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• Unifying recovery dynamics in heterogeneous diseases exemplified by COVID-19

  To model recovery dynamics, using severe COVID-19 as the example, we align heterogeneous recovery trajectories via a novel computational scheme applied to longitudinally sampled blood transcriptomes. We thus generate pseudotime trajectories, which we then link to cellular and molecular mechanisms based on cell deconvolution analysis and molecular pathway prediction, thus presenting a unique framework for studying recovery processes over time.

  Dataset EGAD00001008331

• Pre-diagnostic saliva microbiota of Finnish children with autoimmune diseases

  Pre-diagnostic saliva microbiota samples of Finnish children (aged 11/12 years). This is a case-control study, where case refers to the children who developed Type 1 DM or IBD later in life and control refers to the children who were free from these diseases. The aim of the study was to find biomarkers in saliva microbiota that may help us predict DM or IBD before the onset of these diseases.

  Dataset EGAD00001009984

• Multi-Ethnic Study of Atherosclerosis (MESA) Cohort

  MESA The Multi-Ethnic Study of Atherosclerosis (MESA) is a study of the characteristics of subclinical cardiovascular disease (disease detected non-invasively before it has produced clinical signs and symptoms) and the risk factors that predict progression to clinically overt cardiovascular disease or progression of the subclinical disease. MESA researchers study a diverse, population-based sample of 6,814 asymptomatic men and women aged 45-84. Thirty-eight percent of the recruited participants are white, 28 percent African-American, 22 percent Hispanic, and 12 percent Asian, predominantly of Chinese descent. Participants were recruited from six field centers across the United States: Wake Forest University, Columbia University, Johns Hopkins University, University of Minnesota, Northwestern University and University of California - Los Angeles. Each participant received an extensive physical exam to determine coronary calcification, ventricular mass and function, flow-mediated endothelial vasodilation, carotid intimal-medial wall thickness and presence of echogenic lucencies in the carotid artery, lower extremity vascular insufficiency, arterial wave forms, electrocardiographic (ECG) measures, standard coronary risk factors, sociodemographic factors, lifestyle factors, and psychosocial factors. Selected repetition of subclinical disease measures and risk factors at follow-up visits allows study of the progression of disease. Blood samples have been assayed for putative biochemical risk factors and stored for case-control studies. DNA has been extracted and lymphocytes cryopreserved (for possible immortalization) for study of candidate genes and possibly, genome-wide scanning, expression, and other genetic techniques. Participants are being followed for identification and characterization of cardiovascular disease events, including acute myocardial infarction and other forms of coronary heart disease (CHD), stroke, and congestive heart failure; for cardiovascular disease interventions; and for mortality. In addition to the six Field Centers, MESA involves a Coordinating Center, a Central Laboratory, and Central Reading Centers for Computed Tomography (CT), Magnetic Resonance Imaging (MRI), Ultrasound, and Electrocardiography (ECG). Protocol development, staff training, and pilot testing were performed in the first 18 months of the study. The first examination took place over two years, from July 2000 - July 2002. It was followed by four examination periods that were 17-20 months in length. Participants have been contacted every 9 to 12 months throughout the study to assess clinical morbidity and mortality. MESA Family The general goal of the MESA Family Study, an ancillary study to MESA funded by a grant from NHLBI, is to apply modern genetic analysis and genotyping methodologies to delineate the genetic determinants of early atherosclerosis. This is being accomplished by utilizing all the current organizational structures of the Multi-Ethnic Study of Atherosclerosis (MESA) and Genetic Centers at Cedars-Sinai Medical Center and University of Virginia. In the MESA Family Study, the goal is to locate and identify genes contributing to the genetic risk for cardiovascular disease (CVD), by looking at the early changes of atherosclerosis within families (mainly siblings). 2128 individuals from 594 families, yielding 3,026 sibpairs divided between African Americans and Hispanic-Americans, were recruited by utilizing the existing framework of MESA. MESA Family studied siblings of index subjects from the MESA study and from new sibpair families (with the same demographic characteristics) and is determining the extent of genetic contribution to the variation in coronary calcium (obtained via CT Scan) and carotid artery wall thickness (B-mode ultrasound) in the two largest non-majority U.S. populations. In a small proportion of subjects, parents of MESA index subjects participating in MESA Family were studied but only to have blood drawn for genotyping. The MESA Family cohort was recruited from the six MESA Field Centers. MESA Family participants underwent the same examination as MESA participants during May 2004 - May 2007. DNA was extracted and lymphocytes immortalized for study of candidate genes, genome-wide linkage scanning, and analyzed for linkage with these subclinical cardiovascular traits. While linkage analysis is the primary approach being used, an additional aspect of the MESA Family Study takes advantage of the existing MESA study population for testing a variety of candidate genes for association with the same subclinical traits. Genotyping and data analysis will occur throughout the study. MESA Air The general goal of the Multi-Ethnic Study of Atherosclerosis and Air Pollution ('MESA Air') is to prospectively examine the relation between an individual level assessment of long-term ambient air pollution exposures (including PM2.5 and the progression of subclinical cardiovascular disease in a multi-city, multi-ethnic cohort. MESA Air will also prospectively examine the relationship between an individual level assessment of long-term ambient air pollution exposures and the incidence of cardiovascular disease, including myocardial infarction and cardiovascular death. MESA AIR is funded by a grant from the United States Environmental Protection Agency to the University of Washington and subcontracts from the UW to other participating institutions. MESA Air will assess if ambient air pollution is associated with changes over time in subclinical measures of atherosclerosis and plasma markers of inflammation, oxidative damage, and endothelial activation in a longitudinal data model, adjusting for age, race/ethnicity, socioeconomic status, and specific cardiovascular risk factors (such as diabetes, hypertension, smoking, and diet). The study will similarly assess if the incidence of cardiovascular events is associated with long-term exposure to ambient air pollution, using a proportional hazards model. The study includes refinement of statistical tools, and explores joint/independent effects of acute and long-term pollutant exposure in the occurrence of cardiovascular disease. The MESA Air study is built on the foundation of the ongoing MESA study. The parent MESA Study cohort is located in six geographic areas ('Field Centers') that capture tremendous exposure heterogeneity, comparable to or greater than the variability in locations of prior U.S. cohort studies. In addition to the six Field Centers, the study involves a Coordinating Center, a Central Laboratory, and Reading Centers for Computed Tomography (CT), ultrasound and air pollution data. The cohort for the MESA Air study currently includes 6226 subjects: 5479 enrolled in the parent MESA study; 257 recruited specifically for this study, and 490 recruited from the MESA Family study. The entire MESA Air cohort will be followed over a 10-year project period for the occurrence of cardiovascular disease events. On two occasions over the ten-year study period, 3600 subjects from the MESA Air cohort, residing in nine locales, will undergo computed tomography scanning to assess presence and extent of coronary artery calcification (CAC), and ultrasound of the carotid artery to determine intima-media thickness (IMT). We will also repeatedly assess plasma markers of inflammation, oxidative damage, and endothelial function in 720 subjects. MESA Air adds state-of-the-art air pollution exposure assessment information to the MESA cohort study, and introduces new subjects and outcome measures to achieve our aims. The study will assess long-term individual-level exposure to ambient air pollutants for each subject using community-scale monitoring, outdoor spatial variation, subject proximity to pollution sources, pollutants' infiltration efficiency, and personal time-activity information. The exposure models will be validated using detailed monitoring in a subset of subjects. The MESA 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" box located on the right hand side of this top-level study page phs000209 MESA Cohort. phs000420 MESA SHARe phs000283 MESA CARe phs000403 MESA ESP Heart-GO

  Study phs000209

• Utlizing the RA signature to predict response to TNFi

  This study involves bulk RNA-seq analyses of blood cells from patients with rheumatoid arthritis who have had an inadequate response to methotrexate, collected before and 12 weeks after effective treatment with either etanercept or adalimumab. Peripheral blood mononuclear cells were stimulated with anti-CD3 for 24 hours and sorted into CD4+, CD19+, and CD4-CD19- (DN) populations for bulk RNA-seq.

  Study phs002562

• Inherited T Cell Defects: Diagnosis, Mechanisms and Treatments

  Infants with abnormal newborn screen results for severe combined immunodeficiency (SCID) and their parents were enrolled in UCSF IRB approved protocols with informed consent to have molecular and immunologic investigation to determine the cause of the infant's low T lymphocytes. Studies included exome sequencing of DNA from the infant and both parents. Candidate variants were investigated in mouse and zebrafish model organisms.

  Study phs002968

• Ciliopathies Exome Sequencing Initiative

  The study is aimed at identifying new genes involved in pediatric brain disorders from inbred families originating predominantly in the Middle East. Each patient analyzed to date has a specific and highly unique neurodevelopmental disorder that is likely to be recessive in nature. Many patients have one of the diseases along the "ciliopathy" spectrum of diseases, with evidence of kidney failure, retinal blindness and cerebellar ataxia.

  Study phs000288

• Million Veteran Program (MVP) Summary Results from Non-Sensitive Omics Studies

  MVP is an ongoing prospective cohort study and mega‐biobank in the Department of Veterans Affairs Healthcare System designed to study genetic influences on health and disease among veterans. This is the accession to hold publicly available results. Results from sensitive phenotypes or MVP population subsets can be found at accession phs001672 and will require an application for access.

  Study phs002453

• A prospective pilot study of genome-wide exome and transcriptome profiling in patients with small cell lung cancer progressing after first-line therapy

  In this prospective study, custom genome-wide exome and whole transcriptome sequencing (NGS) was used to identify genomic events and associated expression changes in advanced Small Cell Lung Cancer (SCLC) and attempt to prescribe systemic therapy based on the results. Tumor/normal pairs were sequenced from 12 patients with advanced SCLC for this study.

  Study phs001366

• Developmental Dynamics of Translation in the Human Brain

  We performed ribosome profiling and RNA sequencing from a total of 43 adult brain and 30 prenatal brain samples. The age of adult brain donors ranged from 18 to 82 years (average 39.5 years), with an average post-mortem interval of 9.9 hours. The gestational age of prenatal cortex samples ranged from 12 to 23 weeks, with a mean of 19.9 weeks. 

  Study phs002489

• Investigating Human Placentation and Pregnancy Using First Trimester Chorionic Villi

  Chorionic villus sampling (CVS) is routinely used for prenatal diagnosis of cytogenetic disorders, but also possesses great potential for studying placentation. To better understand villi biology, human placentation, and how these relate to pregnancy outcomes, we examined the morphology and transcriptomes of villi obtained via CVS from 10-14 weeks of pregnancy and correlated these with pregnancy attributes and clinical outcomes.

  Study phs001320

• Genome Wide Association Study of Asthma

  This data forms part of an ongoing genome wide association study into the genetic variants that predispose to pediatric asthma at the Children's Hospital of Philadelphia (CHOP). All cases and controls were recruited at CHOP and genotyped at the Center for Applied Genomics (CAG). The data set includes 793 cases and 1988 controls. The inclusion criteria to this case control study are detailed below.

  Study phs000233

• Next Generation Mendelian Genetics: Auriculocondylar syndrome (ACS)

  This project is part of an ongoing project to identify the molecular genetic basis of rare craniofacial disorders. This specific project involved the collection of DNA samples from four probands with severe manifestations of auriculocondylar syndrome and their parents. Detailed clinical phenotypic data is available on each proband. The sole purpose of this research is to identify the molecular cause(s) of auriculochondylar syndrome.

  Study phs000437

• CD4 T Cell Subsets in Human Metastatic Melanoma

  We used single-cell RNA-sequencing (scRNA-seq) to define CD4+ T-cell subsets in melanoma tumors from patients undergoing tumor resection. All patients received immune checkpoint blockade prior to surgery. We identified multiple subsets in the tumor with transcriptional features of suppressive function, including TR1 cells and FOXP3+ Treg cells. Based on transcriptional profiles, classical helper T cell subsets were not prevalent.

  Study phs003816

• Whole exome sequencing and RNA sequencing of lineage-switched acute myeloid leukemia with KMT2A-AFF1 rearrangement

  We performed whole exome sequencing and RNA sequencing of lineage-switched acute myeloid leukemia (LS AML) with KMT2A-AFF1 rearrangement to elucidate the feature and potential treatment targets. Notably, LS AML possessed gene expression signatures of monocytic myeloid derived suppressor cells (M-MDSCs). Several known genes related to MDSCs were highly expressed in LS AML, which could be novel treatment targets.

  Study JGAS000631

• 1. Identidication of molecular biological mechanism associated with the development and prognosis of uterine cancer, uterine sarcoma, and endometrial hyperplasia / 2. Identification of molecular biological mechanism associated with the development of endometriosis and malignant transformation, ovarian cancer, fallopian tubal cancer, peritoneal cancer, and other malignant tumors in gynecological organs

  To identify molecular subtypes and carcinogenesis in clear cell ovarian carcinomas by whole-exome sequencing, RNA-sequencing, and methylation array, and to characterize high-grade serous carcinomas by NGS-based, integrative genomic analyses, with focus on homologous recombination deficiency, molecular subtypes and prognositic factors.

  Study JGAS000560

• Phylogenetic analysis of combined lobular and ductal carcinoma of the breast

  Breast cancer manifests in diverse forms, with particular reference to various cell types harboring different mutations and gene expression profiles. To elucidate the clonal relationship between cancer cells in tumors composed of both ductal and lobular phenotypes, we analyzed two combined lobular and ductal carcinoma (CLDC) cases, including one mixed ductal-lobular carcinoma (MDL) lesion, by next generation sequencing.

  Study JGAS000300

• Somatic inflammatory gene mutations accumulate in human ulcerative colitis epithelium

  We performed whole exome sequencing and targeted sequencing of ulcerative colitis with/without colitis associated neoplasm and healthy indivisuals. The aim of this study was to calculate the influence of inflammation and age on a count of genetic mutations in colonic epithelium, and to identify the specific signal pathways on which the significant genetic mutations accumulating in ulcerative colitis patients' colonic epithelium.

  Study JGAS000199

• Viral integration analysis of hepatocellular carcinoma using virus capture sequence.

  Hepatitis B viral (HBV) DNA is frequently integrated into the genome of hepatocellular carcinoma (HCC) in patients with chronic HBV infection (chronic HBV, hereafter), whereas it is yet to be clarified in patients after HBV disappearance (prior HBV, hereafter). This study aimed to identify viral integration such as HBV and adeno-associated virus type 2 (AAV2) into the HCC genome as oncogenic event.

  Study JGAS000194

• Excised DNA Circles from V(D)J Recombination Promote Relapsed Leukaemia

  In this study, we show that ESCs replicate and persist through many cell generations. High ESC copies at diagnosis of BCP-ALL strongly correlate with subsequent relapse. These data provide the first demonstration that the V(D)J recombination by-product, when replicated to elevated levels, potently associates with the V(D)J recombinase to cause adverse disease outcomes.

  Study EGAS50000001043

• The Genetic Analysis of multiple sclerosis

  We created these data in order to identify genetic variants associated with increased susceptibility to multiple sclerosis. Cases from many parts of the world were genotyped with the Illumina 660 chip along with Swedish controls. In our analysis we also used control data from the WTCCC2 common UK controls and from other published studies.

  Study EGAS00000000101

• Study of wound response like states in glioblastoma

  In order to investigate wound reponse-like states in glioblastoma, we carried out experiments on primary tissue as well as organoids. Single cell RNA sequencing was performed on core and periphery of three human glioblastoma. Bulk RNA sequencing was performed on glioblastoma-derived organoids subject to treatment for 72h with plasma, hypoxia, or both, and analyzed at 0, 24, 72, and 144h.

  Study EGAS50000001442

• Targeted sequencing data of regulatory regions in 200 Spanish ASD trios

  This study consists of genomic sequencing data obtained through targeted sequencing of regulatory regions (85,394 human cCREs from ENCODE v2, version 2, https://screenv2.wenglab.org/) in 200 ASD (Autism Spectrum Disorder) trios (father and mother unaffected and proband affected). The aim of the project is to detect genomic variants (rare and inherited variants) in regulatory regions that contribute to autism.

  Study EGAS50000001395

• Multimodal analysis of rare BARD1 missense variant

  This project analyzes whole-exome sequencing data from a patient with breast cancer recurrence and endometrial cancer, as well as from the patient’s father’s colon tumor, all harboring a rare germline BARD1 missense variant (p.Gly753Val). The data reveal loss of heterozygosity and homologous recombination deficiency specific to the triple-negative breast cancer recurrence, supporting the variant’s conditional pathogenicity linked to prior treatment.

  Study EGAS50000001682

• Longitudinal Single-cell Genomic Analysis of Initial and Recurrent Meningioma

  This study investigates the genomic evolution of meningioma through single-cell whole genome sequencing analysis of paired tumor samples. We analyzed tumor tissues from initial and recurrent meningiomas from the same patients to understand clonal evolution and tumor progression. The research aims to characterize copy number alterations and genomic heterogeneity at single-cell resolution across different time points of tumor development.

  Study EGAS50000000860

• Bulk RNASeq of metastatic colorectal cancer organoids treated with crenigacestat alone or in combination with cetuximab

  Bulk RNA sequencing was performed on mCRC organoids cultured under untreated conditions or treated with crenigacestat alone or in combination with cetuximab. This dataset was generated to investigate the transcriptional changes associated with combination therapy and to compare these profiles with the adaptive responses observed following cetuximab monotherapy in the corresponding ATOH1 wild-type and knockout organoid models.

  Study EGAS50000001422