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• Epigenomics of Prostate Cancer from Cell Free Plasma

  We sought to perform epigenomic characterization of prostate cancers by profiling circulating nucleosomes isolated from patient plasma using cell free chromatin immunoprecipitation followed by sequencing (cfChIP-seq). Our major findings include identification of prostate-cancer specific regulatory elements using a novel statistical method accounting for variable tumor DNA fraction in plasma, inferring transcription factor activity based on binding motif enrichment within regulatory elements, and epigenetically phenotyping patients based on clinical and genomic features. Data available in dbGaP will include cfChIP-seq and targeted sequencing from approximately 50 patients with a known diagnosis of cancer and healthy patient controls.

  Study phs003482

• Divergent WNT Signaling and Drug Sensitivity Profiles within Hepatoblastoma Tumors and Organoids

  Hepatoblastoma, the most prevalent pediatric liver cancer, almost always carries a WNT-activating CTNNB1 mutation, yet exhibits notable molecular heterogeneity. To characterize this heterogeneity and identify novel targeted therapies, we perform comprehensive analysis of hepatoblastomas and tumor-derived organoids using single-cell RNA-seq/ATAC-seq, spatial transcriptomics, and high-throughput drug profiling. We identify two distinct tumor epithelial signatures: hepatic ‘fetal’ and WNT-high ‘embryonal’, displaying divergent WNT signaling patterns. The fetal group is enriched for liver-specific WNT targets, while the embryonal group is enriched in canonical WNT target genes.

  Study EGAS50000000561

• RNA-seq of longitudinal human blood and nose swab samples from a controlled human infection experiment with SARS-CoV-2 virus

  Controlled human infection experiments enable longitudinal profiling of immune responses to a pathogen. 36 healthy volunteers aged 18-29 years, with no evidence of previous infection or vaccination, were inoculated with SARS-CoV-2 virus and quarantined for 14 days. Blood samples for RNA sequencing were collected into PAXgene tubes before virus challenge, 6 hours after challenge, daily thereafter for 14 days and on day 28. Mid-turbinate nose swabs for RNA sequencing were collected before virus challenge, and on days 1, 3, 5, 7, 10 and 14 after challenge, preserved in RNAprotect.

  Study EGAS50000000667

• Distinct immune cell infiltration patterns in pancreatic ductal adenocarcinoma (PDAC) exhibit divergent immune cell selection and immunosuppressive mechanisms

  Pancreatic ductal adenocarcinoma has a dismal prognosis. A comprehensive analysis of single-cell multi-omic data from matched tumour-infiltrated CD45+ cells and peripheral blood in 12 patients, and two published datasets, reveals a complex immune infiltrate. Patients have either a myeloid-enriched or adaptive-enriched tumour microenvironment. Lymphocyte enrichment is intrinsically linked with highly distinct B and T cell clonal selection, diversification, and differentiation. Using TCR data, we see the largest clonal expansions in CD8 effector memory, senescent cells, and highly activated regulatory T cells which are induced within the tumour from naïve cells. We identify pathways that potentially lead to a suppressive microenvironement, including targets of immunotherapy and checkpoints including TIGIT/PVR and SIRPA/CD47. PDAC patient tumors from the APACT clinical trial revealed that patients with myeloid enrichment had the shorter overall survival compared to those adaptive cell enrichment. We identify multiple therapeutic targets that should form the basis for rational design including boosting of B cell responses, targeting immunosuppressive macrophages, and specific Treg depletion approaches. The dataset is scRNA-seq data from PDAC patients.

  Dac EGAC50000000319

• NHLBI TOPMed - NHGRI CCDG: Groningen Genetics of Atrial Fibrillation (GGAF) Study

  Atrial fibrillation (also called AFib or AF) is a quivering or irregular heartbeat (arrhythmia) that can lead to blood clots, stroke, heart failure and other heart-related complications. The Groningen Genetics of Atrial Fibrillation (GGAF) cohort is a cohort composed from 5 different sources of individuals with atrial fibrillation (AF) and age and sex-matched controls. Written informed consent was provided from all participating individuals, and all 5 studies were approved by the ethical committee at the University Medical Center (www.atrialfibrillationresearch.nl) and Maastricht University. All samples selected for TOPMed WGS are from individuals with atrial fibrillation.

  Study phs001725

• Single-cell Analysis of Neoplastic Plasma Cells Identifies Novel Myeloma Pathobiology Mediators and Potential Targets

  Newly diagnosed symptomatic and relapsed/refractory myeloma is a clonal plasma cell (PC) dyscrasia that arises from precursors which have been studied utilizing bulk or single-cell (sc) techniques. By combining scRNA-sequencing with scB-cell receptor (BCR)-sequencing, we found more dysregulated genes in monoclonal PCs compared with analyses of the entire CD138+ population, which includes non-neoplastic/polyclonal PCs. Paired tumor and non-tumor WGS was performed to evaluate the presence of IgH-associated translocations and hyperdiploidy events, initially detected by FISH, in a subset of samples included in this study.

  Study EGAS50000000801

• Integrated Transcriptomic and Regulatory RNA Profiling Reflects Complex Pathophysiology and Uncovers a Conserved Gene Signature in End Stage Heart Failure RNA-Seq data

  Heart failure (HF) is a complex syndrome. Despite availability of multiple treatment options, the mortality remains high and the quality of life poor. Better understanding of the underlying pathophysiological processes can lead to development of novel therapies. Multiple comparative transcriptomics studies, which revealed gene level changes in the key pathophysiological pathways in failing hearts, point towards heterogeneity from interplay of disease stage, etiologies and ethnicity. Transcriptomic characterization of HF in patients from different ethnicities can potentially help in understanding the heterogeneity imparted by various factors and the core elements in heart failure.

  Study EGAS50000000810

• Enabling sensitive and precise detection of ctDNA through somatic copy number aberrations in breast cancer

  Cell-free DNA (cfDNA) extracted from peripheral blood has emerged as a crucial biomarker source in oncology research. To enhance the detection of somatic copy number alterations (SCNAs) and circulating tumor DNA (ctDNA), we developed eSENSES, a 2Mb breast cancer-targeted NGS panel. It includes 15,000 genome-wide SNPs, 500 focal SNPs in breast cancer driver regions, and exons from 81 commonly altered genes, alongside a custom computational approach. eSENSES provides a reliable, powerful and cost-effective tool for monitoring disease progression and guiding therapeutic decisions in breast cancer patients.

  Study EGAS50000000793

• The Multiethnic Cohort (MEC) Study

  The Multiethnic Cohort (MEC) study of over 215,000 men and women in Hawaii and California is unique in that it is population-based and includes large representations of older adults (45-75 years at baseline) for five US racial/ethnic groups (Japanese Americans, African Americans, European Americans, Latinos and Native Hawaiians) at varying risks of chronic diseases. The MEC has established a large biorepository of mainly blood and urine collected from over 70,000 participants, linked to extensive, prospectively collected risk factors (e.g., diet, smoking, physical activity), biomarkers and clinical data for five racial/ethnic groups.

  Study phs002183

• Feasibility study of enzymatic methylation sequencing of cell-free DNA from cerebrospinal fluid of pediatric brain tumors for classification

  Array-based DNA methylation profiling is the gold standard for molecular classification of brain tumors. However, it relies on significant amount of input DNA extracted from surgical tissue, thus limiting its use for tumors where biopsy is challenging or limited in quantity. Cell-free tumor DNA (cfDNA) in cerebrospinal fluid (CSF) presents alternative opportunities for brain tumor diagnosis and disease monitoring following treatment. Novel enzymatic DNA methylation sequencing (EM-seq) methods may allow us to overcome input DNA limitations and accurately quantify methylation from cfDNA for tumor classification.

  Study EGAS50000000871

• GenomeAsia 100K Project: Human DNA samples collecting and whole genome sequencing of Asian populations

  The number of basal divergences, admixture, and the degrees of isolation among Indigenous North Eurasian and Native South American populations remain debated, with most insights derived from genome-wide genotyping data. This study aims to improve our understanding of the ancient dynamics and shaping of the contemporary populations of North Eurasia and the Americas. Using large-scale whole-genome sequencing of 1,537 individuals across 139 ethnic groups from these regions, we identify population structures, clarify the prehistoric migrations and the role of past environments in the diversification of human populations.

  Study JGAS000781

• RNA-seq data of bone marrow CD34-positive cells from 57 patients with myelodysplastic syndromes (MDS) and 5 healthy individuals (62 participants in total)

  Genetic mutations in hematopoietic neoplasms, seen in disease-specific and non-specific ways, are key drivers in pathogenesis. Typically, these mutations alone don't cause neoplasms; rather, multiple mutations or breakdowns in regulatory mechanisms occur, progressing the disease through stages. Genetic mutation patterns vary even within subtypes, suggesting shared gene expression abnormalities from different mutations may drive neoplasm development. Identifying these "common factors" is vital for effective molecular-targeted therapy development. Our study aims to elucidate neoplasm pathogenesis by analyzing patient genetic abnormalities, pinpointing "common factors" in each subtype for novel targeted therapy development.

  Study JGAS000724

• Single-nuclei histone modification profiling of the adult human central nervous system unveils epigenetic memory of developmental programs

  We profile the adult human CNS from distinct regions, sex and ages, for chromatin accessibility at the single-nuclei level. Tissue was collected from 20 different donors (10 male, 10 female) within the ages of 34 to 74 years old. Additionally we performed Single-cell nanoCUT&Tag H3K27ac and H3K27me3 profiling for 4 of the donors and multiome single cell assay (RNA-seq+ATAC-seq) for 2 of the donors. Each donor donated fresh frozen white matter from the following three tissue regions: primary motor cortex (Brodmann area 4, BA4), arbor vitae cerebelli (CB) and fasciculi cuneatus and gracilis from and cervical spinal cord (CSC). Tissue was processed semi-randomly, ensuring that each batch of experiments had a representation of both sexes and all three tissue regions. Completed libraries were again randomly multiplexed during sequencing to minimize batch effects. We also performed micro-C,2 replicates, of iPS human derived cell cultures of human oligodendrocyte precursor cells (hOPC).

  Dataset EGAD50000000410

• Development of Novel Synovial Sarcoma Organoids Models for Drug Discovery

  Although synovial sarcoma has been studied using established cell lines and mouse models, effective treatments remain limited. We treated five patients with synovial sarcoma between 2022 and 2023 and established organoid cultures from resected tumor specimens using a modified air-liquid interface method. After serial passaging, organoids were successfully xenografted into NOD-scid IL2Rgnull (NSG) mice in three cases. The established organoids retained SS18-SSX fusion transcripts and demonstrated histological and genetic similarities to the original tumors. These organoid models provide a reliable platform for studying synovial sarcoma biology and hold promise for the development of novel therapeutic strategies.

  Study JGAS000806

• Epigenomic analysis of the human placenta and endometrium constituting the fetal-maternal interface

  This study aims to determine the reference epigenomes of the human placenta and endometrium, which constitute the fetal-meternal interface, for future use in studies of human diseases associated with reproduction and development. In the placenta, we focus on cytotrophoblast and syncytiotrophoblast cells (both at first trimester and at term) and, in the endometrium, we focus on epithelial cells (at the follicular and secretory phases) and stroma cells. These reference epigenomic data will be of valuable resource in studying disease-associated differences in epigenomic modification in the reproductive system. JGA submission accessions: JGA000074,JGA00000000074

  Study JGAS000073

• Expression quantitative trait loci analysis using human immune cells in a Japanese population

  Recent evidence suggests that a substantial portion of complex disease risk alleles modify gene expression in a cell-specific manner. Therefore, it is reasonable to expect that cell-specific expression quantitative trait loci (eQTL) analysis can identify the candidate causal mechanisms of complex diseases (an eQTL is a variant whose polymorphism affects gene expression). We fractionated peripheral blood from 105 healthy Japanese volunteers into five major immune cell subsets (CD4+ T cells, CD8+ T cells, B cells, NK cells, and monocytes). We quantified gene and exon expression by RNA sequencing, and tested associations with neighboring common variants (MAF ? 0.05).

  Study JGAS000085

• Epigenomic analysis of the human placenta and endometrium constituting the fetal-maternal interface

  This study aims to determine the reference epigenomes of the human placenta and endometrium, which constitute the fetal-meternal interface, for future use in studies of human diseases associated with reproduction and development. In the placenta, we focus on cytotrophoblast and syncytiotrophoblast cells (both at first trimester and at term) and, in the endometrium, we focus on epitherial cells (at the follicular and secretory phases) and stroma cells. These reference epigenomic data will be of valuable resource in studying disease-associated differences in epigenomic modification in the reproductive system. JGA submission accessions: JGA000117,JGA00000000117

  Study JGAS000107

• Germline pathogenic variant and gastric cancer risk

  Germline pathogenic variants in some genes have been suggested to be associated with gastric cancer risk, although large-scale evaluations were limited. Herein, we analyzed germline variants in 27 cancer-predisposing genes in 10,426 gastric cancer patients and 38,153 controls from BioBank Japan. Following quality control of sequencing data, samples from 10,366 gastric cancer patients and 37,592 controls were further analyzed. We evaluated the association between pathogenic variants and gastric cancer risk and explored the characteristics of the pathogenic-variant carrier. Nine genes were associated with gastric cancer risk. The germline pathogenic variant carriers showed different clinical and demographic characteristics.

  Study JGAS000592

• B cell activation

  To investigate the gene programs involved in B cell activation and antibody switching, we profiled the gene expression at the single cell level as well as the antibody repertoire of human naive and memory B cells at resting and following three time points of activation. Through CRISPR perturbations, we defined IRF4 as a central regulator of both GC and plasma cell fates, acting independently of PRDM1 in GC commitment. Finally, leveraging machine learning classification methods trained solely on transcriptomic profiles, we accurately predicted sister cell relationships, revealing that plasma cell gene expression programs are heritable and tightly conserved within a clone.

  Study EGAS50000001468

• Paired DNA and RNA sequencing uncovers common and rare genomic variants regulating gene expression in the human retina

  In this study, we uncovered common and rare genomic variants shaping retinal expression profiles. This includes 1,483,595 significant cis-expression quantitative trait loci (eQTLs) impacting 9,959 and 3,699 genes in NSR and RPE, respectively, with associated genomic variants enriched to cis-candidate regulatory elements and notable shared eGenes between NSR and RPE. We also detected 1051 expression outliers and prioritised 299 rare non-coding single-nucleotide, structural variants or copy number variants as plausible drivers for 28% of outlier events. This study increases understanding of gene expression regulation in the human retina.

  Study EGAS50000001443

• RNAseq profile of monomorphic epitheliotropic intestinal T-cell lymphoma and enteropathy associated T-cell lymphoma

  Background : Enteropathy-associated T-cell lymphoma (EATL) and monomorphic epitheliotropic intestinal T-cell lymphoma (MEITL) are aggressive malignancies with limited treatment options and poor prognosis. Our research on MEITL has uncovered its genetic portrait including hallmark SEDT2 mutations, expanded its pathological spectrum, and identified molecular biomarkers influencing patients’ outcome. In this study, we aimed to establish and clarify the similar and diverging features of EATL. Methods : A large combined cohort of patients with EATL (n=30) and MEITL (n=52) was assembled and tumor samples were used for whole-exome and RNA sequencing profiling.

  Study EGAS50000001125

• Whole Exome Sequencing of monomorphic epitheliotropic intestinal T-cell lymphoma and enteropathy associated T-cell lymphoma

  Background : Enteropathy-associated T-cell lymphoma (EATL) and monomorphic epitheliotropic intestinal T-cell lymphoma (MEITL) are aggressive malignancies with limited treatment options and poor prognosis. Our research on MEITL has uncovered its genetic portrait including hallmark SEDT2 mutations, expanded its pathological spectrum, and identified molecular biomarkers influencing patients’ outcome. In this study, we aimed to establish and clarify the similar and diverging features of EATL. Methods : A large combined cohort of patients with EATL (n=30) and MEITL (n=52) was assembled and tumor samples were used for whole-exome and RNA sequencing profiling.

  Study EGAS50000001126

• Neuroblastoma Smart-Seq2 Single Nuclei Sequencing Data

  Heterogeneity of tumors, including the presence of resistant clones, represents a great challenge for high-risk neuroblastoma (NB). Currently, there are no treatments that address cancer heterogeneity. Classification of bulk tumors and corresponding predictions are poor and too general. Understanding heterogeneity will provide critical insight for the development of targeted therapeutic strategies. In this study, we collected 10 human neuroblastoma tumor samples and performed whole-transcriptome profiling at single-nucleus resolution using SMART-Seq2 technology. This approach enables comprehensive characterization of transcriptional diversity within individual tumors, allowing us to identify distinct cellular subpopulations.

  Study EGAS50000001103

• Full AfricanNeo ModernDNA Study

  With the largest genomic dataset to date of Bantu-speaking populations, including newly generated data of modern-day and ancient DNA from previously unsampled regions in Africa, we shed fresh light on the expansion of peoples speaking Bantu languages that started ~4000 years ago in western Africa. We have genotyped 1,763 participants, including 1,487 Bantu speakers from 143 populations across 14 African countries. Our comprehensive genetic analysis of the expansion of people speaking Bantu languages reveals a complex history of serial founder events, variable levels of contact with local groups, and spread-over-spread events.

  Study EGAS50000000006

• The molecular landscape of glioma in patients with Neurofibromatosis 1.

  Neurofibromatosis type 1 (NF1) is a common tumor predisposition syndrome in which glioma is one of the most prominent tumor type. Gliomagenesis in NF1 results in heterogeneous spectrum of tumors, from low grade to high grade glioma, occurring during the entire patient lifespan. In this study, we present the molecular landscape of low- and high-grade glioma in children and adults affected by NF1 (NF1-glioma). 59 tumor samples from 56 NF1-glioma patients with 43 matched normal were profiled with Whole Exome Sequencing, DNA Methylation array (31 tumors) and RNA sequencing (29 tumors).

  Study EGAS00001003186