Search Results - EGA European Genome-Phenome Archive

The primary aim of this study is to identify genes related to the occurrence of breast events, defined as occurrence of invasive breast cancer or ductal carcinoma in situ (DCIS), in women at high risk of developing breast cancer who have received a Selective Estrogen Receptor Modulator (SERM - tamoxifen or raloxifene) on the National Surgical Adjuvant Breast and Bowel Project (NSABP) P-1 or P-2 trials. Cases and controls were selected from the tamoxifen arm in the P-1 and from the tamixifen and raloxifene arms in the P-2 trial. For the P-1 trial, cases and controls were required to be 50 years of age or older at time of entry. Cases were females who experienced an invasive breast cancer or DCIS on P-1 or P-2. Controls were females who did not experience an invasive breast cancer or DCIS. A nested matched case-control design was used, with matching on the following factors: 1) trial and treatment arm (P-1 tamoxifen, P-2 tamoxifen, P-2 raloxifene); 2) age at trial entry (when controls could not be exactly matched on age, we incremented the age of matching by +/- 1 year, in sequence until a match was obtained without exceeding +/- 5 years); 5-year predicted breast cancer risk based on the Gail model ( <2.00%, 2.01-3.00, 3.01-5.00, >5.01), 3) history of lobular carcinoma in situ (yes vs. no); 4) history of atypical hyperplasia in breast (yes vs. no); 5) time on study (controls must be on study at least as long as the time to diagnosis of the breast event for the case). Because 94.2% of the participants on P-1 and P-2 treated with tamoxifen or raloxifene were Caucasian, this study was restricted to only Caucasians. Two cases and two controls were randomly chosen as duplicates for quality control of genotype concordance. The DNA samples were plated into 96-well plates, with cases and controls randomly distributed across the plates. A Caucasian parent-child CEPH trio from the HapMap project was included to check for Mendelian transmission of alleles. Genotypes were determined by the RIKEN Center for Genomic Medicine with the Illumina Human610-Quad.

Study phs000305

The Atherosclerosis Risk in Communities (ARIC) Study

The Atherosclerosis Risk in Communities (ARIC) Study, sponsored by the National Heart, Lung and Blood Institute (NHLBI), is a prospective epidemiologic study conducted in four U.S. communities. The four communities are Forsyth County, NC; Jackson, MS; the northwest suburbs of Minneapolis, MN; and Washington County, MD. ARIC is designed to investigate the etiology and natural history of atherosclerosis, the etiology of clinical atherosclerotic diseases, and variation in cardiovascular risk factors, medical care and disease by race, gender, location, and date. ARIC includes two parts: the Cohort Component and the Community Surveillance Component. The Cohort Component began in 1987, and each ARIC field center randomly selected and recruited a cohort sample of approximately 4,000 individuals aged 45-64 from a defined population in their community. A total of 15,792 participants received an extensive examination, including medical, social, and demographic data. These participants were reexamined every three years with the first screen (baseline) occurring in 1987-89, the second in 1990-92, the third in 1993-95, and the fourth and last exam was in 1996-98. Follow-up occurs yearly by telephone to maintain contact with participants and to assess health status of the cohort. In the Community Surveillance Component, currently ongoing, these four communities are investigated to determine the community-wide occurrence of hospitalized myocardial infarction and coronary heart disease deaths in men and women aged 35-84 years. Hospitalized stroke is investigated in cohort participants only. Starting in 2006, the study conducts community surveillance of inpatient (ages 55 years and older) and outpatient heart failure (ages 65 years and older) for heart failure events beginning in 2005. ARIC is currently funded through January 31, 2012. This study is part of the Gene Environment Association Studies initiative (GENEVA, http://www.genevastudy.org) funded by the trans-NIH Genes, Environment, and Health Initiative (GEI). The overarching goal is to identify novel genetic factors that contribute to atherosclerosis and cardiovascular disease through large-scale genome-wide association studies of well-characterized cohorts of adults in four defined populations. Genotyping was performed at the Broad Institute of MIT and Harvard, a GENEVA genotyping center. Data cleaning and harmonization were done at the GEI-funded GENEVA Coordinating Center at the University of Washington.

Study phs000090

National Cancer Institute (NCI) Prostate Cancer Genome-Wide Association Study for Uncommon Susceptibility Loci (PEGASUS)

This genome-wide association study was funded by the National Cancer Institute (NCI) to identify uncommon susceptibility loci for prostate cancer. A total of 4,600 prostate cancer cases and 2,840 controls of European ancestry from the Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Screening Trial were genotyped using the Illumina HumanOmni2.5 and passed rigorous quality control filters. Additional genotype data (available in dbGap under other accession numbers) from 101 independent controls of European ancestry scanned with the HumanOmni2.5 were also included, resulting in a total of 4,600 cases and 2,941 controls for the published analysis. SNPs from the most promising regions, as determined by rank p-value, under multiple different models as well as select candidate genes were taken forward for replication using a custom Iselect chip in 6,575 cases and 6,392 controls of European ancestry. Results from the primary scan after imputation were then meta-analyzed with the Iselect results as well as results from previous GWAS. In a combined meta-analysis of the primary scan together with the custom Iselect replication and a previous GWAS, thirteen loci reached genome-wide significance (P < 5 x 10-8) for prostate cancer overall; however, each of them confirmed a previously reported locus. Although they did not reach genome-wide significance, we found evidence for two new suggestive loci at chromosome 16q22.2 (PKD1L3, rs12597458, P = 9.67 x 10-8) and 6p22.3 (CDKAL1, rs12198220, P = 2.13 x 10-7). In a combined case-only analysis of 12,518 prostate cancer cases, we identified two loci associated with Gleason score, a pathological measure of disease aggressiveness: rs35148638 at 5q14.3 (RASA1, P=6.49x10-9) and rs78943174 at 3q26.31 (NAALADL2, P=4.18x10-8). In a stratified case-control analysis, the SNP at 5q14.3 appears specific for aggressive prostate cancer (P=8.85x10-5) with no association for non-aggressive prostate cancer compared to controls (P=0.57). Only the cases and controls genotyped on the HumanOmni2.5 specifically for this study are included under this accession number. Controls (n=101) genotyped with the HumanOmni2.5 for another study are posted under a different accession number. Please note that the majority of prostate cancer cases and controls genotyped in CGEMS (and posted under a different accession number) are included in this study.

Study phs000882

PRE-DETERMINE: Biologic Markers and MRI SCD Cohort Study

The PRE-DETERMINE Study is a prospective, multi-center study of 5,764 patients with a history of coronary artery disease (CAD) and documentation of either a prior myocardial infarction (MI) or mild to moderate left ventricular dysfunction (LVD) with left ventricular ejection fraction (LVEF) 35-50%. Patients were enrolled at 136 sites where information on baseline demographics, clinical characteristics, pertinent past medical history, lifestyle habits, cardiac test results, and medications were collected via electronic data capture. Electrocardiograms (ECG) along with a blood sample was also collected at baseline, sent to central laboratories, and stored for future analyses. Contrast-enhanced magnetic resonance imaging (CE-MRI) scans were collected on a subset of patients and analyzed. Enrollment closed in November 2013 and patients are now being followed centrally by the Clinical Coordinating Center via mail/phone to document interim non-fatal arrhythmic events and cause-specific mortality. Questionnaires that inquire about intervening implantable cardiac defibrillator (ICD) implantations, ICD therapies, cardiac arrest, and other pertinent cardiovascular endpoints are mailed to participants every six months, and follow-up telephone calls are made to non-responders. Study endpoints are being confirmed through review of medical records, interviews with next-of-kin, and autopsy reports, if available.The primary objective of PRE-DETERMINE is to determine whether biologic markers and ECGs can be utilized to advance sudden cardiac death (SCD) risk prediction in patients with coronary heart disease (CHD) and LVEF >30-35%. The overarching goal of the study is to identify a series of markers that alone or in combination specifically predict risk of arrhythmic death as compared to other causes of mortality among this at risk population of CHD patients with preserved LVEF> 30-35%. If biologic or ECG markers are identified that can specifically predict risk of ventricular arrhythmias, then these markers may serve as relatively inexpensive methods to identify those at risk. The public health impact of identifying markers could be quite substantial, leading to more efficient utilization of ICDs and advances in our understanding of mechanisms underlying SCD.Among the 95% of participants that provided a blood sample at baseline, genome wide genotyping using the Illumina Global Screening Array (GSA) has been performed. A total of 4,335 participants with European ancestry gave consent that allows genetic research and deposition of data into dbGaP.

Study phs002940

Study of Environment, Lifestyle and Fibroids SNP Data

Uterine fibroids are hormonally-dependent benign tumors of the uterine muscle that develop in premenopausal women. Currently, the primary symptoms (pain and bleeding) are treated, but when those treatments fail, major procedures to remove or shrink the fibroids are frequently the only options for women. Fibroids are the leading indication for hysterectomy in the United States. African-American women develop fibroids an average of 10 years earlier than white women in the U.S., and they are approximately three times more likely to have a hysterectomy for fibroids. The known risk factors for fibroids do not explain this disparity.The goal of the Study of Environment, Lifestyle & Fibroids (SELF) is to identify risk factors for uterine fibroid development. It is the first study to identify incident cases based on ultrasound screening. We enrolled a cohort of 1693 women who self-identified as Black or African American, ages 23-35, from the Detroit, Michigan area. Women with a prior diagnosis of fibroids were not eligible. Participants were screened for fibroids with ultrasound at enrollment, and follow-up ultrasounds occurred approximately every 20 months to identify new fibroids. Fibroids that were detected at enrollment and those that arose during follow up were monitored at subsequent visits for fibroid growth. We collected risk factor and symptom data, physical measurements, as well as blood, urine, and vaginal swab specimens at enrollment and follow-up visits.The study was designed to test three primary hypotheses:Vitamin D deficiency is a risk factor for fibroid incidence and/or growth.Reproductive tract infections can increase risk of fibroid development.Genotypic variation in African ancestry may influence fibroid development directly, or through interaction with life-course risk factors.In addition, we collected extensive information to examine other exposures of interest, and our extra specimens can be used to test new hypotheses in the future.With this first prospective study of fibroid development, we aim to identify new preventative factors that could directly benefit women. We anticipate that the detailed data on fibroid development can be used to help design new interval treatment strategies to limit fibroid growth and thus reduce the need for the invasive treatments that remain the standard of care when first-line treatments fail.

Study phs002513

Profiled samples in the study "Chromatin activation profiling of stereotyped chronic lymphocytic leukemias reveals a subset #8 specific signature"

Dac EGAC00001002787

STAT3 ChIPseq of PC-9 and KHM-3S with and without tarceva

Dataset EGAD00001000844

Whole genome sequencing of individuals from Latvia: the first step towards the population-specific reference of genetic variation

Study EGAS00001007406

14314 results for ""Pennsylvania+German"+ACS+study+'Socius'+open+access"

in 16.30 milliseconds.

Genentech Colon Cancer Screen

Enhancer profiling to identify identifies epigenetic markers of endocrine resistance in metastatic castration resistant prostate cancer patients

Longitudinal single-cell RNA-seq data of metastatic ovarian cancer

Methylation data for Genomic landscapes of endometrioid and mucinous ovarian cancers and morphologically similar tumor types

Lower respiratory tract single cell and neutrophil extracellular trap profiling of COVID-19-associated pulmonary aspergillosis

Single-cell multi-omic profiling of glioblastoma-associated myeloid cells

Chordoma Extension Study

CPC-GENE Prostate Cancer Heterogeneity Study

AML-MRD

AngioPredict CNV and Exome data

Bisulphite_MPN_colonies

Identifying_Novel_Fusion_Genes_in_Myeloma

The genomic diversity of Taiwanese Austronesian groups: implications for the ‘Into and Out of Taiwan’ models

RNA-Seq on GeparSixto tissue samples