Search Results - EGA European Genome-Phenome Archive

STAG1 and STAG2-ChIP-seq in RAD21-mutant adult acute myeloid leukemia

Dataset EGAD00001015361

Single-cell multiomics reveals the interplay of clonal evolution and cellular plasticity in hepatoblastoma

spatial transcriptomics

Dataset EGAD00001015262

Dental Caries: Whole Genome Association and Gene x Environment Studies

Dental caries (also known as tooth decay) remains the most common chronic disease of childhood, five times more common than asthma and seven times more common than environmental allergies, with more than 40% of children exhibiting caries when they enter kindergarten. In 2005, it was estimated that dental health care costs were approximately $84 billion, of which 60% or about $50 billion were related to treatment of dental caries. Although overall caries prevalence has declined over the last 40 years, dental caries in the primary dentition and mean caries rates in children ages 2-11 has increased markedly over the past 12 years. Childhood caries is a serious public health issue because of associated health problems and because disparities in oral health have led to substantially higher average disease prevalence among children in poverty and in under-served racial and ethnic groups. These issues are of such concern that in 2005, the American Academy of Pediatrics made children's oral health one of their top areas of focus, as it is for the majority of the NIDCR "Disparities Centers". The etiology of dental caries has been studied for many years. Multiple factors contribute to a person's risk for caries, including: 1) environmental factors such as diet, oral hygiene, fluoride exposure and the level of colonization of cariogenic bacteria and 2) host factors such as salivary flow, salivary buffering capacity, position of teeth relative to each other, surface characteristics of tooth enamel and depth of occlusal fissures on posterior teeth. In spite of all that is known about this disease, there are still individuals who appear to be more susceptible to caries and those who are extremely resistant, regardless of the environmental risk factors to which they are exposed, implying that genetic factors also play an important role in caries etiology. This conclusion is supported by studies in both humans and animals, with the most compelling evidence coming from studies of twins reared apart in which investigators found significant resemblance within monozygotic (MZ) but not dizygotic (DZ) twin pairs for percentage of teeth and surfaces restored or carious and estimated the genetic contribution to caries as 40%. Other recent studies of twins reared together estimated the heritability for caries, adjusted for age and gender, as ranging from 45-64%. Despite the strong evidence of a genetic component to risk for dental caries, there have been only a few studies of candidate genes in caries, and no published genome-wide scans. A comprehensive genome wide search is the only approach that will allow us to identify those genetic regions likely to harbor genes increasing the risk for dental caries, and eventually to identify the etiologic genes and to explore the interaction of those genes with microbiological, dietary, fluoride, and behavioral factors that are known to be associated with caries risk and progression. Therefore, the goal of this study is to perform genome-wide association (GWA) studies of dental caries with a large panel of SNP's (610,000) in families and individuals ascertained through multiple US sites (University of Pittsburgh and University of Iowa). The v2 release of this study includes 96 additional individuals who were genotyped with the CCDG: Dental Caries and CL/P in Guatemala project (dbGaP accession number phs000440) to augment the data initially presented here. These subjects were genotyped on the Illumina 610 platform to make their data comparable. This study is part of the Gene Environment Association Studies initiative (GENEVA, http://www.genevastudy.org), which was developed through the trans-NIH Genes, Environment, and Health Initiative (GEI). The overarching goal is to identify novel genetic factors that contribute to dental caries through large-scale genome-wide association studies of well-characterized families and individuals at multiple sites in the U.S. Genotyping was performed at the Johns Hopkins University Center for Inherited Disease Research (CIDR). The study was supported by the National Institute of Dental and Craniofacial Research (NIDCR, U01-DE018903). Data cleaning and harmonization were done at the GEI-funded GENEVA Coordinating Center at the University of Washington. Samples of some participants in this study were selected for further genomic analysis. These results will be available in the dbGaP CIDR study: Center for Oral Health Research in Appalachia (COHRA) Genomic Studies of Oral Health and Disease (phs001591).

Study phs000095

Risk Assessment of Cerebrovascular Events (RACE) Study

This study includes 1,220 cases with young onset stroke (stroke before age 60 years) who are participants of the larger RACE study. Risk Assessment of Cerebrovascular Events (RACE) is an on-going existing case-control study of stroke now involving over 5000 imaging confirmed cases of stroke and 5000 controls, recruited from seven centers in Pakistan. The study is aimed to investigate the genetic, biomarker and lifestyle determinants of stroke and its subtypes. Cases are eligible for inclusion in the study if they: (i) are aged at least 18 years; (ii) present with a sudden onset of neurological deficit respecting a vascular territory with sustained deficit at 24 hours verified by medical attention within 72 hours after onset (onset is defined by when the patient was last seen normal and not when found with deficit); and (iii) the diagnosis is supported by CT/MRI; and (iv) present with a Modified Rankin Score < 2 prior to the stroke. Findings from patient's history, 12-lead ECG and CT or MRI of the brain. The mandatory procedures for inclusion in this investigation are: (i) clinical verification of cerebrovascular event within 72 hours of onset; (ii) neuroimaging CT (non-contrast) or MRI (MRI is not a mandatory investigation but recorded whenever ordered by the attending physician); and (iii) 12-lead ECG. All other ancillary investigations ordered by the attending physician are recorded as well. The TOAST classification method is used to classify ischemic stroke based on aetiology whereas the Oxfordshire classification is used to classify stroke neuro-anatomically. Control participants for this subset of young onset stroke were individuals enrolled in the Pakistan Risk of Myocardial Infarction Study (PROMIS), a case-control study of acute MI based in Pakistan. RACE capitalizes on the genetic data (including information on GWAS) that has already been collected from the healthy participants enrolled in PROMIS. RACE and PROMIS share similar methodology of recruitment. Participants from both these investigations are derived from similar catchment areas, hence providing an attractive opportunity for RACE to utilize PROMIS controls as common controls for genetic investigations. Controls in PROMIS were recruited following procedures and inclusion criteria as adopted for RACE cases. In order to minimize any potential selection biases, PROMIS controls selected for this stroke substudy were frequency matched to RACE cases based on age and gender and were recruited in the following order of priority: (1) non-blood related or blood related visitors of patients of the out-patient department; (2) non-blood related visitors of stroke patients; (3) patients of the out-patient department presenting with minor complaints (e.g. back pain, minor gastric complaints). Control subjects from the PROMIS study were genotyped at the Wellcome Trust Sanger Institute on the Illumina 660W Quad array. The Center for Non-Communicable Diseases, Pakistan, serves as the coordinating center for both RACE and PROMIS. More information on these research investigations can be found at www.cncdpk.com. This young onset stroke component to the RACE study was funded through the Gene Environment Association Studies initiative (GENEVA, www.genevastudy.org as one of three studies designed to assess the genetics of young onset stroke and modification of genetic effects by smoking. GENEVA is part of the trans-NIH Genes, Environment, and Health Initiative (GEI). Genotyping of 1,220 young onset stroke cases was performed at the Johns Hopkins University Center for Inherited Disease Research (CIDR). Data cleaning and harmonization were done at the GEI-funded GENEVA Coordinating Center at the University of Washington. 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 stroke through large-scale genome-wide association studies of cases and controls recruited within Pakistan. Genotyping was performed at the Johns Hopkins University Center for Inherited Disease Research (CIDR). Data cleaning and harmonization were done at the GEI-funded GENEVA Coordinating Center at the University of Washington.

Study phs000456

A Clinical Trial of Pembrolizumab in Patients with Hepatitis B Virus-related Hepatocellular Carcinoma, with Parallel Study on Baseline and Serial Change in the Immune Environment

This is a single-arm Phase II trial of pembrolizumab in patients with hepatitis B virus-related hepatocellular carcinoma with parallel study on baseline and serial change in the immune environment. Subjects should have a confirmed diagnosis of HCC (in accordance with the AASLD guideline) and confirmed chronic infection with hepatitis B virus as defined by positivity for HBsAg. Antiviral therapy for HBV must be given for at least 12 weeks and HBV viral load must be less than 100 IU/mL prior to first dose of study drug. They must have disease not amenable to a curative treatment approach or loco-ablation. Subject must be fit and agreeable with baseline and post-treatment biopsy of tumor. Subjects must have at least one measurable lesion per Response Evaluation Criteria in Solid Tumors (RECIST) 1.1, an Eastern Cooperative Oncology Group (ECOG) performance score of 0 or 1 and adequate organ functions. 30 subjects will be enrolled to receive pembrolizumab 200 mg IV every 3 weeks(Q3W). Pre-treatment and on-treatment biopsy after 2 cycles of Pembrolizumab will be preformed. Treatment will be stopped when progression of disease or intolerable toxicity occurs. The primary objectives of this trial are to study the efficacy and safety of pembrolizumab in patients with HBV-related HCC and to study the serial change in RNA expression of immune-related gene panel in post-treatment biopsy tissue. The secondary objectives of this trial are to study the serial change in cytokine profile between pre-treatment and post-treatment samples, to study the PD-L1 immunohistochemical (IHC) expression in tumor sample at baseline and post-treatment tissue samples and to study the presence of tumor infiltrating lymphocytes in the baseline and post-treatment tumor samples. The exploratory objective of this trial is to evaluate the possibility of using baseline and the serial change in RNA expression of immune-related gene panel or PD-L1/2 IHC to predict treatment response.

Dataset EGAD50000001872

RNAseq data to study PRPF6 regulated splice forms in colon cancer cell lines

Alternative splicing plays critical roles in differentiation, development, and cancer (Pettigrew et al., 2008; Chen and Manley, 2009). The recent identification of specific spliceosome inhibitors has generated interest in the therapeutic potential of targeting this cellular process (van Alphen et al., 2009). Using an integrated genomic approach, we have identified PRPF6, an RNA binding component of the pre-mRNA spliceosome, as an essential driver of oncogenesis in colon cancer. Importantly, PRPF6 is both amplified and overexpressed in colon cancer, and only colon cancer cells with high PRPF6 levels are sensitive to its loss. Our data clearly point to an important role for PRPF6 in colon cancer growth and suggest that a better understanding of its role in alternative splicing in colon cancer is warranted. To determine the specific alternative splice forms that PRPF6 regulates in colon cancer, we plan three experiments: 1. The first involves knocking down expression of PRPF6 in two different cancer cell lines with 3 different siRNAs, and then completing RNA-seq to determine the gene expression changes that occur relative to a non-targeting control siRNA. Because of the role for PRPF6 in pre-mRNA splicing, we especially want to quantify the changes in splice-specific forms of all genes genome-wide to identify genes whose splicing is altered upon PRPF6 knockdown. 2. The second involves immunoprecipitating PRPF6 from two different cancer cell lines and isolating any RNA that is bound to PRPF6, since PRPF6 is an RNA-binding protein. We then want to carry out RNA-seq to identify which RNA molecules co-immunoprecipitated with PRPF6. This will help us determine possible functions for PRPF6 in regulating colon cancer growth. 3. The third involves overexpressing PRPF6 in cell lines and then carrying out RNA-seq to identify any changes in splice-specific gene expression. This will allow us to determine whether increased PRPF6 expression is sufficient to drive alternative splicing changes.

Dataset EGAD00001000817

Variant call of single Jakun Individual

One Jakun individual was sequenced on IIllumina HiSeq 2000. Variant calling was performed through GATK

Dataset EGAD50000001024

Average_5hmC_TF_sites

Average hydroxymethylation levels on transcription factor binding sites obtained from ENCODE (ChIP-sequencing of GM12878 lymphoblastoid cell line). Data from 6 individuals at different time points.

Dataset EGAD00010002421

Transcriptome of human CD4+ T-lymphyocyte (memory-T-cells - untreated) from donor D2, replicate 2, glucose concentration 5mM

Dataset EGAD00001008048

Transcriptome of human CD4+ T-lymphyocyte (memory-T-cells - untreated) from donor D1, replicate 2, glucose concentration 5mM

Dataset EGAD00001008038

Transcriptome of human CD4+ T-lymphyocyte (memory-T-cells - untreated) from donor D3, replicate 2, glucose concentration 5mM

Dataset EGAD00001008058

RNA-sequençing of 21 inflammatory hepatocellular adenomas and 1 non-tumoral sample

Dataset EGAD00001005284

OT2_Solid_WXS_T

Whole-exome sequencing on AB 5500xl Genetic Analyzer of colorectal cancer primary tumor sample (OT2_cohort)

Dataset EGAD00001003386

HipSci - Monogenic Diabetes - Exome Sequencing - July 2017

Dataset EGAD00001003516

SF11310

SF11310 Oligodendroglioma, IDH-mutant.Tumor Location: Frontal. Age:22. Sex: Female

Dataset EGAD00001006313

CSC DDR dataset

CSC DDR dataset contains 4 bam files of two pairs of colorectal CSCs sensitive and resistant to ATR or CHK1 inhibitor

Dataset EGAD00001006774

Reference epigenome Pancreas-Islet07 WGBS data generated from KEP study

Pancreas-Islet07 WGBS paired end data

Dataset EGAD00001007146

Reference epigenome Fat-adipocyte03 WGBS data generated from KEP study

Fat-adipocyte03 WGBS paired end data

Dataset EGAD00001007147

Reference epigenome Fat-adipocyte04 WGBS data generated from KEP study

Fat-adipocyte04 WGBS paired end data

Dataset EGAD00001007148

Reference epigenome Fat-adipocyte05 WGBS data generated from KEP study

Fat-adipocyte05 WGBS paired end data

Dataset EGAD00001007149

Reference epigenome ADMSC01 mRNA-Seq data generated from KEP study

ADMSC01 mRNA-Seq paired end data

Dataset EGAD00001007150

Reference epigenome ADMSC03 mRNA-Seq data generated from KEP study

ADMSC03 mRNA-Seq paired end data

Dataset EGAD00001007152

Reference epigenome ADMSC05 mRNA-Seq data generated from KEP study

ADMSC05 mRNA-Seq paired end data

Dataset EGAD00001007153

Reference epigenome ADMSC06 mRNA-Seq data generated from KEP study

ADMSC06 mRNA-Seq paired end data

Dataset EGAD00001007154

Reference epigenome ADMSC07 mRNA-Seq data generated from KEP study

ADMSC07 mRNA-Seq paired end data

Dataset EGAD00001007155

Reference epigenome ADMSC08 mRNA-Seq data generated from KEP study

ADMSC08 mRNA-Seq paired end data

Dataset EGAD00001007156

Reference epigenome SMC01 mRNA-Seq data generated from KEP study

SMC01 mRNA-Seq paired end data

Dataset EGAD00001007169

Reference epigenome SMC02 mRNA-Seq data generated from KEP study

SMC02 mRNA-Seq paired end data

Dataset EGAD00001007170

Reference epigenome SMC03 mRNA-Seq data generated from KEP study

SMC03 mRNA-Seq paired end data

Dataset EGAD00001007171

Reference epigenome SMC04 mRNA-Seq data generated from KEP study

SMC04 mRNA-Seq paired end data

Dataset EGAD00001007172

Reference epigenome SMC05 mRNA-Seq data generated from KEP study

SMC05 mRNA-Seq paired end data

Dataset EGAD00001007173

Reference epigenome SMC07 mRNA-Seq data generated from KEP study

SMC07 mRNA-Seq paired end data

Dataset EGAD00001007174

Reference epigenome SMC08 mRNA-Seq data generated from KEP study

SMC08 mRNA-Seq paired end data

Dataset EGAD00001007175

Reference epigenome SMC09 mRNA-Seq data generated from KEP study

SMC09 mRNA-Seq paired end data

Dataset EGAD00001007176

Germline variant analysis in childhood AML

This dataset contains one vcf file with variants from whole exome sequencing of 24 paediatric AML samples at diagnosis.

Dataset EGAD00001008783

Reference epigenome Islet-derived-MSC06 WGBS data generated from KEP study

Islet-derived_MSC06 WGBS paired end data

Dataset EGAD00001007875

Reference epigenome Islet-derived-MSC08 WGBS data generated from KEP study

Islet-derived_MSC08 WGBS paired end data

Dataset EGAD00001007876

Reference epigenome Islet-derived-iPSC04 WGBS data generated from KEP study

Islet-derived_iPSC04 WGBS paired end data

Dataset EGAD00001007877

scRNA-seq of placental immune cells

scRNA-seq analysis of 384 placental immune cells

Dataset EGAD00001010040

STAG1-ChIP-Seq of STAG2-mutated and cohesin wildtype adult AMLs

ChIPseq targeting the cohesin subunit STAG1 in STAG2-mutated AMLs or cohesin wildtype AMLs

Dataset EGAD00001011206

Covacta OLINK LOD

Explore 1536 dataset from serum of patients enrolled in the COVACTA trial. This dataset includes limit of detection values provided by Olink.

Dataset EGAD00001011161

Covacta OLINK NPX

Olink Explore 1536 dataset from serum of patients enrolled in the COVACTA trial. This dataset includes the NPX values provided by Olink.

Dataset EGAD00001011169

Systematic immune cell dysregulation and molecular subtypes revealed by single cell RNA-seq of subjects with type 1 diabetes

Type 1 diabetes mellitus (T1DM) is a prototypic endocrine autoimmune disease resulting from an immune-mediated destruction of pancreatic insulin-secreting beta-cells. A comprehensive immune cell phenotype evaluation in T1DM has not been performed thus far at the single. In this cross-sectional analysis, we generated a single-cell transcriptomic dataset of peripheral blood mononuclear cells (PBMCs) from 46 manifest T1DM (Stage 3) cases and 31 matched controls.Our study reveals a surprisingly strong systemic dimension at the level of immune cell network in T1DM, defines disease-relevant molecular subtypes and has the potential to guide non-invasive test development and patient stratification.

Study EGAS50000000231

CRU-Ukrainian National Research Center for Radiation Medicine Trio Study

Data on transgenerational effects following nuclear accidents are important for understanding fully the consequences of parental exposure to ionizing radiation. Few studies to date have had adequate statistical power to detect effects of the magnitude expected based on animal data, and most have not been of low-dose, protracted exposures associated with nuclear accidents and their aftermath. Although, to date, scant use has been made of the new genomic technologies, in Chernobyl-exposed areas of Ukraine and Belarus, excess minisatellite mutations have been seen in children born after the accident. We propose a study of parent-child trios in which at least one parent was exposed to Chernobyl radiation as a clean-up worker (mean dose>=100 mGy) and/or evacuee from a contaminated area (mean >=50 mGy). The specific aims are to investigate the transgenerational and de novo mutation rates of the spectrum of genetic variants in trios, in particular looking at effects in children and mapping them to possible parental origin of the chromsoome. Together with long-term collaborators at the Research Center for Radiation Medicine (RCRM) in Kiev, epidemiologic data will be collected for up to 450 trios of parents with preconceptional doses and their unexposed offspring. We will use state-of-the-art genomic technologies to characterize the landscape of the genomes of the trios to determine whether parental radiation exposure is associated with genetic mutations transmitted to the offspring, by examining de novo mutation rates, minisatellite mutations, copy number alterations, and variations in telomere length. The analysis will be conducted in peripheral blood and/or buccal samples (when blood is not available) from complete father-mother-child trios. Doses to the gonads from the time of the accident to the time of conception will be reconstructed for all parents using existing records supplemented by interview data. Trio subjects will be selected from representative populations exposed to radiation from Chernobyl who are under active follow-up in the Clinico-Epidemiologic Registry at RCRM. To help identify specific effects of paternal and maternal radiation exposure, we will initially select sets of trio subjects in five categories: (1) exposed father, unexposed mother; (2) unexposed father, exposed mother; (3) both parents exposed; (4) both parents unexposed; and (5) a group of high dose "emergency workers" with acute radiation syndrome. All trio members will be invited to the RCRM outpatient clinic for collection of a 20 ml blood sample (or buccal cells for those who refuse phlebotomy). Both parents will be asked to complete a general questionnaire to obtain demographic and lifestyle data. Then one or both will complete detailed dosimetry questionnaires, based on forms used in previous collaborations with RCRM and administered by specially trained interviewers. Once 50 trios have been recruited (10 from each of the 5 exposure categories), we will conduct an interim evaluation of participation rates, sample collection and quality, and dose reconstruction in order to modify the protocol as needed. The analytical approach will be to correlate the extent, especially for de novo events of genetic alterations in the offspring with parental pre-conceptional radiation dose overall and by parental origin. The statistical power in relation to de novo mutations is very high, in excess of 90%, but somewhat lower for trends in minisatellite mutations. Study findings will contribute importantly to knowledge of the heritable effects of moderate- and low-dose radiation exposure in humans and to radiation risk projection. Eventually data from the Trio Study may be shared with the international community through dbGap.

Study phs001163

HGP-clean

Himalayan population genetic study QC filtered data

Dataset EGAD00010001471

OA_hip-G-1

Genotyping of hip osteoarthritis patients who have undergone total joint replacement

Dataset EGAD00010001292

Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing

Dataset EGAD00001000856

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