining the somatic nature of glioma which will have great potential to impact clinical approaches to disease. This work provides an important step forward in classification of malignant brain tumors using DNA methylation profiling, integrating knowledge regarding IDH1 mutation in gliomas. The epigenetic homogeneity of the IDH1 mutant subclass despite histologic diversity implies that IDH1 mutation is a “driver” or functional determinant of a distinct DNA methylation phenotype, suggesting a novel role for an altered metabolic profile in the brain. This association occurs across histologic subtypes and demonstrates a clear relationship between genetic alteration and epigenetic profile. Fresh frozen tumor tissues were obtained from the University of California San Francisco (UCSF) Brain Tumor Research Center tissue bank with appropriate institutional review board approval. Tumors were diagnosed between 1990 and 2003. Tumor samples were defined as secondary GBM if the patients had prior histological diagnosis of a low-grade glioma. Tumors had previously been reviewed by UCSF neuropathologists to assign histologic subtype and grade. Normal brain tissue samples were from cancer-free patients who underwent temporal lobe resection as treatment for epilepsy at UCSF.
2010-12-20 | E-GEOD-20395 | biostudies-arrayexpress
Project description:Discover homogeneous groups of colon adenocarcinomas associated to clinical and biological characteristics
2012-12-14 | E-TABM-723 | biostudies-arrayexpress
Project description:Uveal melanoma is the most common cancer of the eye arising from melanocytes within the choroid, ciliary bodies and iris. Almost half of uveal melanomas metastasize hematogenously to distant organs, most often the liver, where the disease becomes fatal. One of the first genetic alterations to be identified in primary uveal melanomas was monosomy 3, which was found to be strongly associated with metastasis. We used gene expression profiling to identify two phenotypically distinct classes of uveal melanomas: class 1 tumors with low-grade morphology and low metastatic risk; and class 2 tumors with aggressive morphology and high metastatic risk. Our initial studies suggested that gene expression profiling was a better predictor of metastasis than monosomy 3. For this study, BAC-array comparative genomic hybridization was used to assay genomic DNA isolated from fresh frozen primary uveal melanoma samples of known molecular class based on gene expression profiling. Independent samples were sent to the aCGH cores at the University of California, San Francisco and the Roswell Park Cancer Institute for hybridization, and log2 ratios were reported. Total genomic DNA was obtained from tumor samples that were collected at the time of treatment. Samples were analyzed by the Microarray Shared Resource at the Comprehensive Cancer Center, University of California, San Francisco or by the Microarray and Genomics Facility of the Roswell Park Cancer Institute.
2012-12-06 | E-GEOD-42739 | biostudies-arrayexpress
Project description:Uveal melanoma is the most common cancer of the eye arising from melanocytes within the choroid, ciliary bodies and iris. Almost half of uveal melanomas metastasize hematogenously to distant organs, most often the liver, where the disease becomes fatal. One of the first genetic alterations to be identified in primary uveal melanomas was monosomy 3, which was found to be strongly associated with metastasis. We used gene expression profiling to identify two phenotypically distinct classes of uveal melanomas: class 1 tumors with low-grade morphology and low metastatic risk; and class 2 tumors with aggressive morphology and high metastatic risk. Our initial studies suggested that gene expression profiling was a better predictor of metastasis than monosomy 3. For this study, BAC-array comparative genomic hybridization was used to assay genomic DNA isolated from fresh frozen primary uveal melanoma samples of known molecular class based on gene expression profiling. Independent samples were sent to the aCGH cores at the University of California, San Francisco and the Roswell Park Cancer Institute for hybridization, and log2 ratios were reported. Total genomic DNA was obtained from tumor samples that were collected at the time of treatment. Samples were analyzed by the Microarray Shared Resource at the Comprehensive Cancer Center, University of California, San Francisco or by the Microarray and Genomics Facility of the Roswell Park Cancer Institute.
2012-12-06 | E-GEOD-42738 | biostudies-arrayexpress