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

SNP Genotype Data: Subpopulations of Filipino, Malaysian, and Papua New Guinea

In the context of the study 'Exploring Adaptive Phenotypes for the Human Calcium-Sensing Receptor Polymorphism R990G,' this repository contains 11 VCF files. Each file includes genetic data from 22 autosomes, representing distinct subpopulations. The subpopulations are as follows: Malaysian: Aeta (15 samples) Agta (11 samples) Batak (10 samples) Mamanwa (6 samples) Filipino: Jehai (13 samples) Kintaq (6 samples) Temiar (5 samples) Papua New Guinea: Highlands (2 samples) Koinambe (10 samples) Kosipe (10 samples) Sepik (2 samples) The numbers in parentheses indicate the sample size for each respective subpopulation.

Study EGAS50000000044

Avelumab or M7824 for People with Recurrent Respiratory Papillomatosis

This submission includes genomic data derived from the study of clinical samples from two different phase II trials. These trials evaluated the clinical efficacy and safety of avelumab or M7824 in the treatment of adults with recurrent respiratory papillomatosis (RRP). Subjects with aggressive RRP were treated with three to six doses of avelumab or M7824. Pre-treatment or post-treatment snap frozen papilloma and normal mucosa samples were subjected to whole exome sequencing and bulk RNA-seq. A total of twenty subjects were enrolled and treated. 

Study phs002373

Expression Quantitative Trait Locus Mapping Studies in Mid-Secretory Phase Endometrial Cells Identifies HLA-F and TAP2 as Fecundability-Associated Genes

We performed an unbiased genome-wide expression quantitative trait locus (eQTL) mapping study to identify common regulatory (expression) single nucleotide polymorphisms (eSNPs) in mid-secretory endometrium, corresponding to the luteal phase of the ovarian cycle. Biopsies were collected from 58 women with two or more early pregnancy losses and 53 of these samples passed all quality control. RNA was extracted from endometrial biopsies and DNA was extracted for sequencing from blood. Gene expression data can be found at NCBI GEO Series GSE77688.

Study phs001146

A Somatic Reference Standard for Cancer Genome Sequencing

In this study, we separately performed PCR-free whole genome sequencing on the paired tumor/normal melanoma COLO-829 and lymphoblastoid COLO-829BL cell lines across three separate institutions (TGen, Illumina, Genome Sciences Centre at the British Columbia Cancer Agency). We performed a meta-analysis of all data, in combination with the originally reported analysis of these cell lines by Pleasance et al., and report a somatic reference standard based on consensus events. This standard can be used as a reference for tumor/normal whole genome analyses.

Study phs000932

Leveraging Extended Families for Cardiovascular Disease Genomic Discovery

This study characterizes a large early onset atrial fibrillation family and identifies a rare causative mutation (R231H) in the KCNQ1 gene. The age of this mutation is ~5000 years, as estimated using IBD-coalescent methods. The geographic distribution and demographic history of the mutation is described. Induced pluripotent stem cell derived cardiomyocytes carrying the mutation have abbreviated action potential duration, indicating a gain-of-function. This data resource provides exome or whole genome sequencing data for six patients and RNA-seq data from the cardiomyocyte experiments. 

Study phs002464

Genomic Sequencing of Lung Adenocarcinoma

Lung carcinoma is the leading cause of cancer death in the United States and world-wide; lung adenocarcinoma is the most common cause of lung cancer. Pilot studies of lung adenocarcinoma with hybrid-capture based whole exome sequencing will enable us to identify new targets for therapy and improve diagnosis. We will analyze a blend of whole exome and whole genome sequencing data as well as copy number and somatic mutation calls for 200 tumor and matched normal controls. When completed this study will represent the most comprehensive lung adenocarcinoma genome dataset to date.

Study phs000488

Characterization of CNS Metastases

Metastatic disease to the central nervous system (CNS) is devastating, with a poor prognosis. There are limited treatment options for patients with CNS metastases, and in particular with leptomeningeal carcinomatosis (LMD). In this study, we evaluated the molecular and cellular features of parenchymal brain metastases and LMD. We used single-cell RNA and cell-free DNA profiling of CSF from patients with LMD receiving immunotherapy to demonstrate shifts in the liquid LMD tumor microenvironment. We also characterize the tumor microenvironment of parenchymal brain metastases using single cell sequencing, before and after treatment with immunotherapy.

Study phs002416

Differential Mutations in Matched Primary and Metastatic Colorectal Cancers

This study compares DNA mutations detected in matched primary and metastatic colorectal cancer samples from 18 individuals across 1,321 genes. We found many more mutations were shared between tumor pairs (avg. 33.3 mutations/tumor) than were discordant (avg. 2.3 mutations / tumor). Nearly all tumors showed at least one discordance, and these were observed in genes known to be involved in colorectal cancer progression. Therefore, although primary and metastatic colorectal tumors are highly genetically concordant, evidence exists for discordance, which has clinical implications especially in situations of chemotherapy resistance or insensitivity.

Study phs001084

Breakpoint detection using long insert whole genome sequencing

In this study, we hypothesize that shallow long insert whole genome sequencing (LI-WGS) increases our power for detecting breakpoints compared to shallow short insert WGS. We performed a priori analyses to demonstrate the benefits of LI-WGS, developed a long insert library preparation protocol based off Illumina's protocol, and compared LI-WGS against short insert WGS on test samples. We then used long insert WGS to identify translocations and copy number changes in tumor and germline samples collected from cancer patients with different malignancies.

Study phs000646

Pharmacogenomic Analysis of Microtubule Targeting Agent Response and Toxicity

Microtubule targeting agents are commonly prescribed for early and metastatic breast cancer and other solid tumors. However, interindividual variability in microtubule targeting drug response and toxicity can cause limited therapeutic benefit and impact quality of life. In the present study, genome-wide analyses were performed to investigate how genetic factors can be used to increase prediction of treatment response and toxicity, identify genes or gene pathways associated with chemotherapy-induced neurotoxicity, and inform further in vitro studies that may help isolate differences in response and toxicity of microtubule targeting agents.

Study phs002060

Metagenomic Deep Sequencing in Meningitis and Encephalitis

This is a prospective observational study seeking to identify pathogens in cases of unexplained neurological disease, particularly those in which there is a presumed infectious cause. This next generation analytical approach will hopefully allow for rapid identification of foreign genomic material, and through a sophisticated bioinformatics pipeline developed in the DeRisi lab, these foreign genomic sequences can be aligned to all known sequences in publicly available databases (i.e. GenBank) which may allow for identification of novel pathogens or known pathogens that are not frequently tested for as part of standard diagnostic work-ups.

Study phs001067

The Vaginal Microbiome in Reproductive Age Women

The focus of this cross-sectional study was to characterize the vaginal microbiota of asymptomatic, sexually-active, and reproductive-age women representing four self-reported ethnic groups (White, Black, Asian, and Hispanic). Each woman self-collected two mid-vaginal swabs. The first swab was used to prepare a vaginal smear for Nugent gram stain analysis. The second swab was used for DNA extraction, 16S rRNA gene amplicon sequencing, and detection of Candida albicans. In addition, participants measured vaginal pH and completed a detailed questionnaire on sexual health and behaviors.

Study phs001909

Identification of Putative Neoantigens in Stage III Melanoma

This study of three metastatic melanoma patients utilized exome sequencing and RNA sequencing to help identify putative neoantigen peptides that could be further validated by standard immunological assays before design of a personalized vaccine. For each set of neoantigens identified and verified by standard assays, we designed GMP peptides that correspond to the top neoantigens, then used these to condition dendritic cell isolates from each patient. The conditioned dendritic cells were used as the vaccine in three rounds of vaccination, followed by monitoring for T cell memory response to each of the neoantigens.

Study phs001005

Genomic and Transcriptomic Markers Associated with Response to Immune Checkpoint Blockade

The neoantigen presentation score (NEOPS) study was designed to better understand molecular determinants of response to immunotherapies, including pembrolizumab and nivolumab in stage III or IV melanoma patients. From this work, we developed a composite approach to predicting neoantigens (NEOPS), which takes into account additional escape mechanisms, including HLA LOH (human leukocyte antigen loss of heterozygosity) and the impact of deleterious mutations to the antigen presentation machinery (APM), yielding an improved prediction of response to immunotherapy compared to TMB (tumor mutational burden) or neoantigen burden alone.

Study phs002388

Whole exome sequencing of 184 unrelated subjects with 22q11.2 deletion syndrome (DiGeorge syndrome/velo-cardio-facial syndrome)

Our goal is to find genetic modifiers of major phenotypes in patients with 22q11.2 deletion syndrome, also known as DiGeorge syndrome or velo-cardio-facial syndrome. Whole exome sequencing was performed as part of a contract to the NHLBI, Resequencing and Genotyping Service. We have obtained cardiac phenotype information from the de-identified subjects enrolled in the study, either by echocardiography report or medical doctor report. All of the subjects have a 3 million base pair 22q11.2 deletion flanked by low copy repeats, LCR22, A-D.

Study phs000987

14390 results for ""Pennsylvania+German"+ACS+study+'Socius'+open+access"

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Study2OrangeFiber

Study1PeaFiber

Adaptive single-KIR+NKG2C+ NK cells expanded from superdonors show potent missing-self reactivity and efficiently control HLA-mismatched acute myeloid leukemia

Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from Landen, Stockholm, Sweden.

Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from the Netherlands (posthuma)

Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from Edinburgh, Scotland, UK.

QuantSeq 3'-mRNAseq of pathogen-stimulated PBMCs

Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from Cardiff, UK (O'Donovan)

Transcriptome of insulinomas

Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from the Netherlands (Ophoff)

Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from Stockholm, Sweden (Pedersen)

The BAF chromatin remodeling complex is a novel target of spliceosome dysregulation in SF3B1-mutated chronic lymphocytic leukemia

Elucidating the heterogeneity of immunotherapy response and immune-related toxicities by longitudinal ctDNA and immune cell compartment tracking in lung cancer

Integrative genomic analyses of European intrahepatic cholangiocarcinoma: new ROS1 fusion gene and PBX1 as prognostic marker

Preoperative ipilimumab plus nivolumab in locoregionally advanced urothelial cancer (NABUCCO Cohorts 1 and 2)

Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from Cardiff, UK (Owen)

Comprehensive Characterization of Early Relapse and End-Stage Relapsed Refractory Multiple Myeloma (HIPO K08K/H067/H021+nonHIPO)

HNSCC Patients Treated with Immune Checkpoint Blockade

Kinomics data

Genome-wide DNA Methylation Analysis Reveals a Unique Methylation Pattern for Pleural Mesothelioma Compared to Healthy Pleura and Other Lung Diseases

Chordoma_Extension_Study

Chordoma_Extension__known_cancer_genes_

Giant congenital nevi exome sequencing

Very short reads file for testing purposes

WGS

DLBCLR

SNP array ARID1B patients

LCNEC study - RNAseq data set

Bacteria Lateral sclerosis

Phylogenetic reconstruction of breast cancer