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• MutWP1: CRUK Grand Challenge Mutographs of Cancer: pancreas (2019-04-03)

  The Mutographs project aims to advance our understanding of the causes of cancer through studies of mutational signatures. Led by Mike Stratton, together with Paul Brennan, Ludmil Alexandrov, Allan Balmain, David Phillips and Peter Campbell, this large-scale international research endeavour was awarded a Cancer Research UK Grand Challenge. Different patterns of somatic mutation are generated by the different environmental, lifestyle and genetic factors that cause cancer, many of them are still unknown. Within Mutographs, the International Agency for Research on Cancer is coordinating the recruitment of 5000 individuals with cancer (colorectal, renal, pancreatic, oesophageal adenocarcinoma or oesophageal squamous cancers) across 5 continents to explore whether different mutational signatures explain marked variation in incidence. In brief, through an international network of collaborators around the world, biological materials are collected, along with demographic, histological, clinical and questionnaire data. Whole genome sequences of tumour-germline DNA pairs are generated at the Wellcome Trust Sanger Institute (Illumina HiSeqX, 40X and 20X depth respectively). Somatic mutational signatures are subsequently extracted by non-negative matrix factorisation methods and correlated with risk factors data. Through an enhanced understanding of cancer aetiology, Mutographs unprecedented effort is anticipated to outline modifiable risk factors, lead to new approaches to prevent cancer, and provide opportunities to empower early detection, refine high-risk groups and contribute to further therapeutic development. . This dataset contains all the data available for this study on 2019-04-03.

  Dataset EGAD00001004893

• Spatially confined sub-tumor microenvironments in pancreatic cancer

  Intratumoral heterogeneity is a critical frontier in understanding how the tumor microenvironment (TME) propels malignant progression. Here, we deconvolute the human pancreatic TME through large-scale integration of histology-guided regional multiOMICs with clinical data and patient-derived preclinical models. We discover subTMEs, histologically definable tissue states anchored in fibroblast plasticity, with regional relationships to tumor immunity, subtypes, differentiation, and treatment response. Reactive subTMEs rich in complex but functionally coordinated fibroblast communities were immune-hot and inhabited by aggressive tumor cell phenotypes. The matrix-rich deserted subTMEs harbored less activated fibroblasts and tumor- suppressive features yet were markedly chemoprotective and enriched upon chemotherapy. SubTMEs originated in fibroblast differentiation trajectories and transitory states were notable both in single cell transcriptomics and in situ. The intratumoral co-occurrence of subTMEs produced patient-specific phenotypic and computationally predictable heterogeneity tightly linked to malignant biology. Therefore, heterogeneity within the plentiful, notorious pancreatic TME is not random but marks fundamental tissue organizational units.

  Dataset EGAD00001008155

• Multi-region sequencing of RCC with VTT and metastasis using WES and RNAseq

  This dataset contains multi-region sequencing of 16 RCC patients with venous tumor thrombus (VTT), 11 of which were either metastatic on diagnosis or recurred with metastasis. Whole exome sequencing is available for 94 samples across all 16 patients, including 1 matched normal sample per patient, 2-3 primary tumor samples per patient, 1-2 VTT samples per patient, and 0-3 metastasis samples per patient (metastatic lesions were only sampled for 8 of the 11 metastatic patients). RNAseq, generated by exome capture, is available for 67 samples across 12 patients, including 0-1 matched normal samples per patient, 3 primary tumor samples per patient, 0-1 VTT samples per patient, and 0-3 metastasis samples per patient (RNAseq was only available for 4 of the 8 patients from whom metastatic lesions were sampled).

  Dataset EGAD00001008441

• MutWP1: CRUK Grand Challenge Mutographs of Cancer: Colorectal_LCM (2020-02-20)

  The Mutographs project aims to advance our understanding of the causes of cancer through studies of mutational signatures. Led by Mike Stratton, together with Paul Brennan, Ludmil Alexandrov, Allan Balmain, David Phillips and Peter Campbell, this large-scale international research endeavour was awarded a Cancer Research UK Grand Challenge. Different patterns of somatic mutation are generated by the different environmental, lifestyle and genetic factors that cause cancer, many of them are still unknown. Within Mutographs, the International Agency for Research on Cancer is coordinating the recruitment of 5000 individuals with cancer (colorectal, renal, pancreatic, oesophageal adenocarcinoma or oesophageal squamous cancers) across 5 continents to explore whether different mutational signatures explain marked variation in incidence. In brief, through an international network of collaborators around the world, biological materials are collected, along with demographic, histological, clinical and questionnaire data. Whole genome sequences of tumour-germline DNA pairs are generated at the Wellcome Trust Sanger Institute. Somatic mutational signatures are subsequently extracted by non-negative matrix factorisation methods and correlated with risk factors data. Through an enhanced understanding of cancer aetiology, Mutographs unprecedented effort is anticipated to outline modifiable risk factors, lead to new approaches to prevent cancer, and provide opportunities to empower early detection, refine high-risk groups and contribute to further therapeutic development. . This dataset contains all the data available for this study on 2020-02-20.

  Dataset EGAD00001005994

• Bioinformatic Methods and Bridging of Assay Results for Reliable Tumor Mutational Burden Assessment in Non-Small Cell Lung Cancer

  Tumor mutational burden (TMB) has emerged as a predictive biomarker of response to immune checkpoint inhibitors. Standardization of TMB measurement is essential for implementing diagnostic tools to guide treatment. Here we evaluate bioinformatic TMB analysis by whole exome sequencing (WES) in formalin-fixed, paraffin-embedded samples. In CheckMate 026, TMB was retrospectively assessed in 312 patients with non-small cell lung cancer (58% of the intent-to-treat population) who received first-line nivolumab treatment or chemotherapy. We examined the sensitivity of TMB assessment to bioinformatic filtering methods and assessed concordance between TMB data derived by WES and the FoundationOne CDx™ assay. TMB scores comprising synonymous, indel, frameshift, and nonsense mutations (all mutations) were 3.1-fold higher than data including missense mutations only, but values were highly correlated (Spearman’s r = 0.99). Scores from CheckMate 026 samples including missense mutations only were similar to those generated from data in The Cancer Genome Atlas, but those including all mutations were generally higher. Using databases for germline subtraction (instead of matched controls) showed a trend for race-dependent increases in TMB scores. Parameter variation can therefore impact TMB calculations, highlighting the need for standardization. Encouragingly, WES and FoundationOne CDx outputs were highly correlated (Spearman’s r = 0.90) and differences could be accounted for by empirical calibration, suggesting that reliable TMB assessment across assays, platforms and centers is achievable.

  Dataset EGAD00001005035

• National Cancer Institute (NCI) Biospecimen Pre-analytical Variables (BPV) Analysis

  The Biospecimen Pre-analytical Variables (BPV) Program is a National Cancer Institute-sponsored study to systematically assess the effects of pre-analytical factors on the molecular profile of biospecimens. A robust biospecimen collection infrastructure was established to prospectively collect biospecimens using rigorous standard operating procedures to control for most variables while introducing experimental conditions to study specific biospecimen handling issues, including the cold ischemic time (delay to formalin fixation), time in formalin, freezing methods, and storage temperatures and durations. RNA and DNA from biospecimens collected under these conditions was analyzed on multiple molecular platforms. The potential effects of these pre-analytical conditions on protein integrity and detection of metabolites were also examined. Data from this study will be used to develop evidence-based biospecimen standard operating procedures and best practices for fit-for-purpose collection, processing, and storage of biospecimens. The BPV 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 sub-studies below or in the "Substudies" box located on the right hand side of this top-level study page phs001304 BPV Cohort. The substudy links will be active once they are released by dbGaP. Preanalytical Impacts on Global Metabolite Profiling - plasma (MassSpec by Metabolon) This study was to evaluate the impact of the storage temperature (s) (-80°C and LN2 vapor) and the length of storage on human plasma quality using LC-MS/MS (liquid-chromatography-mass spectrometry/mass spectrometry) based global metabolite profiling. The study includes 240 plasma samples collected from 40 donors. Investigate the effect of the delay to fixation on the proteome and phosphoproteome -FFPE (MassSpec by Caprion). The study is to do proteome and phosphoproteome analysis on Delay to fixation was carried out using FFPE tumor samples from colon and ovarian cancer patients comparing 2, 3, and 12hr delay to fixation to the 1hr time point. The study includes 100 samples 20 donors. Investigate the effect of storage conditions of tumor specimens on the proteome and phosphoproteome profiling- Frozen tissue and plasma (MassSpec by Caprion). The study was to evaluate the effects of storage conditions on tumor specimens. Plasma samples from 40 cancer patients stored at two different temperatures (-80°C and LN2) for a given period (0-2, 6-8, and 12-14 months) were evaluated. Frozen kidney tumor samples from 20 patients were compared for effects of different snap frozen (dry ice vs. LN2) and storage temperatures (-80°C and LN2). The study includes 100 tissue and 240 plasma samples from 60 donors. Preanalytical Impacts on Genomic Sequencing by Next Generation Sequencing (NGS) technology (mRNA/miRNA and WES by Expression Analysis). The goal of the study is to determine the effects of cold ischemic delay-to-fixation (4 time points) and formalin preservation (FFPE) on the nature and quality of genomic profiles using the matched freshly frozen sample as the gold standard, which including WES, RNAseq. The study includes 395 samples from 37 donors. Preanalytical Impacts on Copy Number Variation (CNV) Detection by aCGH technology (aCGH by Georgetown University). This study was to use aCGH to evaluate the effect of variation in cold ischemia time and time in formalin fixation on CNV in DNA extracted from kidney cancer specimens. The study includes 235 samples from 40 donors. Evaluation of frozen conditions on mRNA profiling by TaqMan assay (mRNA expression by Georgetown University). This study was to utilize gene expression profiling, using custom TaqMan arrays, to compare the molecular profiles of RNA from frozen tumor samples collected using two freezing methods (dry ice or LN2), two storage temperatures (-80°C or LN2 vapor), as well as Optimal Cutting Temperature (OCT) compound and non-OCT embedded. The study includes 100 samples from 20 donors. mRNA signature for stratification by cold ischemia time (mRNA expression by IBBL). The study was to determine the effects of cold ischemic time (delay-to-fixation) and formalin preservation (FFPE) on mRNA detection by Taqman assay using tumor tissue specimens from kidney, colon and ovarian cancer patients. There are160 samples from 40 donors. The Biospecimen PV cohort is utilized in the following dbGaP individual studies. To view molecular data, and derived variables collected in these individual studies, please click on the following individual studies below or in the "Sub-studies" box located on the right hand side of this top-level study page phs001304 Biospecimen PV cohort. phs001634 CIT mRNA phs001635 CNV aCGH phs001636 Fixation Delay phs001637 Global Metabolite Profiling phs001638 mRNA TaqMan phs001639 NGS phs001640 Tumor Storage

  Study phs001304

• Resuscitation Outcomes Consortium (ROC) Prehospital Resuscitation Using an Impedance Valve and Early Versus Delayed Analysis (PRIMED) (ROC-PRIMED-BioLINCC)

  Accessing Data: Please refer to “Authorized Access” below regarding accessing data through the BioData Catalyst ecosystem. The data from this accession is not available for download through dbGaP.Objective: The purpose of this study was to examine two different treatments during a cardiac arrest that occurs outside of the hospital and whether either or both treatments would increase the number of people who lived to hospital discharge with satisfactory functional status. The first treatment involved using a device called the Impedance Threshold Device (ITD). The other treatment involved the amount of CPR given before the emergency medical services (EMS) providers first looked at the heart rhythm to determine if a shock is needed.Background: Out-of-hospital cardiac arrest is a common and lethal problem with a low survival rate, leading to an estimated 330,000 deaths each year in the United States and Canada. The traditional approach to out-of-hospital cardiac arrest has been to emphasize early analysis of cardiac rhythm, with delivery of defibrillatory shocks, if indicated, as quickly as possible. It has been suggested, however, that many participants may benefit from a period of CPR before the first analysis of rhythm.The impedance threshold device (ITD) is designed to enhance venous return and cardiac output during CPR by increasing the degree of negative intrathoracic pressure. Previous studies have suggested that the use of an ITD during CPR may improve survival rates after cardiac arrest. This effect is achieved by preventing the passive inflow of air into the chest during chest recoil between chest compressions without impeding active ventilation. The ITD has been found to improve hemodynamics, the perfusion of vital organs, and neurologically intact survival in studies in animals. The results of small, short-term clinical trials have suggested that the ITD can increase systolic blood pressure during resuscitation and improve short-term survival rates. Participants: In the ITD study, 4,345 participants were assigned to sham ITD and 4,373 to active ITD, while in the early versus later rhythm analysis, 5,290 participants were assigned to early cardiac rhythm analysis, and 4,643 were assigned to later cardiac rhythm analysis. This study qualified for exception from informed consent required for emergency research.Design: Most participants were enrolled simultaneously in both the early analysis versus later analysis component and the active ITD versus sham ITD component of the trial.The use of an active ITD was compared with that of a sham ITD in participants at 10 ROC sites in the United States and Canada. Participants, investigators, study coordinators, and all care providers were unaware of the treatment assignments. EMS personnel were trained in ITD function, proper use of the ITD, and all aspects of protocol implementation, with an emphasis on the optimal performance of CPR according to local guidelines. The first EMS responders to arrive at the scene of the arrest who were equipped with a randomly assigned ITD (active or sham) attached the device between the ventilation bag and face mask or between the bag and an advanced airway. Responders were encouraged to implement use of the device within 5 minutes after their arrival or as soon as clinically possible. Each of the 10 participating ROC centers was also divided into approximately 20 clusters. All episodes of cardiac arrest in a cluster were randomly assigned to one CPR strategy; after a set period of time, ranging from 3 to 12 months, all episodes in that cluster were then assigned to the other strategy. Participants in the early-analysis group were assigned to receive 30 to 60 seconds of chest compressions and ventilations (sufficient time to place defibrillator electrodes) before electrocardiographic (ECG) analysis, and those in the late-analysis group were assigned to receive 3 minutes of chest compressions and ventilations before ECG analysis. The start and stop times for CPR were recorded by the responders, and the information was supplemented by the recording of defibrillator time. Conclusions: All 10 sites halted enrollment in November 2009 when the data and safety monitoring board recommended termination because interim analysis showed that the findings were not likely to change with continuation of the study. Neither use of the ITD nor the amount of CPR given before cardiac rhythm analysis significantly improved survival with satisfactory function (i.e., a score of ≤3 on the modified Rankin scale) among participants with out-of-hospital cardiac arrest receiving standard CPR. There were also no significant differences in the secondary outcomes, including rates of return of spontaneous circulation on arrival at the emergency department, survival to hospital admission, and survival to hospital discharge.

  Study phs003825

• University of Alabama at Birmingham (Xenotransplantation Project) - DAC

  This is a Data Access Committee (DAC) developed to govern access to sequence level data produced by the Porrett Lab, University of Alabama at Birmingham (Xenotransplantation Project), and headed by Dr. Jayme Locke, and Dr. Porrett M. Paige, Principal, and Co-Principal Investigators respectively. These data were largely used in the generation of the manuscript: “Spatiotemporal immune atlas of the first clinical-grade gene-edited pig-to-human kidney xenotransplant”. Access to these data will be granted to qualified investigators for appropriate use following data use approval from members of the DAC.

  Dac EGAC50000000188

• Bulk Iso-Seq from brain tissue and exosomes isolated from brain tissue using long-read PacBio sequencing of poly-adenylated transcripts

  Human brain sEVs were isolated from postmortem human brain tissue. RNA was extracted from both the source brain tissue and sEVs and prepared for long-read sequencing. cDNA was sequenced on the PacBio Sequel II. The data provided have undergone processing using the tool ccs (v6.0.0) to generate circula consensus reads. For further processing, it is recommended to follow the guidelines at https://isoseq.how/, starting with using lima to remove cDNA primers.

  Dataset EGAD50000000043

• Long Read sequencing data from 4 tumor/germline samples with non muscle invasive bladder cancer

  A better understanding of the molecular landscape of non-muscle-invasive bladder cancer (NMIBC) is essential to improve risk assessment and identify potential therapeutic targets. Here, we perform a comprehensive genomic analysis of patients diagnosed with NMIBC based on whole-exome- (n=438), shallow whole-genome- (n=362), and total RNA-sequencing (n=414). Additionally, tumor/germline samples from 4 patients were sequenced using Oxford Nanopore technology. This dataset contains 8 BAM files corresponding to the Long read sequencing data.

  Dataset EGAD50000000731