Common Variant GWAS, GECCO
Ontology highlight
ABSTRACT: Genetics & Epidemiology of Colorectal Cancer Consortium (GECCO) is a collaborative effort which aims to accelerate the discovery of colorectal cancer-related variants by discovering, replicating and fine-mapping Genome Wide Association Study (GWAS) findings, conducting a meta-analysis of GWAS data, and investigating how genetic variants are modified by environmental risk factors. The coordinating center for this consortium is based at the Fred Hutchinson Cancer Research Center (Principal investigator: Ulrike Peters). The GECCO Consortium is utilized in the following dbGaP individual studies. To view genotypes, and derived variables collected in these individual studies, please click on the following individual studies below or in the "Sub-studies" box located on the right hand side of this top-level study page phs001078 GECCO Consortium.
SECONDARY ACCESSION(S): PRJNA313337PRJNA313338
REPOSITORIES: dbGaP
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Project description:<p>The Cancer Genome Atlas (TCGA) is a comprehensive and coordinated effort to accelerate our understanding of the molecular basis of cancer through the application of genome analysis technologies, including large-scale genome sequencing. TCGA is a joint effort of the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI), which are both part of the National Institutes of Health, U.S. Department of Health and Human Services.</p> <p>TCGA projects are organized by cancer type or subtype. Click <a href="http://cancergenome.nih.gov/cancersselected" target="_blank">here</a> for a current list of cancer types selected for study in TCGA.</p> <p>Data from TCGA (e.g., gene expression, copy number variation and clinical information), are available via the <a href="https://tcga-data.nci.nih.gov/tcga/" target="_blank">TCGA Data Portal</a>, EXCEPT for the genomic sequence data (.bam files), which are hosted at the <a href="https://cghub.ucsc.edu/" target="_blank">Cancer Genomics Hub (CGHub)</a>.</p> <p>Data from TCGA projects are organized into two tiers: <b>Open Access and Controlled Access</b>. <ul> <li>Open Access data tier contains data that cannot be attributed to an individual research participant. The Open Access data tier does not require user certification. Data in Open Access tier are available in the TCGA Data Portal.</li> <li>Controlled Access data tier contains individual-level genotype data that are unique to an individual. Access to data in the Controlled Access data tier requires user certification through <a href="https://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?login=&page=login" target="_blank">dbGaP Authorized Access</a>.</li> <li>Controlled Access data types consist of the following: <ul> <li>Individual germline variant data (SNP .cel files)</li> <li>Primary sequence data (.bam files), which are available at CGHub</li> <li>Clinical free text fields</li> <li>Exon Array files (for Glioblastoma and Ovarian projects only)</li> </ul> </li> </ul> </p> <p><b>NOTE: TCGA strives to release most data in the open access tier. Individual genotype or sequence files are prominent exceptions. Commonly requested files such as descriptions of somatic mutations or clinical data are open access.</b></p> <p><b>The TCGA study is utilized in the following dbGaP substudies.</b> To view genotypes and other molecular data collected in these substudies, please click on the following substudies below or in the "Substudies" box located on the right hand side of this top-level study page phs000178 TCGA study. <ul> <li><a href="./study.cgi?study_id=phs000441">phs000441</a> Integrated Genomic Analyses of Ovarian Carcinoma (OV)</li> <li><a href="./study.cgi?study_id=phs000489">phs000489</a> Comprehensive Genomic Characterization Defines Human Glioblastoma Genes and Core Pathways</li> </ul> </p>
| phs000178.v6.p6 | EGA
Project description:This SuperSeries is composed of the SubSeries listed below. The raw sequencing data is available through dbGaP (controlled access) due to patient privacy concerns. https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001961.v1.p1
2020-11-23 | GSE161383 | GEO
Project description:<p>Within the framework of the International Lymphoma Epidemiology Consortium (InterLymph) Consortium and NCI-sponsored Cohort Consortium, investigators from 22 studies came together to conduct a genome-wide association study (GWAS) of non-Hodgkin lymphoma (NHL). The goal of the study was to identify common genetic variants associated with the risk of NHL. As described previously (Berndt SI et al., Nature Genetics, 2013, PMID: <a href="http://www.ncbi.nlm.nih.gov/pubmed/?term=23770605">23770605</a> ), cases and controls from 22 studies, including nine prospective cohort studies, eight population-based case-control studies, and five clinic or hospital-based case-control studies were included in this effort. Cases of NHL were ascertained from cancer registries, clinics or hospitals, or through self-report verified by medical and pathology reports. The phenotype information for all NHL cases was reviewed centrally at the InterLymph Data Coordinating Center and harmonized according to the hierarchical classification proposed by the InterLymph Pathology Working Group based on the World Health Organization (WHO) classification (2008). Controls were frequency matched to cases on age and gender by study, and the study was limited to subjects of European ancestry. Participants were genotyped using the Illumina Omni Express.</p> <p><b>The NCI Non-Hodgkin Lymphoma GWAS is utilized in the following dbGaP sub-studies.</b> To view genotypes and derived variables collected in these sub-studies, please click on the following sub-studies 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=phs000801">phs000801</a> NCI Non-Hodgkin Lymphoma GWAS. <ul> <li><a href="study.cgi?study_id=phs000802">phs000802</a> NCI Non-Hodgkin Lymphoma GWAS: CLL</li> <li><a href="study.cgi?study_id=phs000818">phs000818</a> NCI Non-Hodgkin Lymphoma GWAS: Controls</li> <li><a href="study.cgi?study_id=phs000889">phs000889</a> NCI Non-Hodgkin Lymphoma GWAS: DLBCL</li> <li><a href="study.cgi?study_id=phs000890">phs000890</a> NCI Non-Hodgkin Lymphoma GWAS: FL</li> <li><a href="study.cgi?study_id=phs000891">phs000891</a> NCI Non-Hodgkin Lymphoma GWAS: MZL</li> </ul> </p>
| phs000801 | dbGaP
Project description:<p>Shankha Satpathy, Eric J. Jaehnig, et al., <a href="https://www.nature.com/articles/s41467-020-14381-2" target="_blank">Nature Communications volume 11, Article number: 532 (2020)</a></p><p>Cancer proteogenomics promises new insights into cancer biology and treatment efficacy by integrating genomics, transcriptomics and protein profiling including modifications by mass spectrometry (MS). A critical limitation is sample input requirements that exceed many sources of clinically important material. Here we report a proteogenomics approach for core biopsies using tissue-sparing specimen processing and microscaled proteomics. As a demonstration, we analyze core needle biopsies from ERBB2 positive breast cancers before and 48-72 h after initiating neoadjuvant trastuzumab-based chemotherapy. We show greater suppression of ERBB2 protein and both ERBB2 and mTOR target phosphosite levels in cases associated with pathological complete response, and identify potential causes of treatment resistance including the absence of ERBB2 amplification, insufficient ERBB2 activity for therapeutic sensitivity despite ERBB2 amplification, and candidate resistance mechanisms including androgen receptor signaling, mucin overexpression and an inactive immune microenvironment. The clinical utility and discovery potential of proteogenomics at biopsy-scale warrants further investigation.<br><br><em>Genomic Data</em> for samples in the Microscaled Proteogenomic Methods Publication are available from the NIH Database of Genotypes and Phenotypes (dbGaP), Study Accession: phs001907.v1.p1, <a href="https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001907.v1.p1" target="_blank">here</a></p>
<ul><li>Dataset imported into MassIVE from <a href="https://cptac-data-portal.georgetown.edu/study-summary/S051">https://cptac-data-portal.georgetown.edu/study-summary/S051</a> on 06/02/21</li></ul>
2021-06-02 | MSV000087566 | MassIVE
Project description:We performed RRBS and WGBS on primary human chronic lymphocytic leukemia and normal healthy donor B cell samples Due to patient privacy concerns, the raw data is being made available via controlled access in dbGaP (http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000435.v1.p1).
2015-01-01 | GSE58889 | GEO
Project description:<p>Comparison and Reference (CompRef) Samples, initially characterized in the <a href="https://cptac-data-portal.georgetown.edu/cptac/s/S010">System Suitability Study</a>, were analyzed along with the <a href="https://cptac-data-portal.georgetown.edu/cptac/s/S016">TCGA colorectal cancer tumor samples</a> and with the <a href="https://cptac-data-portal.georgetown.edu/cptac/s/S019">normal colon epithelium samples</a>. These interstitial CompRef experiments are global proteomic profiling of the P6 (luminal) and P5 (basal) human-in-mouse xenograft breast carcinoma pooled samples.</p><p>One CompRef sample was run after every 5 samples of TCGA colorectal cancer tumor tissue, alternating between the P6 and P5 CompRef samples to generate 20 total data sets (designated as 01CompRef_P6_VU through 20CompRef_P5_VU).</p><p>Twelve CompRef samples were run with the 30 normal colon epithelium samples to produce 12 data sets (designated as 21CompRef_P6_VU through 32CompRef_P5_VU).</p>These experiments were used to monitor the consistency of laboratory protocols and mass spectrometry instrument performance during the TCGA colorectal cancer analysis.<ul><li>Dataset imported into MassIVE from <a href="https://cptac-data-portal.georgetown.edu/cptac/s/S017" target="_blank">https://cptac-data-portal.georgetown.edu/cptac/s/S017</a> on 08/31/18</li></ul>
2018-08-31 | MSV000082875 | MassIVE
Project description:<p>The Women's Health Initiative (WHI) is a long-term national health study that has focused on strategies for preventing heart disease, breast and colorectal cancer, and osteoporotic fractures in postmenopausal women. The original WHI study included 161,808 postmenopausal women enrolled between 1993 and 1998. The Fred Hutchinson Cancer Research Center in Seattle, WA serves as the WHI Clinical Coordinating Center for data collection, management, and analysis of the WHI.</p> <p>The WHI has two major parts: a partial factorial randomized Clinical Trial (CT) and an Observational Study (OS); both were conducted at 40 Clinical Centers nationwide.</p> <p>The CT enrolled 68,132 postmenopausal women between the ages of 50-79 into trials testing three prevention strategies. If eligible, women could choose to enroll in one, two, or all three of the trial components. The components are: <ul> <li><b>Hormone Therapy Trials (HT)</b>: This double-blind component examined the effects of combined hormones or estrogen alone on the prevention of coronary heart disease and osteoporotic fractures, and associated risk for breast cancer. Women participating in this component with an intact uterus were randomized to estrogen plus progestin (conjugated equine estrogens [CEE], 0.625 mg/d plus medroxyprogesterone acetate [MPA] 2.5 mg/d] or a matching placebo. Women with prior hysterectomy were randomized to CEE or placebo. Both trials were stopped early, in July 2002 and March 2004, respectively, based on adverse effects. All HT participants continued to be followed without intervention until close-out.</li> <li><b>Dietary Modification Trial (DM)</b>: The Dietary Modification component evaluated the effect of a low-fat and high fruit, vegetable and grain diet on the prevention of breast and colorectal cancers and coronary heart disease. Study participants were randomized to either their usual eating pattern or a low-fat dietary pattern.</li> <li><b>Calcium/Vitamin D Trial (CaD)</b>: This double-blind component began 1 to 2 years after a woman joined one or both of the other clinical trial components. It evaluated the effect of calcium and vitamin D supplementation on the prevention of osteoporotic fractures and colorectal cancer. Women in this component were randomized to calcium (1000 mg/d) and vitamin D (400 IU/d) supplements or a matching placebo.</li> </ul> </p> <p>The <b>Observational Study (OS)</b> examines the relationship between lifestyle, environmental, medical and molecular risk factors and specific measures of health or disease outcomes. This component involves tracking the medical history and health habits of 93,676 women not participating in the CT. Recruitment for the observational study was completed in 1998 and participants were followed annually for 8 to 12 years.</p> <p>The original protocol allowed for follow-up until March 2005, after which participants were invited to enroll in the first WHI Extension Study for follow-up through 2010. Participants were invited again to participate in the second WHI Extension Study with continued follow up from 2010 to 2015. As of March 31, 2011 there were 93,122 women enrolled in the second extension. As part of the second Extension, 80+ year old women were asked to consent to an In Person Visit at their homes during which additional blood samples were collected and various measurements were taken (such as blood pressure, height, weight, waist circumference, grip strength, etc).</p> <p><b>The WHI Cohort is utilized in the following dbGaP substudies.</b> To view genotypes, analysis, expression data, other molecular data, and derived variables collected in these substudies, please click on the following substudies below or in the "Substudies" box located on the right hand side of this top-level study page phs000200 WHI Cohort. <ul> <li><a href="./study.cgi?study_id=phs000386">phs000386</a> WHI SHARe</li> <li><a href="./study.cgi?study_id=phs000281">phs000281</a> GO-ESP WHISP</li> <li><a href="./study.cgi?study_id=phs000315">phs000315</a> WHI GARNET</li> <li><a href="./study.cgi?study_id=phs000503">phs000503</a> WHISE</li> </ul> </p>
| phs000200.v7.p2 | EGA
Project description:We performed RRBS and WGBS on primary human chronic lymphocytic leukemia and normal healthy donor B cell samples Due to patient privacy concerns, the raw data is being made available via controlled access in dbGaP (http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000435.v1.p1). cross-sectional/longitudinal
2015-01-01 | E-GEOD-58889 | biostudies-arrayexpress
Project description:Previous studies in bulk tissue suggest that there are abundant expression quantitative trait loci (eQTLs) in human brain. This sample series is of cerebellar Purkinje cells isolated using laser capture microdissection from human cases without neurological disease but of known genotypes. These data may be helpful in confirming eQTLs in bulk tissue or in mapping other gene expression traits in an enriched neuronal population. Authorized Access data: Mapping of GEO sample accessions to dbGaP subject/sample IDs is available through dbGaP Authorized Access, see http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000249
2013-01-01 | GSE37205 | GEO
Project description:<p>This project includes data derived from subjects enrolled in the BASIC3 (Baylor College of Medicine Advancing Sequencing in Childhood Cancer Care) study. BASIC3 is a National Genome Human Research Institute (NHGRI) and National Cancer Institute-funded Clinical Sequencing Exploratory Research (CSER) consortium project that focused on prospective implementation of clinical whole exome sequencing in the pediatric oncology clinic. The primary study objective were to integrate information from CLIA-certified germline and tumor exome sequencing into the care of newly diagnosed solid tumor patients at Texas Children's Cancer Center, and to perform parallel evaluation of the impact of tumor and germline exomes on families and physicians. </p> <p>Blood and frozen tumor (if available) samples were collected from children undergoing surgery or biopsy of newly diagnosed solid tumors and subjected to exome sequencing in a CLIA-certified laboratory. Germline and tumor (if applicable) exome sequencing reports were generated and submitted into the electronic health record and returned to each patient/family by their primary oncologist.</p> <p>In addition to the clinical exome sequencing, specific (optional) consent was requested for research sequencing studies. If this consent was obtained then research studies of some of the children and parents participating in the BASIC3 study (including tumor transcriptome and whole genome sequencing of blood and/or tumor) are performed.</p> <p><b>The Clinical Sequencing Exploratory Research Consortium Cohort is utilized in the following dbGaP sub-study.</b> To view molecular data, and derived variables collected in this sub-study, please click on the following sub-studies below or in the "Sub-study" box located on the right hand side of this top-level study page <a href="study.cgi?study_id=phs001683">phs001383</a> Clinical Sequencing Exploratory Research Consortium Cohort. <ul> <li><a href="study.cgi?study_id=phs001026">phs001026</a> BASIC3</li> <li><a href="study.cgi?study_id=phs001878">phs001878</a> GMKF BASIC3</li> </ul> </p>
| phs001683 | dbGaP