15075 results for "cancer studies using rna-seq"

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• Nanopore sequencing from liquid biopsy: analysis of copy number variations from cell-free DNA of lung cancer patients

  Study EGAS00001004975

• WGS of oesophagogastric cancer

  Illumina short read WGS of 12 oesophagogastric cancer samples

  Dataset EGAD50000002239

• Study on rectal mucus sampling for colorectal cancer diagnostics

  DAC for a study on rectal mucus sampling for colorectal cancer diagnostics

  Dac EGAC50000000643

• Long-read WGS of three cancer cell lines

  Long-read WGS of three cancer cell lines

  Dataset EGAD00001005184

• Exome sequencing of high-risk prostate cancer

  Exome sequencing of high-risk prostate cancer

  Dataset EGAD00001002009

• SNP data for Ovarian cancer PRS

  SNP data for Ovarian cancer PRS (cases)

  Dataset EGAD00001008143

• prostate cancer plasma cfRNA

  Dataset contains mRNA capture sequencing data from plasma of 180 different human donors: 132 prostate cancer patients (PRAD) and 48 cancer-free controls. Samples were sequenced on a NovaSeq X and sequencing data is provided in FASTQ format.

  Dataset EGAD50000001805

• Non-invasive bladder cancer cfDNA dataset

  The dataset contains 30 primary bladder cancer patients, 28 recurrent bladder cancer patients and 31 hematuria controls. Shallow WGS of cell-free DNA enzymatic methyl sequencing libraries was performed on an Illumina Novaseq S4 PE150bp. Samples are provided as raw reads without any prior processing.

  Dataset EGAD50000001935

• ctDNA detectability and representativeness in seven body liquids from female patients with metastatic breast cancer - lpWGS

  low-pass Whole Genome Sequencing (lpWGS) to assess the representativeness of seven body liquids from female patients with metastatic breast cancer.

  Study EGAS50000001302

• ctDNA detectability and representativeness in seven body liquids from female patients with metastatic breast cancer - WES

  Whole Exome Sequencing (WES) to explore the mutational status of seven body liquids from female patients with metastatic breast cancer.

  Study EGAS50000001303

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

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

  Study EGAS00001000566

• Osteosarcoma_Whole_Genome

  We propose to definitively characterise the somatic genetics of Osteosarcoma cancer through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing.

  Study EGAS00001000147

• Linked Read Sequencing of Gastric Cancer Metastases for Complex SV Resolution

  In this study, linked read sequencing was performed on two ovarian metastases and matched normal tissue, from a patient with primary diffuse gastric cancer. Linked read sequencing is a DNA preparation technology whereby high molecular weight molecules of DNA are uniquely barcoded prior to fragmentation and sequencing, thus retaining information about genomic contiguity. This study performed an extended analysis of linked read sequencing data to resolve the complex structures of structural variants in the cancer genomes. Complex structural rearrangements were identified in the genomic region surrounding the known oncogene FGFR2, and the association between FGFR2 and gastric cancer metastasis was demonstrated in an organoid model.

  Study phs001362

• 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

• Foundation Medicine Adult Cancer Clinical Dataset (FM-AD)

  The Foundation Medicine adult cancer clinical dataset consists of 18,004 unique solid tumor samples that underwent genomic profiling on a single uniform platform as part of standard clinical care. The dataset is derived from the FoundationOne® genomic profiling assay version 2 that interrogates exonic regions of 287 cancer-related genes and selected introns from 19 genes known to undergo rearrangements in human cancer. Genomic DNA samples were sequenced to over 500x median coverage, and custom computational analyses identified all classes of genomic alterations (base substitutions, insertions and deletions, copy number alterations, and rearrangements). Since matched normal tissue was unavailable for analysis, these data underwent additional filtering to enrich for cancer-related events. The reported data includes genomic alterations that are known and suspected tumor drivers, as well as variants of unknown significance. To preserve patient anonymity, all known or suspected germline variants were removed from the data unless known to be associated with cancer development. The dataset contains genomic alteration profiles generated by FoundationOne version 2 testing for adult cancer patients (over 18 y.o.), and represents a vast diversity of tumor subtypes, including many rare diseases not profiled as part of large-scale profiling efforts. Cases are grouped into 16 broad disease categories containing tumors from 162 unique disease subtypes. Since specimens were profiled as part of clinical care, limited clinical parameters were available, including age, gender, tissue of origin, % of tumor nuclei, and diagnosis. Publication of this dataset is intended to allow the broad scientific community access to this unique cohort for use in scientific research projects of common and rare types of cancer, both for generating leads regarding causal mechanisms as well as cross-testing and confirming existing hypotheses. A pediatric cancer clinical dataset consisting of data from 1,215 patients under 18 y.o. is available separately at: FOUNDATION MEDICINE

  Study phs001179

• Breast Cancer Whole Genome Sequencing

  Breast Cancer Whole Genome Sequencing

  Dataset EGAD00001000121

• Breast cancer SNP6 arrays_more

  Affymetrix SNP6.0 array breast cancer data

  Dataset EGAD00010001079

• genome-wide cfDNA methylation analysis

  To characterise cfDNA methylome in metastatic prostate cancer

  Study EGAS00001003958

• Genome-wide association study of esophageal squamous cell cancer identifies shared and distinct risk variants in African and Chinese populations

  Study EGAS00001007477

• Homologous recombination repair status in metastatic prostate cancer by next-generation sequencing and functional tissue-based immunofluorescence assays

  - WES files from primary or metastatic prostate cancer biopsies, from patients with metastatic prostate cancer. - This dataset includes those cases profiled by WES and included in the manuscript Homologous recombination repair status in metastatic prostate cancer by next-generation sequencing and functional tissue-based immunofluorescence assays, Arce-Gallego et al, Cell Rep Med 2024 - The dataset includes WES for 80 tumor biopsies from 65 different patients, including paired tumor/normal samples.

  Dataset EGAD50000001018

• Comparison of HCC cell lines and primary HCCs

  There are concerns about whether cancer cell lines could faithfully represent the matched primary cancer cells. Comparison of the HCC cell lines and primary HCCs demonstrated that, during long-term in vitro culture, cell lines retain the genetic landscape of the matched primary HCCs.

  Study EGAS00001001678

• Cancer and germline exomes consisting of FASTQ reads from melanoma, lung and colon cancer samples

  Cancer and germline exomes consisting of FASTQ reads from 6 individuals (4 melanoma, 1 lung and 1 colon cancer). Exome sequencing was performed on illumina with a depth of 100x to 200x. 2 Melanoma datasets contain reads from 2 different tumor regions 2 Melanoma datasets contain reads from 1 tumor region and from a tumor derived cell line 1 Melanoma dataset contains reads from 2 healthy tissues Colon and lung datasets contain both 1 matched germline-tumor pair

  Dataset EGAD00001007950

• EGAD00010000602

  WTCCC2 Reading and Mathematics ability (RM) samples from UK using the Affymetrix 6.0 array

  Dataset EGAD00010000602

• Myeloproliferative Neoplasms (MPN) Exome Validation Study

  Experiments using targeted pulldown methods will be sequenced to validate findings in the exomes of patients with Myeloproliferative Neoplasms (MPN).

  Dataset EGAD00001000619

• Russian_TB_6.0

  Russian Tuberculosis samples using Affymetrix 6.0

  Dataset EGAD00010000901

• UAE genotype dataset

  This dataset contains PLINK processed (PED and MAP) genotype data, from 1000 samples from the UAE using the Illumina Omni5 Exome Bead Chip

  Dataset EGAD00010001886

• SNParray_ASD

  ASD samples using Illumina Infinium Human Core-24 BeadChip platform

  Dataset EGAD00010002229

• Data used in "BaTwa" populations from Zambia retain ancestry of past hunter-gatherer groups

  BaTwa genotype data using the H3Africa array.

  Dataset EGAD50000000555

• PBAT sequencing of human embryonic stem cells

  To assess the DNA methylation landscape of naïve human embryonic stem cells derived from ERKi or control blastocysts using PXGL or UXGL media.

  Dac EGAC50000000606

• aplastic anemia

  Clonal hematopoiesis was investigated in patients with aplastic anemia using next-generation sequencing and single-nucleotide polymorphism (SNP) array-based karyotyping.

  Dataset EGAD00001001256

• NCI COVID-19 in Cancer Patients Study (NCCAPS): A Longitudinal Natural History Study

  NCCAPS is a longitudinal prospective cohort study designed to assess patient, disease and treatment factors associated with short- and long-term outcomes in patients with cancer who develop COVID-19. We also aimed to describe COVID-19 symptoms and treatments, and to describe disruptions in cancer treatment due to COVID-19. The study enrolled patients with cancer on active treatment or with a history of stem cell transplant or CAR-T cell therapy with new, active COVID-19, defined as being within 14 days of their first positive SARS-CoV-2 test. The study found that receipt of chemotherapy and baseline history of stroke, atrial fibrillation or pulmonary embolism were associated with a higher risk of hospitalization for COVID-19. Vaccination for SARS-CoV-2 was associated with a lower risk of hospitalization. Death due to COVID-19 was highest in patients with lymphoma, intermediate in those with acute leukemia and lung cancer, and lowest in those with other solid tumors and other hematologic cancers. Disruptions of cancer treatment were frequent in the first 30 days after SARS-CoV-2 infection.

  Study phs004178

• Genome-wide cell-free DNA fragmentation in patients with cancer

  Cell-free DNA (cfDNA) in the blood provides a noninvasive diagnostic avenue for patients with cancer. However, characteristics of the origins and molecular features of cfDNA are poorly understood. We developed an approach to evaluate fragmentation patterns of cfDNA across the genome and found that cfDNA profiles of healthy individuals reflected nucleosomal patterns of white blood cells, while patients with cancer had altered fragmentation profiles. We applied this method to analyze fragmentation profiles of 236 patients with breast, colorectal, lung, ovarian, pancreatic, gastric, or bile duct cancers and 245 healthy individuals. A machine learning model incorporating genome-wide fragmentation features had sensitivities of detection ranging from 57% to >99% among the seven cancer types at 98% specificity, with an overall AUC of 0.94. Fragmentation profiles could be used to identify the tissue of origin of the cancers to a limited number of sites in 75% of cases. Combining our approach with mutation based cfDNA analyses detected 91% of cancer patients. The results of these analyses highlight important properties of cfDNA and provide a proof of principle approach for screening, early detection, and monitoring of human cancer.

  Study EGAS00001003611