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• Plasma DNA aberrations in systemic lupus erythematosus revealed by genomic and methylomic sequencing

  We performed a high-resolution analysis of the biological characteristics of plasma DNA in systemic lupus erythematosus (SLE) patients using massively parallel genomic and methylomic sequencing. A number of plasma DNA abnormalities were found. First, aberrations in measured genomic representations (MGRs) were identified in the plasma DNA of SLE patients. The extent of the aberrations in MGRs correlated with anti-double–stranded DNA (anti-dsDNA) antibody level. Second, the plasma DNA of active SLE patients exhibited skewed molecular size-distribution profiles with a significantly increased proportion of short DNA fragments. The extent of plasma DNA shortening in SLE patients correlated with the SLE disease activity index (SLEDAI) and anti-dsDNA antibody level. Third, the plasma DNA of active SLE patients showed decreased methylation densities. The extent of hypomethylation correlated with SLEDAI and anti-dsDNA antibody level. To explore the impact of anti-dsDNA antibody on plasma DNA in SLE, a column-based protein G capture approach was used to fractionate the IgG-bound and non–IgG-bound DNA in plasma. Compared with healthy individuals, SLE patients had higher concentrations of IgG-bound DNA in plasma. More IgG binding occurs at genomic locations showing increased MGRs. Furthermore, the IgG-bound plasma DNA was shorter in size and more hypomethylated than the non–IgG-bound plasma DNA. These observations have enhanced our understanding of the spectrum of plasma DNA aberrations in SLE and may provide new molecular markers for SLE. Our results also suggest that caution should be exercised when interpreting plasma DNA-based noninvasive prenatal testing and cancer testing conducted for SLE patients.

  Study EGAS00001000962

• Trial of Onco-Panel for Geneprofiling to Estimate both Adverse events and Response by cancer treatment (TOP-GEAR)

  Bam files and fastq files in a hospital-based prospective study (TOP-GEAR project, the 2nd stage) to investigate the feasibility and utility of NGS-based analysis of 114 cancer-associated genes (the NCC Oncopanel test). DOI: 10.1111/cas.13969

  Study JGAS000662

• Whole exome sequencing of Ewing sarcoma and CIC-DUX4 sarcoma

  Whole exome sequencing of a collection of 6 Ewing sarcoma and 3 CIC-DUX4 sarcoma tumoroids plus 4 matched patient tumors and normal tissue. Tumoroids were established from digested patient tumor material as 3D culture in Matrigel. After 2-3 month of growth, Genomic DNA was isolated from individual tumoroid models using the DNeasy Blood & Tissue Kit (Qiagen) and used for whole exome sequencing. Genomic DNA from corresponding patient tumors and matched normal tissue was tested in parallel, if available.

  Dataset EGAD50000000556

• Single-cell RNA and TCR sequencing of 16 PSCC and 6 non-malignant samples

  We included 16 fresh tumor samples of biopsy-proven invasive penile squamous cell carcinomas and 6 adult non-malignant inner prepuce samples. Single-cell RNA sequencing was performed (10x genomics). An HPV reference genome of 15 high-risk HPV types was generated and we mapped all single cell reads to the GRCh38 human and HPV reference genome using CellRanger. Targeted next-generation sequencing (tNGS) was performed for the detection of TP53 loss-of-function mutations.

  Dataset EGAD50000000317

• Whole-genome enzymatic DNA methylation sequencing and single-cell RNA sequencing data from nasal cells of COVID-19 patients

  Nasal swabs were collected from COVID-19 patients during the acute phase of infection as well as 3 and 12-months post-infection. Cells isolated from nasal swabs were subjected to whole-genome enzymatic DNA methylation sequencing (n=33) and scRNA-seq (n=24). For n=12 former COVID-19 pateints, follow-up samples were collected at 3 and 12 months post-infection and subjected to scRNA-seq.

  Dataset EGAD50000000398

• ETMR_Nanostring

  Total RNA (100ng) from 21 ETMRs with C19MC structural alterations and 28 other PBTs was prepared with nCounter miRNA Sample Prep Kit according to standard protocol. miRNA expression profiling was conducted with human v1, v2, or v3 miRNA panel on nCounter miRNA expression platform (NanoString Technologies, Seattle, WA) according to manufacturer’s protocol. Signal normalization was done using nSolver Analysis and batch corrected using ComBat (Johnson et al. Biostatistics. 2007). 565 miRNAs overlapped between all three versions and was used for further analyses. Fold change and supervised t-test with FDR correction was calculated between the ETMRs and other PBTs.

  Dataset EGAD00010001701

• Cell-free MeDIP-seq of plasma samples from lymphoma patients and healthy controls

  This dataset contains cell-free methylated DNA immunoprecipitation sequencing (cfMeDIP-seq) data generated from plasma samples of lymphoma patients and healthy controls. The study aims to characterize genome-wide methylation patterns of circulating cell-free DNA and identify hypermethylated regions associated with lymphoma. Sequencing libraries were prepared using cfMeDIP with anti-5-methylcytidine antibody enrichment and sequenced on an Illumina platform. The dataset supports differential methylation analyses and the development of classification models for lymphoma detection.

  Dataset EGAD50000002108

• Whole-transcriptome sequencing of MPN patients and controls.

  This dataset contains whole-transcriptome sequencing data of 113 myeloproliferative neoplasms (MPN) patients and 15 controls. Patients were diagnosed with essential thrombocythemia, polycythemia vera, primary myelofibrosis, and secondary acute myeloid leukemia. The data were pooled from 5 different sequencing experiments as indicated using an Illumina HiSeq2000 machine. All samples were sequenced paired-end. Sequenced samples were processed with custom workflows for discovery of fusion genes, SNVs and Indels calling, and identification of splicing abnormalities.

  Dataset EGAD00001004788

• Comprehensive single cell study of lung adenocarcinoma from early to metastatic stages

  We performed single cell RNA sequencing (scRNA-seq) for 208,506 cells derived from 58 lung adenocarcinomas from 44 patients, which covers primary tumour, lymph node and brain metastases, and pleural effusion in addition to normal lung tissues and lymph nodes. The extensive single cell profiles depicted a complex cellular atlas and dynamics during lung adenocarcinoma progression which includes cancer, stromal, and immune cells in the surrounding tumor microenvironments.

  Dataset EGAD00001005054

• Detection of Gene Fusions using Targeted Next-Generation Sequencing

  Five commercially available parallel sequencing assays were evaluated for their ability to detect gene fusions in eight cell lines and 18 FFPE tissue samples carrying a variety of known gene fusions. Four RNA-based assays and one DNA-based assay were compared; two were hybrid capture-based, TruSight Tumor 170 Assay (Illumina) and SureSelect XT HS Custom Panel (Agilent), and three were amplicon-based, Archer FusionPlex Lung Panel (ArcherDX), QIAseq RNAscan Custom Panel (Qiagen) and Oncomine Focus Assay (Thermo Fisher Scientific).

  Dataset EGAD00001006913

• Whole Exome and RNA-Sequencing of Germline, Small Bowel Carcinoid Primary Tumor, and Liver Metastasis Trios

  This dataset includes trios of germline/constitutional, primary tumor (small bowel carcinoid), and metastatic tumor (liver) trios for 5 patients (i.e. 15 samples total). Constitutional, primary tumor, and metastatic tumor samples all underwent whole exome sequencing (WES or WXS). Primary and metastatic tumor samples underwent RNA sequencing (RNA-seq).

  Dataset EGAD00001010036

• Circulating tumor DNA, pathological and immunologic responses to neoadjuvant nivolumab or nivolumab plus relatlimab and chemoradiotherapy in resectable esophageal/gastroesophageal junction cancer

  The dataset for the study “Circulating tumor DNA, pathological and immunologic responses to neoadjuvant nivolumab or nivolumab plus relatlimab and chemoradiotherapy in resectable esophageal/gastroesophageal junction cancer” includes 173 bam files from hybrid capture targeted error-correction next-generation sequencing (TEC-Seq) from plasma cell-free DNA and matched white blood cell DNA from 32 individuals with esophageal/gastroesophageal junction cancer, who received immunotherapy-containing regimens.

  Dataset EGAD00001011822

• Bam files from whole exome sequencing (WES)from multiple laser microdissected regions from tumor and paired biopsies from metastatic lesions.

  In this study we characterized genomic alterations in three bladder cancer patients with metastatic disease courses. Multiple regions were procured by laser microdissection or punctures from primary tumor, lymph node metastases and from distant metastases. Data provided here consist of 35 Bam files for WES (32 Tumors and 2 blood, 1 adjacent normal)

  Dataset EGAD00001002772

• RData

  The file data.RData contains data objects needed to run the .rmd template that generates the manuscript's figures. These include ExpressionSets for the training and test sets, module content and annotations, PCA results, the lasso58 signature with coefficients, and Foundation Medicine CDKN2A copy-number alteration data.

  Dataset EGAD00001007585

• NHLBI TOPMed: Australian Familial Atrial Fibrillation Study

  In the Australian Familial AF Study, a cohort of probands with familial AF was recruited for genetics studies at the Victor Chang Cardiac Research Institute. Familial AF cases were identified from in-patient and out-patient populations at St. Vincent's Hospital and by referral from collaborating physicians throughout Australia. Study subjects underwent clinical evaluation with history, ECG and echocardiogram, and informed consent was obtained from all participants. 151 probands aged <66 years at the time of diagnosis were included in this analysis. The control cohort was comprised of age- and sex-matched individuals (n=151) who had no history of cardiovascular disease. In the current TOPMed study, we have performed whole genome sequencing in European Ancestry cases with early-onset atrial fibrillation (defined as atrial fibrillation onset prior to 61 years).

  Study phs001435

• SARS-CoV2 mRNA-vaccination-induced Immunological Memory in Human Non-Lymphoid and Lymphoid Tissues

  SARS-CoV2 mRNA vaccination-induced CD4+ Th cells were isolated based on activation marker expression from human bone marrow (n=3), lung (n=5), liver (n=4) and paired blood samples (to liver donors, n=4) of virus-naive vaccinees after Spike peptide mix stimulation in vitro. The 10X platform was used for single cell transcriptome analysis, along with T cell receptor clonotype analysis in a total of 1985 cells. Samples were sequenced on a NovaSeq 6000 (Illumina).

  Study EGAS50000000045

• Combined targeting of BRD4-associated Promoter Activation and NFKB Immunomodulation in ARID1A-mutated Gastric Adenocarcinoma

  Gastric cancer (GC) a leading causes of cancer-related deaths worldwide, with ARID1A identified as the second most frequently mutated driver gene in GC. This study involves comprehensive genomic profiling of a Singaporean cohort of over 200 GC patients to characterize the mutational signatures associated with ARID1A inactivation across various molecular subtypes of GC. The findings highlight a potential therapeutic approach for ARID1A-mutated GCs, targeting both tumor-intrinsic mechanisms (BRD4-associated promoter activation) and extrinsic immunomodulatory pathways (NFKB signaling).

  Study EGAS00001006397

• This study aims to evaluate the relationship between cardiometabolic risk factors and the most common genetic variation (SNPs)

  Comprehensive data on lifestyle-related modifiable factors, sociodemographic, anthropometric, economic, biochemical, and genetic markers related to the occurrence of cardiometabolic diseases as part of the observational cross-sectional survey “2015 Health Survey of Sao Paulo with Focus on Nutrition (2015 ISA-Nutrition)”, a population-based study. Data of 805218 SNPs for 841 individuals was genotyped using the Axiom™ 2.0 Precision Medicine Research Array in the Thermo Fisher Scientific laboratory (Affymetrix Inc, Santa Clara, CA).

  Study EGAS00001007818

• Patient tumour data (RNAseq, WGBS, ChIPseq, WGS)

  Content: 60 GB patient tumours and 4 normal brain samples combined in pairs by region (x2=8 total input samples). RNAseq: 1 lane per sample, total strand-specific rRNA-depleted (normal samples were combined = 2 lanes/samples per brain region). WGBS: 2 lanes per sample (normal samples were combined = 2 lanes/samples per brain region). ChIPseq (histone mark): a subset of 20 GB samples were profiled. For the same modification were multiplexed and sequenced on 4 lanes each (H3K27ac, H3K4me1) or a single lane (all others). WGS: used as matching input control for the 20 ChIPseq samples. Data type and technology: RNA-seq: PE 100bp sequenced on HiSeq2000. WGBS: PE 100bp sequenced on HiSeq2000/4000. ChIPseq: SE 50bp sequenced on HiSeq2000/4000. WGS: PE 150bp sequenced on HiSeq X.

  Dataset EGAD00001005492

• RNAseq of 7 MPNSTs

  RNAseq of 7 MPNSTs for Magallon-Lorenz 2026. Contains 5 samples sequenced with DNBseq at BGI (four 2x100bp and one 2x150bp) and 2 samples sequenced with Illumina stranded mRNA-seq technology. BGI samples have been prefiltered with SOAPnuke. Two fastq files provided per sample with no additional filtering or QC.

  Dataset EGAD50000002493

• ctDNA diva aggregate data

  ctDNA biomarker and relevant clinical data for divarasib phase I GO42144 study, including tumor type, KRAS G12C mutation detectability in plasma at baseline, baseline SLD, sites of metastasis, lines of therapy, best response, confirmed best response, PFS, ctDNA tumor fraction and KRAS G12C VAF at baseline/C1D15/C3D1.

  Dataset EGAD50000000454

• WES dataset used for the study "Longitudinal Multi-Omics Study Reveals Molecular Drivers and Tumor Microenvironment in Extramedullary Multiple Myeloma"

  This dataset contains 72 paired fastq files of raw Whole exome sequencing data from 14 patients with Extramedullary myeloma, 8 paired samples from the same patients at the time of Newly diagnosed myeloma, and the corresponding normal samples

  Dataset EGAD50000000052

• ATAC Dataset for 19 T-ALL patient samples and 1 normal control sample

  19 ATAC-seq from T-ALL patient samples and one healthy normal control sample. Reads were aligned to HG38 reference

  Dataset EGAD50000000024

• Whole-exome sequencing of additional thyroid disease cases (2018-08-13)

  Whole-exome sequencing of a cohort of families (probands and affected/unaffected relatives) suffering from one of two rare thyroid disorders: congenital hypothyroidism (CH) and resistance to thyroid hormone (RTH). . This dataset contains all the data available for this study on 2018-08-13.

  Dataset EGAD00001004293

• Whole-exome sequencing of additional thyroid disease cases (2017-05-11)

  Whole-exome sequencing of a cohort of families (probands and affected/unaffected relatives) suffering from one of two rare thyroid disorders: congenital hypothyroidism (CH) and resistance to thyroid hormone (RTH). This dataset contains all the data available for this study on 2017-05-11.

  Dataset EGAD00001003331

• Gene regulation of human CD4+ Treg ChM-seq

  This dataset maps gene expression regulation in human primary regulatory CD4+ T cells (Tregs). It includes whole genome sequence data for ChM-seq (118 H3K4me3, 118 H3K27ac and 6 inputs). The final quality filtered set included 91 individuals with H3K27ac ChM-seq and 88 with H3K4me3 ChM-seq.

  Dataset EGAD00001004828

• PFA ependymoma study -WGS data

  WGS bam file for the 18 samples used in Michealraj et al. Cell 2020. The dataset includes PFA ependymoma tissue, derived line and blood samples of 6 patients WGS data were aligned with BWA to the hg38 human reference genome (igenome) and further processed according to the GATK best practice pipeline.

  Dataset EGAD00001006045

• Genome-wide array and mtDNA data Mercheros

  This dataset includes genome-wide autosomal array data and whole mtDNA sequences for 24 Merchero individuals.

  Dataset EGAD00001007763

• Whole genome sequencing generated from 11 glioma patient samples

  This dataset includes 22 BAM files for tumor tissue and matched normal blood from 6 IDH-mutant, 5 IDH-wild-type glioma patient samples of unmatched initial and recurrent timepoints profiled using whole genome sequencing.

  Dataset EGAD00001007771

• Platelet RNAseq data for SLFN14 K219N patients

  RNAseq dataset containing 20 control and 2 SLFN14 K219N patient samples, derived from platelets. Sequencing libraries were constructed using an Illumina TruSeq stranded Ribo Zero Gold kit and paired end sequenced at a read depth of 30 million reads on an Illumina NovaSeq 6000 platform.

  Dataset EGAD00001008965

• Human Spermatogenesis Methylome

  The dataset contains the methylome EM-sequencing raw data (fastq) of different spermatogenic cells from 5 human males (three controls and two crypotzoospermic). The datasets correspond to the following cell types: undifferentiated spermatogonia, differentiating spermatogonia, 4C spermatocytes, and 1C spermatids (this cell type only for the control individuals)

  Dataset EGAD00001011180

• Single-cell RNA sequencing of Small Intestinal Neuroendocrine Tumors (SI-NET)

  Single-cell RNA sequencing (scRNA-seq) was performed on cells isolated from intestinal mucosa and small intestinal neuroendocrine tumors (SI-NETs) to compare their transcriptomic profiles. Tumor and adjacent normal tissues were collected from two SI-NET patients, enzymatically dissociated, and processed into single-cell suspensions. Single-cell libraries were generated using the Chromium Single Cell 3′ Reagent Kit v3 and sequenced on an Illumina platform to produce FASTQ files for downstream analysis.

  Dataset EGAD50000002265

• Small RNA-Seq of MicroRNA's in extracellular vesicles of Ushers Syndrome patients

  Small RNA-Seq dataset of MicroRNA's found in tear extracellular vesicles (EVs) and hiPSC-derived retinal pigment epithelium (RPE) cells of Ushers Syndrome patients and control samples. 14 samples were isolated and assessed for quality before preparing libraries using the miReasy and TruSeq Small RNA Library Preparation Kit. Sequencing was performed on the Illumina NextSeq 2000 platform, generating paired end FASTQ files.

  Dataset EGAD50000001709

• Profiling of gene expression and epigenomics in the fetal brain

  scRNA-seq and Cut&Tag from a sample of the human fetal brain. To compare neurogenesis in the primary human brain with that in organoids, we profiled transcriptome and chromatin accessibility (10X multiome) as well as bulk Cut&Tag of histone modifications H3K27me3, H3K27ac and H3K4me3. We used a human brain sample from GW 19 for all experiments.

  Dataset EGAD50000000225

• Valid reads

  Valid reads obtained after analyzing in situ Hi-C data of 16 normal B cells (3 naive B cells, 3 germinal center B cells, 3 plasma cells, and 3 memory B cells, together with a merge file for each subpopulation), 7 chronic lymphocytic leukemias (2 unmutated IGHV and 5 mutated IGHV), and 5 mantle cell lymphomas (2 conventional and 3 leukemic non-nodal).

  Dataset EGAD00001006486

• Single-cell Transcriptomic and Immune Receptor Profiling of PBMCs from Dengue-Infected Individuals with Varying Disease Severities

  This dataset comprises single-cell RNA sequencing (scRNA-seq) and immune receptor (TCR/BCR) profiling of peripheral blood mononuclear cells (PBMCs) collected from individuals infected with dengue virus (DENV) exhibiting different clinical severities: asymptomatic dengue (AD), dengue fever (DF), and dengue hemorrhagic fever (DHF). PBMCs were collected during the acute phase and, in some cases, during convalescence. The data provide a resource for understanding protective versus pathogenic immune responses in dengue infection.

  Dataset EGAD00001015634

• Decoding Human Endogenous Retrovirus Expression in Liver Metastatic Colorectal Cancers: Implications for Diagnosis and Prognosis

  The association between Human Endogenous RetroVirus (HERV) expression and cancer can be considered to both reflect the epigenetic deregulation of cancer and facilitate oncogenesis through its promoter/enhancer action on genes. More than 50% of colorectal cancers develop liver metastases and HERV has never been studied in this setting. We collected 400 RNAseq samples from more than 200 patients with primary and liver metastases from published and unpublished databases. We corroborated our findings with tandem mass spectrometry from primary colorectal cancer and single-cell RNAseq from liver metastatic colorectal cancer (lmCRC). We identified global stability in HERV expression between liver metastases and primary colorectal cancers, suggesting an early oncogenic footprint. Therefore, we proposed a list of seventeen HERV loci for lmCRC characterization with ERV-derived peptides but no expression in normal tissues. Among them, we discovered six prognostic markers after surgical resection of lmCRC. Four of them, HERVH_Xp22.32a, HERVH_20p11.23b, HERVH_13q33.3, HERVH_13q31.3, showed poor prognostic value when expressed (log-rank p-value 0.028, 0.0083, 9e-4, 0.05, respectively). HERVH_Xp22.2c (log-rank p-value 0.032) and HERVH_8q21.3b (only in multivariate models) were associated with better prognosis when expressed. These markers showed a cumulative effect on survival when expressed. Some HERVs were associated with decreased cytotoxic immune cells and most of them correlated with cell cycle pathways. Our findings provide new insights into lmCRC classification and suggest novel prognostic biomarkers and potential therapeutic targets.

  Study EGAS50000000307

• Barcelona kids with melanoma

  This set of samples is composed of eight young people (7-16 years old) that have developed melanoma with first-degree relatives that have also developed cancer, which suggests a genetic component to their disease. Here we want to sequence these samples in order to find the causative mutations. As these samples do not carry any of the high-penetrance mutations known to date, finding the genes(s) responsible will offer new insights into the genetic mechanisms underlying predisposition to melanoma.

  Dataset EGAD00001002198

• XP patients NGS data collection from Gustave Roussy.

  This dataset is composed of NGS data from 33 XP patients studied by WGS.

  Dataset EGAD00001009693

• Genetic Association Studies in the Solomon Islanders

  The goal of this study was to determine the genetics underlying blond hair in the Solomon Islands, which has the highest prevalence of blondism outside of Europe. Participants in the study were of self-reported Solomon Islands ancestry and were 6-36 years of age at enrollment. Individuals with blond (N = 43) and dark hair (N = 42) were selected, approximately matched for age, sex and local geography, and spectrophometric measurements of hair pigmentation were made as a single measurement taken from hair at the crown. Individuals with gray, white, thin, bleached or artificially colored hair were excluded from analysis. All 85 participants were evaluated in a genome-wide scan to detected association to hair pigmentation in the Solomon Islands.

  Study phs000493

• Screening for tryptophan conversion in human stool samples

  The goal of this study was to compare the tryptophan metabolism of different human fecal microbiota. To this end we enriched human stool samples in culture medium and measured growth and metabolite concentrations after 48h of culture. We quantified the consumption of tryptophan and the production of typical tryptophan derivaties.

  Study EGAS50000000548

• Transcriptome data of WS patients and controls

  Fibroblasts of 4 WS patients and 4 sex matched controls were transformed into iPSCs, which were then differentiated to Neuroepithelial Stem Cells (NESCs), and further differentiated into neurons. RNA sequencing was performed at the NESC stage and after 4 and 8 weeks of neural development for 3 replicates per individual using the Illumina TruSeq stranded library polyA method on the NovaSeq6000 platform at NGI Stockholm. The data was preprocessed using the nf-core/rnaseq (https://nf-co.re/rnaseq) that includes quality control, data cleaning, and read alignment to GRCh38 (STAR, v2.6.1d)

  Dataset EGAD50000001728

• Establishing multiple omics baselines for three Southeast Asian populations in the Singapore Integrative Omics Study

  In this study, we established population reference measurements across multiple omic technologies and investigated the inter-population variations in each omic and phenotypic measurements in three major populations in Singapore. The measurements include genome-wide SNPs, gene probesets expression, lipid species and circulating miRNAs.

  Study EGAS00001002527

• Angiopredict: predicting response for bevacizumab treatment

  In ANGIOPREDICT, academic cancer biologists and industry-based biotechnology researchers worked with clinicians to identify biomarkers to predict whether individual metastatic colorectal cancer patients will respond positively to bevacizumab containing therapy. In this retrospective study, copy number profiles were determined using whole genome shallow sequencing, and progression free survival and treatment data was collected.

  Study EGAS00001002724

• Sequence data for study: Mobilization of tissue-resident memory CD4+ T lymphocytes from bone marrow and their contribution to a systemic secondary immune reaction

  Short Description: This study contains 7 RRBS samples, including 3 ex vivo CD4+ Trm (2 x spleen and 1 x bone marrow) and 4 blood tetanus (TT) and measles (Me) antigen-reactive memory CD4+ cells before and one day post DTaP (diphtheria-tetanus-pertussis) and MMR (measles-mumps-rubella) vaccination, respectively (1 x tetanus D0, 1 x tetanus D1, 1 x measles D0, 1 x measles D1). Technology: Illumina HiSeq 2500 Filetype: fastq format

  Dataset EGAD00001007886

• Dataset for identification of the dismal subtype of B-ALL with dysregulation of CDX2 and UBTF

  WGS (tumor and germline samples) was performed to identify structural variants in the UBTF/CDX2 subgroup. RNA-seq was performed to detect gene fusion in the UBTF/CDX2 subgroup. HiChIP was performed to investigate 3D chromatin architecture and enhancer landscapes of representative patient samples and cell lines harboring Type I and II FLT3-PAN3 deletions and amplifications.

  Dataset EGAD00001008416

• Phase 2 Study of Nivolumab and Entinostat in Unresectable or Metastatic Cholangiocarcinoma and Pancreatic Adenocarcinoma

  The study was a single-center, open-label, phase II trial (registration no. NCT03250273) designed to evaluate the efficacy of entinostat in combination with nivolumab in patients with advanced pancreatic ductal adenocarcinoma (PDAC). The aim was to assess the objective response rate using RECIST v1.1 criteria as the primary endpoint. A total of 27 patients with advanced PDA were enrolled from November 2017 to November 2020. Their treatment involved a 14-day lead-in with entinostat monotherapy, followed by a combination with nivolumab. The study utilized several molecular technologies to assess immune profiles and tumor microenvironment (TME) changes: high-dimensional mass cytometry by time of flight (CyTOF), Luminex for chemokine analysis in plasma, multiplexed immunohistochemistry (mIHC), image cytometry-based quantification, bulk RNA sequencing analysis. The objective response rate (ORR) was 11% with three patients showing a partial response (PR). The median duration of response was 10.2 months. Grade ≥ 3 treatment-related adverse events (TRAEs) occurred in 63% of patients, with the most common being decreased lymphocyte count, anemia, hypoalbuminemia, and hyponatremia. Gene expression analysis showed an enrichment in inflammatory response signaling pathways with the combination treatment. RNA sequencing data with clinical and demographic patient information will be available through dbGaP. For expression summaries, please refer to GEO submission GSE248014.

  Study phs003615

• Single-Cell RNA-Seq Profiling of Peripheral Immune Responses to Severe Infection in Uganda

  We conducted a prospective observational study (RESERVE-U-2-TOR) of adults admitted to Tororo General Hospital in eastern Uganda with severe, undifferentiated infection (i.e., suspected sepsis). Peripheral blood mononuclear cells (PBMCs) were isolated from freshly collected heparinized whole-blood samples (4 - 5 mL) using a standard density-gradient protocol (STEMCELL Technologies). PBMCs were aliquoted, cryopreserved in CryoStor CS10 (STEMCELL Technologies), stored overnight at -80°C, and transferred to liquid nitrogen for longer-term storage. Upon thawing, viability was assessed using the Nexcelom Cellaca Cell Counter, and cells were diluted to optimal concentrations for loading onto the Chromium Controller (10X Genomics). Each sample targeted the capture of ~10,000 GEMs (gel bead-in-emulsions). Single-cell RNA libraries were prepared using the Chromium Single Cell 3' Reagent Kit v3.1 following the manufacturer's standard protocol. Libraries were quality-assessed using an Agilent TapeStation and quantified using both Qubit 2.0 Fluorometer (Invitrogen) and qPCR (Applied Biosystems). Sequencing was performed on the NovaSeq X Plus platform (Illumina) using a 28×91 read configuration per 10X guidelines, targeting ~50,000 reads per cell. Data from this study available through dbGaP include raw single-cell RNA-seq data generated from PBMC samples collected from a subset of RESERVE-U-2-TOR participants at study enrollment (N=8).

  Study phs004100

• scRNA-seq of LN and lymphoma stroma

  The activities of non-haematopoietic cells (NHCs), including mesenchymal stromal cells and endothelial cells, in lymphomas, reportedly underlie lymphomagenesis. However, understanding of lymphoma NHCs has been hampered by unexplained NHC heterogeneity, even in normal human lymph nodes (LNs). Here, we constructed a single-cell transcriptome atlas of >100,000 NHCs collected from 27 human samples, including LNs and various nodal lymphomas, revealing 30 distinct subclusters, including some that were previously unrecognized. Notably, this atlas was highly useful for comparative analysis with lymphoma NHCs, which revealed an unanticipated landscape of subcluster-specific changes in gene expression and interaction with malignant cells in follicular lymphoma NHCs, facilitating our understanding of stromal remodelling in lymphoma and potentially suggesting novel biomarkers. Our study largely updates NHC taxonomy in human LNs and pertains to analysis of disease status, providing a rich resource and deeper insights into LN and lymphoma biology and offering to advance lymphoma management and therapy.

  Study EGAS00001005732

• Comprehensive genomic and transcriptomic analysis of three synchronous primary tumours and a recurrence from a head and neck cancer patient

  Synchronous primary malignancies occur in a small proportion of head and neck squamous cell carcinoma patients. Here, we analysed three synchronous primaries and a recurrence from one patient, by comparing the genomic and transcriptomic profiles among the tumour samples and determining the recurrence origin. We found remarkable levels of heterogeneity among the primary tumours, and through the patterns of shared mutations, we traced the origin of the recurrence. Interestingly, the patient carried germline variants which might have predisposed him to carcinogenesis, together with a history of alcohol and tobacco consumption. Mutational signature analysis confirmed the impact of alcohol exposure, with Signature 16 present in all tumour samples. Characterisation of immune cell infiltration highlighted an immunosuppressive environment in all samples, which exceeded the potential activity of T cells. Studies such as the one described here have important clinical value and contribute to personalised treatment decisions for patients with synchronous primaries and matched recurrences.

  Study EGAS00001004857