13380 results for ""60+mice"+"6+weeks"+diet+study+2014+2017+DOI"

in 183.19 milliseconds.

• Premalignant SOX2 overexpression in the fallopian tubes of ovarian cancer patients: Discovery and validation studies

  To identify early driver mutations in ovarian cancer cells, we used dense whole genome sequencing of micrometastases and microscopic residual disease collected at three time points from a single patient during treatment for high-grade serous ovarian cancer (HGSOC). Laser capture microdissection of tumour islets was performed on samples prior to chemotherapy, after three cycles of chemotherapy and at recurrence. Long frament read whole genome sequencing was performed and mutations were identified. To our knowledge, this is the first longitudinal study that attempts to investigate spatial and temporal micro-heterogeneity in cancer.

  Study EGAS00001001909

• Transcriptome sequencing of intravenous leiomyomatosis and uterine myoma

  Up to now, there are two hypothesis about the pathogenesis of the relationship of intravenous leiomyomatosis and uterine myoma. One theory suggests that the IVL comes from the smooth muscle cell in the vessel wall.The other theory indicates that the IVL derives from the uterine myometrium. However, limited to the technology, few studies have been deeply explore the underlying relation. In this study, we employ the RNA sequencing to explore the molecule relationship between IVL and uterus myoma. In order to identify the molecule relationship between IVl and uterine myoma we conducted transcriptome sequencing and bioinformaitc analysis

  Study EGAS00001002504

• Transcriptome profiling of human plucked frontal and occipital hair follicles

  Androgenetic alopecia (AGA) is characterized by a progressive and androgen-dependent loss of hair from the frontal and vertex regions of the scalp. Although large-scale genetic analyses have identified >300 genetic risk factors, the underlying causal genes and pathways, and their involvement in core pathophysiological mechanisms, remain unclear. In the present study, systematic profiling of differential mRNA and microRNA expression was performed in human hair follicle samples from frontal and occipital scalp regions. Taken together, the present data improve understanding of the genomic regions, genes, and pathways that are implicated in AGA pathobiology.

  Study EGAS00001002832

• Single cell exome sequencing of lung adenocarcinoma

  Single cell exome sequencing was performed on 200 single cells isolated from a lung adenocarcinoma, female, non-smoker patient. The cells were derived from two distant tumour sectors and a far normal sector. The single cells were amplified on the Fluidigm C1 machine using the GE Healthcare illustra GenomiPhi V2 DNA Amplification Kit prior to sequencing library preparation. In addition, bulk exome sequencing was also conducted for each tumour sectors. For this study, somatic variations were detected from the single cells and phylogenetic clustering was conducted to elucidate the evolutionary trajectory of lung cancer.

  Study EGAS00001002972

• Panbody_nanoseq

  Different cell types within the human body are subject to different endogenous and exogenous exposures which may result in distinct patterns of mutagenesis. In non-clonal tissues, it is difficult to assess these mutational patterns, including the rate at which they occur. This study will examine the mutational rates and signatures operating across a wide range of normal tissues using the nanoseq technology to reliably call variants, irrespective of their clonal composition. Each cell type will be enriched for using laser capture microdissection. This will serve as a reference against which future work on benign and malignant disease entities can be compared.

  Study EGAS00001005521

• Genome-wide Ancestry and Demographic History of African-Descendant Maroon Communities from French Guiana and Surname.

  The transatlantic slave trade (TAST) was the largest forced migration in world history. However, the origins of the enslaved Africans and their admixture dynamics remain unclear. To investigate the demographic history of African-descendant Marron populations, we generated genome-wide SNP data (4.3 million markers) from 107 individuals from three African-descendant populations in South America, as well as 124 individuals from six west African populations to complement underrepresented African data sets. Our study sheds additional light on the demographic consequences of the TAST and illustrates how genetic data can complement historical sources.

  Study EGAS00001002535

• T-cell reconstitution after reduced dose ATLG induction in kidney transplant recipients

  Pre-sensitized kidney transplant recipients have a higher risk for rejection following kidney transplantation and therefore receive a lymphodepletional induction therapy with anti human T-lymphocyte globulin (ATLG). The time course of lymphocyte reconstitution with regards to overall and donor-reactive T-cell receptor (TCR) specificity remains elusive. In this study we aimed to describe the TCR repertoire in a reduced dose ATLG regimen making it possible to evaluate shifts in the shape of the immune repertoire and to detect the reappearance of donor-reactive T-cells following reduced lymphodepletional induction therapy.

  Study EGAS00001005941

• Understanding_hematopoietic_stem_cell_mobilization_and_engraftment_

  This study looks at patients undergoing gene therapy for genetic blood and immune disorders, in particular sickle cell disease. From each patient, single blood HSPC colonies are grown from patient blood mononuclear cells, bone marrow mononuclear cells, or CD34+ at multiple time points: pre gene transduction, post-transduction, and post-infusion (at several time points). Whole-genome sequencing will be performed on DNA from these colonies and somatically-acquired mutations will be called. Using these mutations, a phylogeny of these cells can be inferred and further inferences can be made about the gene therapy transduction and engraftment steps.

  Study EGAS00001004620

• molecular profiles of serum-derived extracellular vesicles in high-grade serous ovarian cancer

  Patients with high-grade serous ovarian cancer (HGSC) who have no visible residual disease (R0) after primary surgery have the best clinical outcomes, followed by patients who undergo neoadjuvant chemotherapy (NACT) and have response enabling interval cytoreductive surgery. Clinically useful predictive biomarkers for such distinctions are still lacking. Extracellular vesicles (EVs) have been recognized as liquid biopsy-based biomarkers for early cancer detection and disease surveillance in other disease settings. In this study, we performed extensive molecular characterization of serum-derived EVs and correlated them with therapeutic outcomes in patients with HGSC.

  Study EGAS00001006350

• Multiple Tissue Monitoring in Huntington disease - RNAseq skeletal muscle

  We examined whether peripheral tissues can serve as a source of readily accessible biological signatures at the RNA and protein level in Huntington disease (HD) patients. Under the MTM-HD study we generated large, high-quality human datasets from skeletal muscle, skin and adipose tissue, as well as primary human fibroblast lines to probe molecular changes in human pre-manifest and early manifest HD patients. We document the involvement of inflammation, energy metabolism and extracellular vesicle homeostasis. This demonstrates the potential to identify biological signatures from peripheral tissues in HD suitable as biomarkers in clinical trials.

  Study EGAS00001006474

• SARS-CoV-2 host genetics and COVID-19 outcomes in admixed Brazilians with extreme phenotypes

  COVID-19 comprises clinical outcomes of SARS-CoV-2 infection and is highly heterogeneous, ranging from asymptomatic individuals to deceased young adults without comorbidities. There is growing evidence that host genetics play an important role in COVID-19 severity, including inborn errors of immunity, age-related inflammation and immunosenescence. This study proposes a strategy of subject’s ascertainment based on phenotypic extremes to take part in genomic studies and elucidate intrinsic risk factors involved in COVID-19 severe outcomes. Different cohorts were collected and submitted to Next-Generation Sequencing (Whole exome and whole genome sequencing).

  Study EGAS00001006376

• NOTCH-mutations drive immune-escape mechanisms in B cell malignancies

  Here we provide access to MCL expression data that were used for interrogating the molecular functions of NOTCH1 and NOTCH2, which are two of the most commonly mutated genes in CLL and MCL and associated with a poor clinical outcome. The mechanisms underlying how NOTCH1 contributes to disease progression, resistance to treatment and Richter’s transformation remain largely unknown. The main goal of this study is to compare the gene expression profile of primary MCL cells transduced with the intracellular part of NOTCH1 or NOTCH2 lacking of the PEST domain vs cells transduced with an empty vector.

  Study EGAS00001005793

• Discovery and capture of novel dynamic DNA methylation in human sperm with preferential links to altered folate metabolism

  The sperm DNA methylation landscape is unique and critical for offspring health. If gamete-derived DNA methylation escapes reprogramming in early embryos, epigenetic defects in sperm may be transmitted to the next generation. Current techniques to assess sperm DNA methylation show bias towards CpG dense regions and do not target areas of dynamic methylation, those predicted to be environmentally sensitive and tunable regulatory elements. Thus, this study aim to assess variation in human sperm DNA methylation and design a targeted capture panel to interrogate the human sperm methylome.

  Study EGAS00001003617

• Multiple Tissue Monitoring in Huntington disease - RNAseq fibroblasts

  We examined whether peripheral tissues can serve as a source of readily accessible biological signatures at the RNA and protein level in Huntington disease (HD) patients. Under the MTM-HD study we generated large, high-quality human datasets from skeletal muscle, skin and adipose tissue, as well as primary human fibroblast lines to probe molecular changes in human pre-manifest and early manifest HD patients. We document the involvement of inflammation, energy metabolism and extracellular vesicle homeostasis. This demonstrates the potential to identify biological signatures from peripheral tissues in HD suitable as biomarkers in clinical trials.

  Study EGAS00001006472

• Multiple Tissue Monitoring in Huntington disease - RNAseq adipose tissue

  We examined whether peripheral tissues can serve as a source of readily accessible biological signatures at the RNA and protein level in Huntington disease (HD) patients. Under the MTM-HD study we generated large, high-quality human datasets from skeletal muscle, skin and adipose tissue, as well as primary human fibroblast lines to probe molecular changes in human pre-manifest and early manifest HD patients. We document the involvement of inflammation, energy metabolism and extracellular vesicle homeostasis. This demonstrates the potential to identify biological signatures from peripheral tissues in HD suitable as biomarkers in clinical trials.

  Study EGAS00001006473

• Characterization of chromatin accessibility in metastatic prostate cancer

  The development of resistance to second-generation AR-signaling inhibitors (ARSIs) and progression to metastatic castrate-resistant prostate cancer (mCRPC) represents a huge obstacle to the improvement of patients’ clinical outcomes. Lineage plasticity is a common mechanism that drives the development of mCRPC by changing chromatin conformation at regulatory elements affecting downstream gene activity. ATAC-seq is a popular technique that measures accessible chromatin regions. To better understand of potential epigenomic mechanisms of ARSI resistance in prostate cancer, in this study, we performed ATAC-seq on 70 mCRPC tissue biopsies from the SU2C/PCF West Coast Dream Team (WCDT) cohort.

  Study EGAS00001006698

• Selective advantage of mutant stem cells in human clonal hematopoiesis is associated with attenuated response to inflammation and aging

  In this study we characterised the consequences of DNMT3A- and TET2-mutations in human clonal haematopoiesis. We screened 195 bone marrow samples for mutations by targeted DNA sequencing, and sequenced 99 paired peripheral blood samples to compare mutation detection between bone marrow and blood. We performed single-cell analysis with TARGET-seq+ on 13 samples (4 controls and 9 clonal haematopoiesis samples), which combines single-cell genotyping for targeted mutations with whole transcriptome sequencing on FACS sorted cells. Single-cell genotyping and transcriptomes were sequenced separately and linked by common single-cell identifiers.

  Study EGAS00001007358

• Single-cell proteogenomics of MDS upon AZA

  To study the evolution of the clonal molecular and cellular architecture of MDS upon the treatment with AZA, we performed scDNA-seq of an amplicon panel of 53 genes recurrently mutated in myeloid malignancies, as well as typically lost or gain DNA regions, and scProt-seq of 42 cell-surface proteins to provide a simultaneous landscape of the genetic setting and immunophenotype using the Tapestri platform (MissionBio). We sequenced thousands of cells from 14 MDS patients, where paired bone marrow samples were obtained at the timepoint of diagnosis and after AZA treatment.

  Study EGAS00001007427

• Organ_maturation_in_preparation_for_birth__Peds_RFA__to_develop_a_tissue__resource_and_a_single_cell_atlas_of_organ_development_and_maturation_for__dissemination_among_the_scientific_and_clinical_community__RNA

  Knowledge about abnormal organ development is important to understand pathology and to develop novel treatment approaches for individuals with congenital and acquired disease. Most of our current understanding is based on examination of tissues from the embryo and early foetus, collected from women undergoing termination of pregnancy in the first trimester (third) of pregnancy. There is very little known about normal and abnormal organ development from a developmental perspective during the crucial last two-thirds of pregnancy when much remodelling of foetal tissues occurs. This study will generate a single-cell atlas of late-foetal lungs, blood, heart, bone and immune organs.

  Study EGAS00001008256

• NOUS-209 off-the-shelf immunotherapy has the potential to hit primary and metachronous colorectal and urothelial cancer in Lynch syndrome

  Lynch syndrome is an inherited cancer predisposition characterized by the development of microsatellite-instable tumors, most commonly colorectal and urothelial cancers. These cancers harbor recurrent frameshift mutations (FSMs) that generate shared neoantigens, creating opportunities for targeted immunotherapy. NOUS-209 is a viral-vector–based cancer vaccine encoding 209 of these shared neoantigen peptides. This study investigated the presence and evolution of NOUS-209 target FSMs in Lynch syndrome–associated tumors, revealing their persistence across primary and metachronous cancers and supporting the rationale for NOUS-209 as a preventive immunotherapy.

  Study EGAS50000001336

• miRNA-seq of paired Follicular Lymphoma (FL) patient samples before and after high-grade transformation to DLBCL (FL vs. tFL) from FFPE tissues

  The aim of this study was to analyze transcriptional changes in paired samples of follicular lymphoma (FL) and its histological transformation (tFL). Transformation of FL is an adverse event in the course of the disease and is associated with poor outcome. Several genetic aberrations have been linked to tFL pathogenesis, but gene expression changes and microenvironmental interactions have not been well characterized. We performed miRNA profiling of FL and paired tFL samples transformed to DLBCL (n=10 pairs). For miRNA profiling, we utilized libraries prepared using RNA isolated from archival FFPE tissues.

  Study EGAS50000000942

• mRNA-seq of paired Follicular Lymphoma (FL) patient samples before and after high-grade transformation to DLBCL (FL vs. tFL) from FFPE tissues

  The aim of this study was to analyze transcriptional changes in paired samples of follicular lymphoma (FL) and its histological transformation (tFL). Transformation of FL is an adverse event in the course of the disease and is associated with poor outcome. Several genetic aberrations have been linked to tFL pathogenesis, but gene expression changes and microenvironmental interactions have not been well characterized. We performed RNA profiling of FL and paired tFL samples transformed to DLBCL (n=11 pairs). For RNA profiling, we utilized libraries prepared using RNA isolated from archival FFPE tissues.

  Study EGAS50000000941

• Oesophageal adenocarcinoma WGS from LUD2015-005 study (NCT02735239, EudraCT 2015-005298-19)

  This dataset contains whole genome sequencing (WGS) generated from the inoperable cohorts of the LUD2015-005 study (NCT02735239, EudraCT 2015-005298-19). WGS data were generated with the aim to assess previously reported (e.g. tumour mutational burden) and novel predictive genomic markers for immunochemotherapy treatment in this setting. Using these data, mutation and copy number profiles were generated for the LUD2015-005 study, which were assessed for correlation with patient outcomes from this trial.

  Dataset EGAD00001009400

• Whole blood RNA sequencing of individuals from Nepal

  This study utilized blood samples collected in Lalitpur, Nepal as part of the Strategic Typhoid Alliance across Africa and Asia (STRATAA) study. The dataset comprises whole blood RNAseq of 376 febrile individuals from Nepal. Blood was collected in PAXgene tubes and sent to Monash University (Melbourne, Australia) where RNA was extracted using the PAXgene Blood RNA kit before being sent to the Wellcome Sanger Institute (Hinxton, UK) for sequencing. Library prep used NEBNext Ultra II RNA custom kits on an Agilent Bravo WS automation platform with poly(A) pulldown. After PCR, plates were purified using Agencourt AMPure XP SPRI beads and libraries were quantified using Biotium Accuclear Ultra high sensitivity dsDNA Quantitative kits. Pooled libraries were normalised to 2.8 nM. Samples were globin depleted using KAPA RNA HyperPrep with RiboErase. Libraries were then subjected to 2x100bp paired-end sequencing on Illumina NovaSeq. Each library was sequenced to an average of 80 million reads. The STRATAA study was approved by the Nepal Health Research Council (NHRC, ref 283 306/2015) and OxTREC (Oxford Tropical Research Ethics Committee, ref 39-15). All participants provided informed consent for human genetic tests.

  Dataset EGAD00001011131

• Framingham Cohort

  Startup of Framingham Heart Study. Cardiovascular disease (CVD) is the leading cause of death and serious illness in the United States. In 1948, the Framingham Heart Study (FHS) -- under the direction of the National Heart Institute (now known as the National Heart, Lung, and Blood Institute, NHLBI) -- embarked on a novel and ambitious project in health research. At the time, little was known about the general causes of heart disease and stroke, but the death rates for CVD had been increasing steadily since the beginning of the century and had become an American epidemic. The objective of the FHS was to identify the common factors or characteristics that contribute to CVD by following its development over a long period of time in a large group of participants who had not yet developed overt symptoms of CVD or suffered a heart attack or stroke. Design of Framingham Heart Study. In 1948, the researchers recruited 5,209 men and women between the ages of 30 and 62 from the town of Framingham, Massachusetts, and began the first round of extensive physical examinations and lifestyle interviews that they would later analyze for common patterns related to CVD development. Since 1948, the subjects have returned to the study every two years for an examination consisting of a detailed medical history, physical examination, and laboratory tests, and in 1971, the study enrolled a second-generation cohort -- 5,124 of the original participants' adult children and their spouses -- to participate in similar examinations. The second examination of the Offspring cohort occurred eight years after the first examination, and subsequent examinations have occurred approximately every four years thereafter. In April 2002 the Study entered a new phase: the enrollment of a third generation of participants, the grandchildren of the original cohort. The first examination of the Third Generation Study was completed in July 2005 and involved 4,095 participants. Thus, the FHS has evolved into a prospective, community-based, three generation family study. The FHS is a joint project of the National Heart, Lung and Blood Institute and Boston University. Research Areas in the Framingham Heart Study. Over the years, careful monitoring of the FHS population has led to the identification of the major CVD risk factors -- high blood pressure, high blood cholesterol, smoking, obesity, diabetes, and physical inactivity -- as well as a great deal of valuable information on the effects of related factors such as blood triglyceride and HDL cholesterol levels, age, gender, and psychosocial issues. Risk factors have been identified for the major components of CVD, including coronary heart disease, stroke, intermittent claudication, and heart failure. It is also clear from research in the FHS and other studies that substantial subclinical vascular disease occurs in the blood vessels, heart and brain that precedes clinical CVD. With recent advances in technology, the FHS has enhanced its research capabilities and capitalized on its inherent resources by the conduct of high resolution imaging to detect and quantify subclinical vascular disease in the major blood vessels, heart and brain. These studies have included ultrasound studies of the heart (echocardiography) and carotid arteries, computed tomography studies of the heart and aorta, and magnetic resonance imaging studies of the brain, heart, and aorta. Although the Framingham cohort is primarily white, the importance of the major CVD risk factors identified in this group have been shown in other studies to apply almost universally among racial and ethnic groups, even though the patterns of distribution may vary from group to group. In the past half century, the Study has produced approximately 1,200 articles in leading medical journals. The concept of CVD risk factors has become an integral part of the modern medical curriculum and has led to the development of effective treatment and preventive strategies in clinical practice. In addition to research studies focused on risk factors, subclinical CVD and clinically apparent CVD, Framingham investigators have also collaborated with leading researchers from around the country and throughout the world on projects involving some of the major chronic illnesses in men and women, including dementia, osteoporosis and arthritis, nutritional deficiencies, eye diseases, hearing disorders, and chronic obstructive lung diseases. Genetic Research in the Framingham Heart Study. While pursuing the Study's established research goals, the NHLBI and the Framingham investigators has expanded its research mission into the study of genetic factors underlying CVD and other disorders. Over the past two decades, DNA has been collected from blood samples and from immortalized cell lines obtained from Original Cohort participants, members of the Offspring Cohort and the Third Generation Cohort. Several large-scale genotyping projects have been conducted in the past decade. Genome-wide linkage analysis has been conducted using genotypes of approximately 400 microsatellite markers that have been completed in over 9,300 subjects in all three generations. Analyses using microsatellite markers completed in the original cohort and offspring cohorts have resulted in over 100 publications, including many publications from the Genetics Analysis Workshop 13. Several other recent collaborative projects have completed thousands of SNP genotypes for candidate gene regions in subsets of FHS subjects with available DNA. These projects include the Cardiogenomics Program of the NHLBI's Programs for Genomics Applications, the genotyping of ~3000 SNPs in inflammation genes, and the completion of a genome-wide scan of 100,000 SNPs using the Affymetrix 100K Genechip. Framingham Cohort Phenotype Data. The phenotype database contains a vast array of phenotype information available in all three generations. These will include the quantitative measures of the major risk factors such as systolic blood pressure, total and HDL cholesterol, fasting glucose, and cigarette use, as well as anthropomorphic measures such as body mass index, biomarkers such as fibrinogen and CRP, and electrocardiography measures such as the QT interval. Many of these measures have been collected repeatedly in the original and offspring cohorts. Also included in the SHARe database will be an array of recently collected biomarkers, subclinical disease imaging measures, clinical CVD outcomes as well as an array of ancillary studies. The phenotype data is located here in the top-level study phs000007 Framingham Cohort. To view the phenotype variables collected from the Framingham Cohort, please click on the "Variables" tab above. The Framingham Cohort is utilized in the following dbGaP substudies. 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" section of this top-level study page phs000007 Framingham Cohort. phs000342 Framingham SHARe phs000282 Framingham CARe phs000363 Framingham SABRe phs000307 Framingham Medical Resequencing phs000401 Framingham ESP Heart-GO phs000651 Framingham CHARGE-S phs000724 Framingham DNA Methylation phs001610 Framingham T2D-GENES phs002558 Framingham ADSP phs002559 Framingham BRIDGET phs002560 Framingham Cholesterol phs002611 Framingham Post-Mortem Brain Tissue phs002938 Framingham Molecular QTL The unflagging commitment of the research participants in the NHLBI FHS has made more than a half century of research success possible. For decades, the FHS has made its data and DNA widely available to qualified investigators throughout the world through the Limited Access Datasets and the FHS DNA Committee, and the SHARe database will continue that tradition by allowing access to qualified investigators who agree to the requirements of data access. With the SHARe database, we continue with an ambitious research agenda and look forward to new discoveries in the decades to come.

  Study phs000007

• Efficacy of a Therapeutic Treatment Trial in Angelman Syndrome

  This study has been designed to evaluate the possible therapeutic benefits of L-5-methyltetrahydrofolate (Metafolin), vitamin B12, creatine and betaine in children with Angelman Syndrome (AS). This study is based on the hypotheses 1) that dietary manipulation may increase global DNA methylation; 2) that increased methylation of the paternal chromosome in AS participants may increase expression of the Angelman gene causing clinical benefit; and 3) that dietary interventions with Metafolin in conjunction with creatine, betaine, and vitamin B12 would represent little risk, but some chance for benefit. The dietary regimen is felt to be quite benign and safe. The clinical response will be measured by recording: changes in seizure activity, changes in communication skills, changes in developmental skills and changes in behavioral patterns as indicated by formal developmental assessments and clinical evaluations. We will assess the progress of the participants by monitoring their changes from baseline throughout their participation in the study and measure their improvement in particular in the developmental parameters. As a secondary aim, we plan to measure the biochemical response to these compounds by obtaining levels of homocysteine, methionine, S-adenosyl-methionine (SAM), and S-adenosyl-homocysteine (SAH). The molecular response will be measured by global DNA methylation analysis. As an exploratory aim, we hope to use control data we have previously obtained from a double blind placebo-controlled trial done in the past using betaine and folic acid to compare the development of those children who have and those who have not received medications. More specifically, we wish to compare differences in the rate of development for those children who have never received study medications (from the first trial) with those who have received medications from the present trial. Developmental parameters used in the previous trial will be consistent with those used in the present trial in order to permit these comparisons. The previous trial was conducted at Baylor College of Medicine, Rady San Diego Children's Hospital and Boston Children's Hospital whereas a group of AS participants received folic acid and betaine or placebo in a randomized double-blind basis. All the participants for the study will include patients who have a documented molecular diagnosis of AS. The participants will be seen at Baylor College of Medicine, Rady Children's Hospital of San Diego, Boston Children's Hospital and the Greenwood Genetics Center at 0 months and at 12 months for follow-up. Clinical and relevant historical data will be collected during the clinical visit and examination and also by reviewing medical and laboratory records. This information will then be entered into a HIPAA compliant clinical research database.

  Study phs000701

• NIDA Genetic Epidemiology of Opioid Dependence in Bulgaria (GEODB)

  The study was conducted in Bulgaria as a collaboration between the Molecular Medicine Center (Medical University, Sofia), the Bulgarian Addictions Institute (Sofia), the Initiative for Health Foundation (Sofia) and Washington University School of Medicine (Saint Louis, MO, USA). This is a case-population control study. Participants (N=2,499 interviews; N=1,995 with GWAS data) in our study are primarily active heroin users (78%) aged 18 and over, with a median 8.9 years of daily heroin use (minimum of 12 months). Virtually all participants (99.1%) qualified for a lifetime DSM-IV diagnosis of dependence, symptom endorsement probabilities ranging from 77% to 99.3%; and 61% endorsing all symptoms. 85% were heroin injectors and 97% reported using (or having used) heroin daily. Anonymized, population-representative control samples (no phenotypic data, N = 1,062 with GWAS data) were drawn from the MMC repository. Unlike other studies, where samples are clinically ascertained (e.g., from ORT programs), our participants are primarily untreated. PTSD, major depression, suicidality, mania, alcohol, nicotine and substance dependence (separating heroin and opioids) were assessed using the MAGIC (Todd et al., 2003, PMID: 14627881), a broad semi-structured psychiatric assessment tool with good reliability and prospective stability. The onset of (any) illicit drug use in this sample is not particularly remarkable (age~16), but the age of onset of heroin use is much lower than in the USA: 25% by age 16; 50% by age 19, with no differences between ethnicities or gender. This is consistent with findings from other studies in Bulgaria. In contrast, in 2008, SAMHSA estimated an average age of 23.4 for new heroin initiates in the USA. Further, progression from first use to regular use appears to be more rapid, with the majority of participants reporting onset of dependence problems within one year of initiation. Another unique aspect of this study population are the comparatively low levels of polysubstance use (outside of nicotine and alcohol). This early-use, fast-transition and monosubstance heroin pattern stands in sharp contrast to what is reported in many studies in the Western World. In our study, 47% of Ethnic Bulgarians and 66% of Roma used only opioids, even years after the onset of drug use. 15.4% of Ethnic Bulgarians and 66.2% of Roma reported heroin as the very first illicit drug used. Lifetime, 12.5% of Ethnic Bulgarians and 52.8% of Roma report never having used another illicit drug other than heroin more than five times. While both Roma and Ethnic Bulgarians certainly experiment with other drugs, abuse/dependence rates for these drugs are low in Ethnic Bulgarians (from 8.4% for inhalants to 28% for stimulants) and in the Roma population (from 1.3% for hallucinogens to 11.2% for stimulants).

  Study phs001804

• GSA pilot raw data

  Unfiltered genotype data for a pilot study (Batch 1) of 1,140 DDD Study participants (and 12 "Empty" samples). Samples include 380 mothers, 382 fathers and 378 probands, and form 376 trios. Most of the probands have been previously genoyped on the llumina HumanCoreExome BeadChip (EGAD00010001598) or the Illumina InfiniumCoreExome Beadchip (EGAD00010001600). All samples were genotyped on the Illumina Global Screening Array.

  Dataset EGAD00010002567

• Family-Based Study on Ulcerative Colitis with Whole Exome Sequencing

  Genetic risk factors for ulcerative colitis are not well understood. We performed a family-based whole exome sequencing analysis to identify potential causal mutations. In the proband, we found a heterozygous de novo mutation in the gene HSPA1L. Our results indicate that the de novo mutation in HSPA1L is associated with ulcerative colitis.

  Study phs001251

• Sex Differences in MAGEL2 Gene Promoter Methylation in High Functioning Autism - Trends from a Pilot Study Using Nanopore Cas9 Targeted Long Read Sequencing

  Using DNA extracted from peripheral blood, Cas9-targeted nanopore DNA sequencing was used to analyze MAGEL2 gene, including its entire regulatory construct (chr15:23639316-23651466), for sequence variation and 5-methyl-cytosine (5mC) modification in a cohort of adults with HFA compared to sex- and age-matched NC.

  Study EGAS50000000508

• Pilot study towards the development of a Companion/Complimentary Diagnosis platform using liquid biopsy with cfDNA for immune checkpoint inhibitor therapy in advanced urothelial cancer

  Preliminary analysis was conducted to develop a cfDNA-based platform capable of predicting gene mutation profiles, TMB, gene expression profiles (molecular subtype diagnosis), and immunohistochemical findings (PD-L1 expression) using the primary lesion tissue of bladder cancer and upper urinary tract epithelial cancer, verifying the feasibility of such development.

  Study JGAS000714

• RNA-seq from B-ALL patients treated on the ALLG ALL09 study

  Dataset contains RNA-sequencing data (fastq files) from 46 patients treated on the Australasian Leukaemia and Lymphoma Group (ALLG) ALL09 study (ACTRN12618001734257). All patients were diagnosed with CD19 positive B-cell acute lymphoblastic leukaemia and were negative for Philadelphia chromosome positive disease. Patient samples (bone marrow or peripheral blood) were taken at diagnosis. mRNA was extracted from lymphoblasts and underwent paired-end sequencing using either the illumina NextSeq (75 bp PE) or MGI DNABSEQ-G400 (100bp PE) platforms. Transcriptomic data was used for identification of genomic drivers of acute lymphoblastic leukaemia (ALL).

  Dataset EGAD50000001603

• single nuclei multiomics (ATAC-RNA) of KOLF2.1J human induced pluripotent stem cells-derived differentiated dopaminergic neurons

  We processed nuclei from hIPSCs differentiated optimized protocols for generating dopaminergic neurons. Cells differentiated with a first iteration were RNA and ATAC-sequenced, to understand our protocol caveats to address for optimization. Cells differentiated with a second protocol and in vivo were RNA-sequenced to validate the identities of our cells.

  Study EGAS50000001418

• R compatible Seurat's objetc .rds files with count data and metadata from single cell RNA seq analysis to characterize the prostate cancer tumoral microenviroment of 31 fusion biopses.

  Pre-processed Seurat objects with cellular and functional annotation information from the scRNAseq study on PC fusion biopsy samples. The data consists of rds files composed of normalised counts matrices, normalised and scaled counts, functional enrichment counts at the cellular level and metadata with patient grouping and cellular annotation variables. There are 3 .rds files, one with the total cells (SCP_data_analysis), with the selection of cells annotated as cancerous (selected_cancer_analysis) and cancer-associated fibroblasts (selected_caf_analysis).

  Dataset EGAD50000001298

• Spinocerebellar ataxia type 3 RNA-sequencing study

  RNA-Sequencing from human post-mortem Spinocerebellar ataxia type 3 patients. This sequencing experiment was carried out to validate that the transcriptional changes of an Ataxin-3 knock-in mouse model (expressing an expansion of 304 CAG/CAAs either heterozygous or homozygous in the murine Ataxin-3 locus) represent that transcriptional changes seen in the human disease.

  Study EGAS00001004241

• ADAPTeR Study: scRNA and scTCR data from TILs from two ccRCC patients treated with anti-PD1

  TILs were extracted from two ccRCC patients treated with (Nivolumab) anti-PD1, one was responsive to treatment, the other non-responsive. IgG4 staining was used to separate cells into anti-PD1 bound and unbound, the samples then underwent paired scRNA and scTCR sequencing on the 10x Genomics platform.

  Study EGAS00001005640

• The gut microbiota in prediabetes and diabetes: a population-based cross-sectional study

  The link between the gut microbiota and type 2 diabetes (T2D) warrants further investigation because of known confounding effects from antidiabetic treatment. Here we profiled the gut microbiome in a discovery (n=1011) and validation (n=484) cohort comprising Swedish subjects naive for diabetes treatment and grouped by glycemic status.

  Study EGAS00001004480

• scRNA-seq to study interactions between HSPCs, BMSCs and immune microenvironment

  Mechanisms of clonal evolution in myeloid neoplasms remain incompletely understood. Darwinian theory predicts that the (micro)environment of clone-propagating stem cells may contribute to clonal selection. Here, we provide data fitting this model, establishing a relationship between stromal niche inflammation, inflammatory stress in HSPCs, clonal resistance and leukemic evolution in human MDS.

  Study EGAS00001008181

• Whole genome sequence of third generation family member (SFHS)

  Previously we performed deep WGS on 6 parents and 13 children from 3 large families from the Scottish Family Health Study to identify de novo mutations. This prelim is cover the additional sequencing of one grandchild from one of these three families. The inclusion of a third generation individual will provide additional experimental validation for the de novo mutations found in the initial trio. As in the previous study, the DNA will be WGS to a depth of approximately 25X to achieve this purpose.These data can only be used for the investigation of the genetic causes of the reported clinical phenotypes in these patients

  Dataset EGAD00001001454

• MutWP5: CRUK Mutographs of Cancer: Breast: Cancer Mastectomy (Targeted) (2020-01-29)

  Sequencing of LCM-derived microbiopsies from 30 women who mastectomies due to Breast Cancer. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Targeted data will be used as a driver and clonality screen, highly clonal or driver-containing samples will subsequently be sent for whole-genome sequencing. Results from this portion of the study will be compared to women who had cosmetic breast reduction surgeries and those with germline BRCA 1/2 mutations. . This dataset contains all the data available for this study on 2020-01-29.

  Dataset EGAD00001005923

• MutWP5: CRUK Mutographs of Cancer: Breast: BRCA Carriers (Targeted) (2020-01-29)

  Sequencing of LCM-derived microbiopsies from 20 women who underwent risk-reducing reduction mastectomies due to germline BRCA1/2. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Targeted data will be used as a driver and clonality screen, highly clonal or driver-containing samples will subsequently be sent for whole-genome sequencing. Results from this portion of the study will be compared to women who had cosmetic breast reduction surgeries and those with cancer. . This dataset contains all the data available for this study on 2020-01-29.

  Dataset EGAD00001005920

• MutWP5: CRUK Mutographs of Cancer: Breast: BRCA Carriers (Exome) (2020-01-29)

  Sequencing of LCM-derived microbiopsies from 20 women who underwent risk-reducing reduction mastectomies due to germline BRCA1/2. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Exome data will be used as a driver and clonality screen, highly clonal or driver-containing samples will subsequently be sent for whole-genome sequencing. Results from this portion of the study will be compared to women who had cosmetic breast reduction surgeries and those with cancer. . This dataset contains all the data available for this study on 2020-01-29.

  Dataset EGAD00001005921

• MutWP5: CRUK Mutographs of Cancer: Breast: Cancer Mastectomy (Exome) (2020-01-29)

  Sequencing of LCM-derived microbiopsies from 30 women who underwent mastectomies due to a breast cancer diagnosis. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Exome data will be used as a driver and clonality screen, highly clonal or driver-containing samples will subsequently be sent for whole-genome sequencing. Results from this portion of the study will be compared to women who had cosmetic breast reduction surgeries and those with germline BRCA 1/2 mutations. . This dataset contains all the data available for this study on 2020-01-29.

  Dataset EGAD00001005924

• Whole Genome-sequencing of rhabdomyosarcoma tumour tissue (2025-09-30)

  This study investigates high-risk rhabdomyosarcoma (RMS) using multiple single-cell and spatial genomic technologies. We generated and analysed single-cell and single-nucleus RNA-sequencing, chromatin accessibility, and spatial transcriptomics data from primary tumours and validation samples. These datasets characterise cellular diversity within rhabdomyosarcoma and identify cell states associated with aggressive disease. The data support research into tumour biology, risk stratification, and therapeutic target discovery. This repository houses the whole-genome sequencing of RMS tumours data. . This dataset contains all the data available for this study on 2025-09-30.

  Dataset EGAD00001015712

• ParityImmune

  Blood transcriptome from women participating in the Norwegian Women and Cancer study (NOWAC)

  Dataset EGAD00010001412

• Duplex sequencing

  A total of 387 buccal swab samples were subjected to error-corrected sequencing (duplex sequencing).

  Study EGAS50000000054

• Mutant p53 confers gain-of-function transcriptional activity in liver cancer

  Mutant p53 confers gain-of-function transcriptional activity in liver cancer

  Study EGAS00001005779

• DAC for TFHL single-cell analysis project at Department of Hematology, University of Tsukuba

  DAC for study of tumor heterogeneity and immune-evasive microenvironment in T follicular helper cell lymphomas

  Dac EGAC50000000201

• Chromatin immunoprecipitation followed by sequencing combined with transcription factor (TF) motif identification and transcriptome analyses revealed different patterns of REST binding and its proximal TF motifs in IDH wild-type and mutant gliomas

  Study EGAS00001006366

• RNA-sequencing from duodenal bipsies of Celiac disease patients

  Total RNA was extracted from the PaxFPE biopsy specimens (n = 116)

  Study EGAS50000000337