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• Genomic determination for Homologous Recombination Deficiency (HRD) by shallow Whole Genome Sequencing (sWGS)

  Genomic determination for Homologous Recombination Deficiency (HRD) by shallow Whole Genome Sequencing (sWGS) with shallowHRD (PMID : 32315385) on 55 triple-negative breast cancer Patient Derived-Xenograft (PDX) treated with platinum.

  Study EGAS00001005926

• Sequencing data for Hepatoblastoma samples

  This dataset contains DNA sequencing data for twelve hepatoblastoma tumor samples, four of which have matched normals. Nine of the samples also have RNA sequencing data from the tumor sample. The dataset comprises six samples from patient tissues and six from cell lines; see metadata for details.

  Dataset EGAD00001006621

• Learning from the thymic human cell atlas for T cell engineering: Paediatric RNA (2025-10-02)

  T cells are central to adaptive immunity and thus crucial for understanding and treating human disease. While extensively studied in model organisms, translating this knowledge to humans can sometimes be limited by their rapid cross-species evolution and diverse . This dataset contains all the data available for this study on 2026-03-10.

  Dataset EGAD00001015720

• Genome-wide genotype data for 1,433 ni-Vanuatu

  Here, we generated genome-wide genotype data for 1,433 contemporary ni-Vanuatu and assessed their fine-scale genetic structure, in order to address central questions about the settlement of western Remote Oceania.

  Study EGAS00001005910

• Personalized Treatment of Sezary Syndrome through a CTLA4:CD28 Fusion

  We sequenced two tumor and one normal whole genome libraries for a Sezary syndrome patient and also sequenced RNA libraries for each tumor. We identified a novel, highly expressed CTLA4:CD28 gene fusion that is predicted to results in a leading to stimulatory T-cell signaling in the presence of an inhibitory signal.

  Study phs000773

• Comprehensive molecular and clinicopathological profiling of salivary duct carcinoma

  Molecular targets and predictive biomarkers for prognosis in salivary duct carcinoma (SDC) have not fully identified. We conducted comprehensive molecular profiling to discover novel biomarkers for SDC. A total of 67 SDC samples were examined with DNA sequencing of 464 genes and transcriptome analysis in combination with the clinicopathological characteristics of the individuals.

  Study JGAS000534

• Clonal structure and oncogenic potential of liver cirrhosis tissues.

  Hepatocellular carcinoma (HCC) recurrently develops in cirrhotic liver composed of numbers of regenerative nodules (RNs). The biologic or genetic basis of RNs for hepatocarcinogenesis remains unclear at present. Thus, to uncover the basis of cirrhotic liver for multicentric tumorigenesis, we investigated the oncogenic potential of RNs in LC tissues using multi-omics analysis.

  Study JGAS000134

• Comprehensive genomic analysis of patient derived orthotopic xenograft model in primary central nervous system lymphoma

  The purpose of this study is to investigate genetic background of orthotopic xenograft cells and aseess consistency with parent tumor cells. For exome sequencing, we used two distinct PCNSL cells (YML9 and YML11). We also performed RNA sequencing for 7 PCNSL patient tumor cells to compare NF-kB pathway activation.

  Study JGAS000178

• An Organoid Biobank of Rare Human Neuroendocrine Neoplasms Enables Genotype-Phenotype Mapping

  We performed whole genome sequencing and RNA-sequencing of neuroendocrine neoplasm. The aim of this study was to provide genetic landscape of neuroendocrine neoplasm, to construct available animal models, and to engineer neuroendocrine neoplasm from normal colon epithelium. The reference genomes used are GRCh37 for whole genome sequencing and GRCh38 for RNA-sequencing.

  Study JGAS000237

• Comprehensive NGS Profiling to Enable Detection of ALK Gene Rearrangements and MET Amplifications in Non-Small Cell Lung Cancer

  We evaluate the analytical performance of the PGDx™ elio™ tissue complete assay, a 505 gene next-generation sequencing (NGS) tissue-based assay, that has now been FDA-cleared for use by physicians to help guide treatment decisions for cancer patients, using a NSCLC cohort of 38 patients.

  Study EGAS50000000010

• single nuclei multiomics (ATAC-RNA) of KOLF2.1J human induced pluripotent stem cells-derived differentiated dopaminergic neurons

  We processed nuclei from hIPSCs differentiated optimized protocols for generating dopaminergic neurons. Cells differentiated with a first iteration were RNA and ATAC-sequenced, to understand our protocol caveats to address for optimization. Cells differentiated with a second protocol and in vivo were RNA-sequenced to validate the identities of our cells.

  Study EGAS50000001418

• Single nuclei ATAC-Seq data from the human ganglionic eminences

  We performed the single nuclei Assay for Transposase-Accessible Chromatin with Sequencing (snATAC-Seq) to map potential regulatory genomic regions operating in individual cell populations of the human GE, using these to test for enrichment of schizophrenia common genetic variant liability and to functionally annotate non-coding variants associated with the disorder.

  Study EGAS50000000411

• Emirati Phased Diploid T2T Trio-Assembly of a Female Individual

  This dataset contains a telomere-to-telomere (T2T), trio-based genome assembly in FASTA format for a single female Emirati individual (proband) generated using parental information for accurate phasing. Sequencing data comprised PacBio HiFi (>60X per parent, >120X offspring), ONT ultra-long reads (>110X offspring), and Illumina short-read WGS (>100X for all three individuals). The offspring genome was assembled in a trio framework and finished with NTLink (initial scaffolding), RagTag (reference-guided refinement), and Quartett (gap filling). The resulting contiguous assembly serves as a high-quality, population-relevant reference suitable for downstream variant discovery and integration into the pangenome.

  Dataset EGAD50000001754

• scRNA-seq dataset, RCC

  scRNA-seq dataset for the study "Surgery in combination with immune checkpoint therapy as an effective treatment for patients with metastatic cancer." The dataset comprises 38 samples from 19 patients, with each pair includes a baseline (BL) sample and a post-biopsy or post-surgery sample. Each sample corresponds to an R1 (read 1) and an R2 (read 2) files (.fastq.gz) for paired reads. Beside procedure (biopsy or surgery), another important phenotype is response (PR and PD in this case, no SD for these patients), included in the description of the samples. The sequencing was performed using Illumina NovaSeq 6000 platform., as seen in the experiment description.

  Dataset EGAD50000000566

• Neutrophil myeloperoxidase as a functional biomarker for RSV severity: implications for in vitro therapeutic screening

  This study investigates gene expression profiles in neutrophils from healthy adult donors using RNA sequencing. The aim is to define baseline transcriptional variation in circulating neutrophils. Samples were collected from peripheral blood and processed under standardised conditions. The dataset provides a reference for studies of immune function and inflammatory disease.

  Study EGAS50000001844

• Benchmark and validation of whole exome sequencing of a trio and singleton

  Whole exome paired-end sequencing data was obtained for a trio and a fourth unrelated individual sequenced to high depth (95x) using a paired-end library with the Illumina HiSeq platform and aligned by BWA 0.5.9. The bam files were analysed and experimentally vaidated for the novel insertion of mobile elements.

  Study EGAS00001000852

• Y_phylogeny_haplogroupDE

  High-coverage whole genome sequences using Hiseq X for 4 individuals to investigate their Y chrosmosmes' relationship to the known phylogeny. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001002674

• Mutator phenotype and specific mutational signature explain an increased risk of hematological malignancies in patients with Xeroderma Pigmentosum

  In this study we report for the first time the unique collection of 6 leukemias and two sarcomas from XP-C. Comprehensive WGS-based mutational analysis provides genetic explanation for the increased incidence of leukemia in XP-C and describes an unique mutational process in internal tumors associated with NER deficiency.

  Study EGAS00001004511

• Mutation tracking in single cell RNA-Seq reveals consequences of subclonal evolution in acute myeloid leukemia

  Total bone marrow from AML patients was FACS index sorted with staining for Lineage markers (Lin), CD33, CD34, CD38, CD45RA, CD90, CD99, Tim3 and GPR56, and enrichment for Lin- and Lin-CD34+ cells. Single cells were subjected to a modified smart-seq2 protocol with targeting of mutant sites of interest ("MutaSeq”).

  Study EGAS00001003414

• Exome sequencing of patients with rare neurological disorders

  Exome sequencing of patients and their families with diverse rare neurological disorders. Some families have prior linkage data identifying a specific chromosomal interval or interest, other families do not have linkage data available. Many of these families come from special populations whose demography or preference for consanguineous marriages make them particularly tractable for genetic studies.

  Study EGAS00001000159

• CRISPR_Screening_of_Brazilian_Acral_Melanoma_Cell_Lines

  Perform CRISPR Screening in acral melanoma cell lines, using a genome-wide gRNA library, aiming to identify genes essential for their survival and proliferation. The results will aid the identification of key genes and pathways implicated in acral melanoma progression, paving the way to understand the disease and offer potential targets for precision therapies to this subtype of melanoma.

  Study EGAS00001008230

• A somatic reference standard for cancer genome sequencing.

  Paired PCR-free whole genome sequencing data of a matched metastatic melanoma cell line (COLO829) and normal across three lineages and across separate institutions, with independent library preparations, sequencing, and analysis. The data was generated with mean mapped coverages of 99X for COLO829 and 103X for the paired normal across three institutions. Overall, common events include >35,000 point mutations, 446 small insertion/deletions, and >6,000 genes affected by copy number changes. We present this reference to the community as an initial standard for enabling quantitative evaluation of somatic mutation pipelines across institutions.

  Dataset EGAD00001002142

• Smoking and the Vaginal Microbiome

  The focus of this study was to better understand the effects of cigarette smoking on the vaginal microbiome. There were two phases of the study, cross-sectional and longitudinal, conducted at the Center for Health Behavior Research at the University of Maryland School of Public Health. In the cross-sectional phase, 20 smokers and 20 non-smokers collected mid-vaginal swabs, measured their vaginal pH, prepared a vaginal smear on a slide for Nugent Gram stain analysis, and completed questionnaires about demographics, tobacco use, and reproductive and sexual health history. Smoking status was confirmed through self-report, carbon monoxide exhalation and saliva cotinine measures. Secretions from the mid-vaginal swabs were tested for presence/absence of HPV strains and GC-MS was used to quantify the levels of over 600 metabolites. In the longitudinal phase, 7 participants who were current smokers and motivated to quit smoking were recruited and followed for up to 12 weeks. On a daily basis, participants collected mid-vaginal swabs, measured their vaginal pH, and prepared a mid-vaginal smear on a slide for Nugent Gram stain analysis, and completed daily diaries on tobacco use and reproductive health. Carbon monoxide exhalation and saliva cotinine measures were collected at weekly clinical visits. In addition, participants had weekly behavioral counseling sessions about smoking cessation and used Nicoderm CQ patches to aid in quitting smoking. The self-collected vaginal swabs were used for DNA extractions,16s rRNA sequencing and measurement of metabolites in vaginal fluid.

  Study phs001386

• The Chromatin Landscape of Pathogenic Transcriptional Cell States in Rheumatoid Arthritis

  In this study, we characterized 24 rheumatoid arthritis (RA) synovial tissue chromatin classes (i.e., cell states defined by chromatin accessibility) across 5 cell types (T, B/plasma, myeloid, stromal, and endothelial). We also investigated the transcription factors that may regulate these chromatin classes, their connections to transcriptional cell states in a proposed superstate model, and their interplay with RA pathology through associations with histological parameters and risk variants.As part of the Accelerating Medicines Partnership (AMP) network, we obtained 18 synovial tissue samples from 14 RA and 4 osteoarthritis (OA) patients for this study. Samples were collected from 7 clinical sites. We performed a 10x single cell ATAC-seq experiment on each sample.We further collected synovial tissue samples from 11 RA patients and 1 OA patient from 2 clinical sites; each sample was used for a 10x single cell multimodal ATAC and Gene Expression experiment.For additional support of the proposed superstate model, we also collected peripheral blood mononuclear cells (PBMCs) from 4 RA patients, sorted for 4 populations (CD4+CD127-CD25hi Tregs, CD4+CD127-CD25int Tregs, CD4+CD25-PD1+CXCR5- TPH, CD4+CD25-PD1+CXCR5+ TFH), tagged each population with a hashing antibody, and pooled populations for one multimodal sequencing run.The FASTQ files are available for controlled access via dbGaP. Additional data can be found on Synapse.The presence of pooled subjects inflates the automatically-generated subject count; the actual consented subject count for this data is 34.

  Study phs003417

• Geriatric Oncology Database of genotypes and methylation, gene expression, clinical data, and survey results on psychosocial and physical conditions in Japanese elderly cancer patients to establish truly effective treatment strategy

  Owing to the advent of super-aged society, cancer mortality in Japan is forecasted to become an all-time high. The management of elderly patients with cancer is a serious health issue and the need for specific care guidelines for this population is critical in Japan. The significant individual differences in comorbidity, physical and mental functioning, and social problems among aging individuals are obstacles to the progress. The response to cancer treatment varies significantly among patients, even in the same stage of the same type of cancer. Older aged patients are still less likely to be offered participation in clinical trials, thus the number of clinical evidences is limited. The molecular mechanisms regulating the physiological process of ageing and senescence, and cancer are far from understood. To establish a truly effective treatment algorithm, we attempted to develop a geriatric oncology database for genotypes and methylation, gene expression, clinical data, and survey results on psychosocial and physical conditions in Japanese elderly cancer patients in this retrospective study. The genomic analysis was performed in 62, 106, and 173 cases, respectively for gastric, colon and lung cancers. The clinical data and survey results on psychosocial and physical conditions were collected from 166, 313, and 344 patients respectively for gastric, colon and lung cancers, and also collected from 357, 49, and 300 benign cases respectively for cardiovascular disorder, respiratory dysfunction, diabetes and nephropathy as the analysis control.

  Study JGAS000061