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• Circulating cell-free DNA analysis in Small Cell Lung Cancer

  Small cell lung cancer (SCLC) accounts for ~250,000 deaths worldwide each year. Acquisition of adequate tumour biopsies is challenging and liquid biopsies present the best option for patient stratification and response monitoring. We present genome-wide and targeted plasma DNA sequencing data that identifies tumour related changes in 91% of limited (LS-SCLC) and 100% of extensive stage (ES-SCLC) patients. Parallel analysis of circulating tumour cells (CTCs, by CellSearch) based on ≥ 1 CTC/7.5ml blood increased tumour detection frequencies to 98% patients (95% for LS-SCLC) where CTC count and plasma DNA readouts correlated with disease stage and overall survival (OS). Targeted plasma DNA sequencing identified potential therapeutic targets in >50% of patients. This approach will support trials of targeted therapies where improved patients outcomes are urgently required.

  Study EGAS00001003110

• Raw sequencing of single-cell RNA-seq data of a phase II clinical trial (NCT03419481)

  This is a single-arm Phase II trial of pembrolizumab in patients with hepatitis B virus-related hepatocellular carcinoma with parallel study on baseline and serial change in the immune environment.

  Study EGAS50000001315

• Targeted sequencing data of cfDNA, archival tissue, and WBC from 208 patients with mUC

  Targeted tissue (n=81), cfDNA (n=319), and WBC (n=208) Illumina sequencing of metastatic urothelial carcinoma patients. All cfDNA is collected in the metastatic setting, while archival tissue is from across the disease course. White blood cell (WBC) samples are used as patient matched germline samples. All files are in paired-end fastq format.

  Dataset EGAD50000002089

• Targeted sequencing data of cfDNA, archival tissue, and WBC from 226 patients with mUC

  Targeted tissue (n=210), cfDNA (n=402), and WBC (n=245) Illumina sequencing of metastatic urothelial carcinoma patients. All cfDNA is collected in the metastatic setting, while archival tissue is from across the disease course. White blood cell (WBC) samples are used as patient matched germline samples. All files are in paired-end fastq format.

  Dataset EGAD50000001571

• RNA-seq data of breast cancer HCI011 model from Ros et al (2020)

  RNA-seq data of the HCI011 and HCI011R models, GDC032 treated and control (total of 21 samples), from the paper: FOXM1 is a biomarker of resistance to PI3Kα inhibition in ER+ breast cancer that is detectable using metabolic imaging (Ros et al, 2020)

  Dataset EGAD00001006245

• C-MACH reduced-representation bisulfite sequencing (RRBS)

  Umbilical cord blood (CB) has been commonly used as an epigenetic surrogate of fetuses. Here, we propose umbilical cord tissue (UC) as an alternative surrogate for epigenetic studies on fetuses. To explore the feasibility to examine UC epigenome by deep sequencing, we determined CpG methylation profiles of human postnatal UC by reduced representation bisulfite sequencing. We compared DNA methylomes between UC and CB. To investigate the effect of folate during pregnancy on fetal DNA methylation, we compared fetal UC DNA methylation between low and high levels of maternal plasma folate. Our study suggests that UC is useful as an alternative surrogate for studying environmental effects on DNA methylation in human fetuses, compensating CB by providing additional information about epigenetic regulation of genes.

  Study JGAS000171

• Prevention and Early Treatment of Acute Lung Injury Network - Reevaluation of Systemic Early Neuromuscular Blockade (PETAL ROSE-BioLINCC)

  Data Access NOTE: Please refer to the "Authorized Access" section below regarding accessing data through the BioData Catalyst ecosystem. The data from this accession is not available for download through dbGaP. Available Data: The data available for request now include Long Term Outcome data.Biospecimens: Access to Biospecimens is through the NHLBI Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC). Biospecimens from PETAL ROSE include Plasma, DNA, Whole Blood, and Urine. Please note that use of biospecimens in genetic research is subject to a tiered consent.Objectives: To determine the efficacy and safety of early neuromuscular blockade with concomitant heavy sedation as compared with a strategy of usual care with lighter sedation targets in patients with moderate-to-severe ARDS.Background: It has been well established that the approaches used for the application of mechanical ventilation in patients with acute respiratory distress syndrome (ARDS) can affect survival and outcomes after discharge from the intensive care unit (ICU). A large, multicenter trial conducted a decade before this study reported that the early administration of a 48-hour infusion of neuromuscular blockade in patients with moderate-to-severe ARDS (defined by a ratio of the partial pressure of arterial oxygen [Pao2] to the fraction of inspired oxygen [Fio2] of Participants: There were 1006 participants.Design: PETAL-ROSE was a multicenter, unblinded, randomized trial of patients with moderate-to-severe ARDS. Participants were randomly assigned in a 1:1 ratio to receive 48 hours of continuous neuromuscular blockade with concomitant deep sedation (intervention group) or to receive usual care without routine neuromuscular blockade and with lighter sedation targets (control group).Patients in the intervention group who were not under deep sedation at baseline were deeply sedated within 4 hours after randomization. Subsequently, patients in this group received an intravenous bolus of 15 mg of cisatracurium, followed by a continuous infusion of 37.5 mg per hour for 48 hours. After the 48-hour trial intervention period, decisions regarding further use of neuromuscular blockade, including the choice of agent, were left to the discretion of the treating clinician. Neuromuscular blockade could be stopped early if the patient met the criteria for freedom from mechanical ventilation (Fio2 ≤0.40 and PEEP ≤8 cm of water) for at least 12 hours. All patients were treated with a strategy of low tidal volume ventilation within 2 hours after randomization and a high PEEP strategy for up to 5 days after randomization. Assessors who were unaware of the group assignment interviewed surviving patients or their proxies at 3, 6, and 12 months after randomization. The primary end point was in-hospital death from any cause at 90 days (in-hospital was defined as the time in the trial hospital plus transfer to another hospital, including the time in long-term acute care facilities). Conclusions: After the second interim analysis, the decision to stop the trial for futility was made independently by the data and safety monitoring board.In critically ill patients identified shortly after the diagnosis of moderate-to-severe ARDS, the addition of early continuous neuromuscular blockade with concomitant deep sedation did not result in lower mortality than a usual-care approach to mechanical ventilation that included lighter sedation targets.

  Study phs003878

• Peking University BIOPIC Data Access Committee (PUBDAC).The DATA ACCESS AGREEMENT is provided at https://github.com/zhangyybio/single-T-cell-data-access. Applicants can request access to the data by directly downloading it or by sending an email to cancerpku@pku.edu.cn. The process that is used to approve an application includes verifying the institution, participants and research purposes of the application. In general this process will take about two weeks. In principal, any academic research institutions complying with the laws and bioethic regulation policies of China will be approved.

  Dac EGAC00001000551

• Mexican Biobank Project

  In this study, we present the data from the Mexican Biobank Project: 50 WGS from individuals with Native American ancestry, and 6000 genotypes from samples from this project. This project highlights the necessity of better diversity representation in genomic databases is a scientific imperative.

  Study EGAS00001005797

• DNA Methylation Characterization of Fusion-Positive and Fusion-Negative Rhabdomyosarcoma

  Rhabdomyosacoma (RMS) is a common pediatric soft tissue tumor that is associated with the skeletal muscle lineage. RMS comprises two major subtypes: fusion-positive (FP, most commonly PAX3- FOXO1 or PAX7-FOXO1) and fusion-negative (FN, frequently associated with mutations in RAS pathway). Our previous study demonstrated that FP and FN tumors exhibit distinct DNA methylation profiles. In this study, further investigation of genome-wide DNA methylation profiles in RMS tumors revealed DNA methylation differences between AX3-FOXO1 and PAX7-FOXO1 subsets in FP RMS, and between RAS mutation and RAS wild-type subsets in FN RMS. These data provide new insight into the relationship of DNA methylation with mutational changes and transcriptional organization in FP and FN RMS.

  Study phs001970