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• The PRIME-AIR Study: Positive End-Expiratory Pressure, Recruitment, Incentive Spirometry, Muscle Relaxant Optimization, Preoperative Education, Postoperative Early Ambulation, Individualized, and Reinforced

  Data Access NOTE: Please refer to the "Authorized Access" section below for information about how access to the data from this accession differs from many other dbGaP accessions.The PRIME-AIR study ("Positive end-expiratory pressure, Recruitment, Incentive spirometry, Muscle relaxant optimization, preoperative Education, postoperative early Ambulation, Individualized, and Reinforced") was a prospective multi-center randomized controlled pragmatic trial, with a blinded assessor, to compare post-operative pulmonary complications (PPCs) in patients with an individualized anesthetic-centered intervention (including individualized mechanical ventilation positive end-expiratory pressure (PEEP) management to maximize respiratory system compliance and minimize driving pressures, a neuromuscular agent and subsequent reversal, and post-operative lung expansion and early mobilization) versus usual care.

  Study phs003926

• Construction of endoscopic biopsy banking for understanding the intestinal environment in colorectal diseases and exploratory studies using these banking systems.

  Colorectal cancer is the most common type of cancer in Japan. Although some colorectal cancers have a genetic background, most colorectal cancers are sporadic. Known risk factors for colorectal cancer include smoking, obesity, lack of exercise, and red and processed meat. Furthermore, although it has been suggested that changes in the intestinal environment due to changes in diet and lifestyle may be involved in the increased incidence of colorectal cancer in Japan, the molecular mechanism has not yet been fully elucidated. The main objective of this study is to elucidate the changes in the intestinal environment that cause colorectal tumors, and also to contribute to the establishment of colorectal mucosal tissue banking in Japan.

  Study JGAS000655

• Research on the identification of cancer stem cells for peidatric and adult malignancies.

  In recent years, "cancer stem cells" have been reported to exist in many cancers. Many reports have shown that they are the main cause of cancer recurrence. The aim of this study is to test whether cancer stem cells can be identified using patient samples. We will perform omics analysis of rare pediatric cancers by integrating genomics, transcriptomics, proteomics and metabolomics, including somatic and germline mutations, to deepen our understanding of the biological characteristics of the target disease. Based on the knowledge gained and clinical information from patients, we will conduct preclinical pharmacological studies using mouse models and in vitro models to investigate the therapeutic effects of novel therapeutic agents and novel therapeutic strategies such as cellular therapies.

  Study JGAS000623

• Target resequencing of LQTS-related 100 genes in Japanese patients

  Some of the fatal familial arrhythmias cause sudden death in seemingly healthy individuals. It is not easy to make a pre-symptomatic diagnosis of these diseases using only clinical examinations such as an electrocardiogram. The purpose of this study is to elucidate the cause of lethal arrhythmia and/or the genetic factors that influence its susceptibility, thereby enabling early diagnosis and selection of effective treatment methods, and preventing sudden death. The most important purpose of this study is to identify the sites of genetic abnormalities and disease-related genes in pre-symptomatic cases. If a genetic abnormality is found, it is expected that the functional abnormality can be evaluated and appropriate measures to prevent sudden death can be taken.

  Study JGAS000579

• Integrated genomic analysis identifies recurrent mutations and evolution patterns driving the initiation and progression of follicular lymphoma.

  follicular lymphoma (FL), the most common indolent non-Hodgkin’s lymphoma, remains incurable. A well-recognized complication of FL is its transformation to a diffuse large B-cell lymphoma (DLBCL)-morphology in a subset of patients, for which the clinical outcomes are poor. Recent genetic profiling and single case studies of donor-derived FL following stem cell transplantation had alluded to the putative existence of a ‘long lived’ tumor-initiating progenitor cell compartment from which successive disease events occurred. To chronicle the genetic changes associated with progression to transformation, we conducted whole-genome sequencing (WGS) of FL-tFL pairs and matched germline (GL) samples from six patients, a total of 20 genomes.

  Study EGAS00001000399

• Single cell transcriptome and TCR sequencing of EBNA1, ANO2 and CRYAB-reactive T cells in multiple sclerosis.

  Molecular mimicry between Epstein-Barr virus (EBV) and self antigens in the brain has been suggested as a mechanism for how adaptive immune responses to EBV may contribute to multiple sclerosis (MS) disease pathogenesis. Anoctamin-2 (ANO2) and ɑ-crystallin B (CRYAB) have been identified as having homologous peptide sequences with the EBV antigen EBNA1. To explore T cell cross-reactivity, we stimulated PBMC from four natalizumab-treated persons with MS with full-length bead-coupled antigens and sorted proliferating CD4+ T cells by flow cytometry after 8 days. Single cell RNA sequencing was performed on T cells reacting to EBV EBNA1, ANO2, CRYAB, albumin binding domain (ABD, irrelevant protein control) and anti-CD3.

  Study EGAS50000001531

• Mutational_landscape_in_haemochromatosis__WGS_

  Somatic mutation has recently been shown to play a role in disease other than cancer. Driver mutations associated with lipid metabolism and insulin pathway have been identified in non-alcoholic fatty liver disease (NAFLD). It is plausible that driver mutations seen in NAFLD are a consequence of selection pressure exerted on hepatocytes in the context of excess fat accumulation. It has not been investigated whether selection pressure and driver landscape varies between chronic liver diseases of different aetiologies. This study aims to investigate mutational landscape in haemochromatosis, which is a disorder caused by a build-up of iron in the liver. We aim to use data generated by whole-genome sequencing of laser-dissected microbiopsies from diseased livers to characterize driver landscape and mutational signatures in haemochromatosis patients.

  Study EGAS00001005157

• Single cell RNAseq data of human neurons, Bouwen et al Nat Comm 2025

  Brain tumor patients often suffer from epilepsy, but the underlying neuronal changes leading to this neurological symptom are not well understood. This study examined the transcriptomic profiles of human cortical neurons collected from brain tumor patients with or without seizures. The goals of the study were to identify the molecular identities of the recorded neurons and confirm that they are layer 2/3 pyramidal neurons rather than neuron-like tumor cells; and to compare the differential gene expression profiles between patients with and without epilepsy. For each patient, cortical neurons were rapidly isolated from surgically resected tissue and prepared using the Smart-seq2 protocol. Samples from 12 patients were sequenced on an Illumina HiSeq 2500 platform to generate their transcriptomic profiles.

  Study EGAS50000001369

• Hematopoietic differentiation at single-cell resolution in NPM1-mutated AML

  To investigate the relationship between somatic mutations and phenotypic hematologic differentiation at the single-cell level, we used a droplet-based multi-omics single-cell platform on eleven NPM1-mutated AML diagnostic samples. We developed a bioinformatics framework to perform phylogeny-driven genotype correction, that allowed us to study 52 103 single cells. Intra-leukemic genetic heterogeneity was detectable in all patients, including a branched architecture in nine of them, always owing to co-occurring signaling mutations. We identified two groups of NPM1-mutated AML, one characterized by a progenitor immunophenotype and a second one with a predominant monocytic differentiation. We also identified various degrees of intra-leukemic immunophenotype heterogeneity, sometimes associated with strong genetic/phenotype correlations.

  Study EGAS00001006565

• Longitudinal analysis of bone marrow heterogeneity reveals the co-evolution of malignant B cells and their T-cell niche supporting follicular lymphoma persistence

  Follicular Lymphoma (FL) is an indolent lymphoid malignancy characterized by cycles of remission and relapse, reflecting the inability of current therapies to fully eradicate tumor cells. Our hypothesis is that rare cancer precursor/persister cells (CPCs) evade treatment by homing to a protective tumor microenvironment, particularly within the bone marrow (BM), and/or by adopting specific cellular states, and form a rare reservoir of residual cells seeding lymphoma recurrence. To adress this, we collected paired BM samples at diagnosis and one year post-therapy from a clinical trial (FLIRT trial, NCT02303119) and applied multi-modal single-cell analysis to dissect the transcriptomics determinants of rare drug-tolerant persister cells and their surrounding T-cell niche.

  Study EGAS50000001295