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• WGS data subfolder HF3J5CCXY from multifocal ileal NETs study

  This dataset includes linked-read whole-genome sequencing data (subfolder HF3J5CCXY) for multifocal ileal tumor samples from one patient. Samples were sequenced using the 10x Genomics linked-read whole-genome sequencing (WGS) approach.

  Dataset EGAD00001008493

• The University of Hong Kong Colon Cancer Ganciclovir Study WGS Data

  Human clonal intestinal organoids were treated with 1µM MMF (Roche), 20 μM GCV (Hainan Poly Pharm Co Ltd), or in combinations (1 µM MMF + 20 μM GCV or 1 µM MMF + 40 μM GCV) continuously for 4-6 weeks. DNA was extracted after drug treatment. WGS was performed with 150 bp PE sequencing at 30X using an Illumina Novaseq sequencer.

  Dataset EGAD00001009667

• BCG Molecular Subtyping

  Dataset for the paper: Non-muscle Invasive Bladder Cancer Molecular Subtypes Predict Differential Response to Intravesical Bacillus Calmette-Guérin

  Dataset EGAD00001010065

• Neoantigen responses to Immunotherapy in Prostate Cancer

  To determine whether antigen-specific T cell responses can be elicited following treatment with ICT in cancers that have a low TMB, a clinical trial with ipilimumab (anti-CTLA-4) was conducted in 30 patients with metastatic castration-resistant prostate cancer (CRPC). We identified 2 distinct groups of patients divided by clinical outcomes, which consisted of a cohort with Favorable and Unfavorable outcomes. Compared to the Unfavorable cohort, the patients in the Favorable cohort were more likely to have higher intratumoral CD8 T cell density and/or IFN-γ response gene signature, including five patients who had antigen-specific T cell responses that were only detectable after ipilimumab therapy. Three patients had T cell responses against tumor-associated antigens (PSMA and PAP). Importantly, two patients with a relatively low TMB had T cell responses against unique neoantigens. Collectively, our data indicate that a subset of patients with metastatic prostate cancer benefit from ICTs, particularly those who have immunological biomarkers associated with effector T cell responses. Publication: Sumit K. Subudhi, Luis Vence, Hao Zhao, Jorge Blando, Shalini S. Yadav, Qing Xiong, Alexandre Reuben, Ana Aparicio, Paul G. Corn, Brian F. Chapin, Louis L. Pisters, Patricia Troncoso, Rebecca Slack Tidwell, Peter Thall, Chang-Jiun Wu, Jianhua Zhang, Christopher L. Logothetis, Andrew Futreal, James P. Allison and Padmanee Sharma, 2020, Neoantigen responses, immune correlates, and favorable outcomes after ipilimumab treatment of patients with prostate cancer. Science Translational Medicine, 01 Apr 2020:Vol. 12, Issue 537, eaaz3577DOI: 10.1126/scitranslmed.aaz3577. https://pubmed.ncbi.nlm.nih.gov/32238575/

  Study EGAS00001004050

• National Heart, Lung, and Blood Institute (NHLBI) Bench to Bassinet Program: The Pediatric Cardiac Genetics Consortium (PCGC)

  Multi-center, prospective observational cohort study of individuals with congenital heart defects (CHD). Phenotypic data and source DNA derived from 10,000 probands, parents, and families of interest are being collected to investigate relationships between genetic factors and phenotypic and clinical outcomes in patients with CHD.

  Study phs000571

• Nurminen et al ("GP2Men") Study Primary and Metastatic Prostate Cancer Whole Genome Sequence Data

  We used novel processing techniques to obtain whole genome data together with 3D anatomic and histomorphologic analysis in two men (GP5 and GP12) with high risk PrCa undergoing radical prostatectomy. A total of 22 whole genome-sequenced sites (16 primary cancer foci and 6 lymph node metastatic) were analyzed using evolutionary reconstruction tools and spatio-evolutionary models. Probability models were used to trace spatial and chronological origins of the primary tumor and metastases, chart their genetic drivers, and distinguish metastatic and non-metastatic subclones.

  Dataset EGAD50000000005

• Whole exome sequencing in patients with ALS and concomitant FTD lacking the C9orf72 repeat expansion

  Dac EGAC00001000656

• Effect of aging on chromatin accessibility and gene expression in immune cells, The Jackson Laboratory

  Dac EGAC00001000721

• The European MAPPYACTS trial: Precision Medicine Program in Pediatric and Adolescent Patients with Recurrent Malignancies

  Dac EGAC00001003276

• Genomic validation of the revised Bethesda criteria in terms of pathogenesis and oncologic significance

  Study EGAS00001003959

• Genotype data from 'Evidence of the interplay of genetics and culture in Ethiopia'

  Study EGAS00001005171

• Exome data from 154 patients with childhood or adolescent cutaneous melanoma

  This dataset contains sequence data from 154 patients in Australia diagnosed with cutaneous melanoma before the age of 20. Each patient was exome sequenced on the illumina platform. Generated sequence reads were aligned against version 19 of the human genome assembly and stored in bam files made available here.

  Dataset EGAD50000001868

• Single cell mRNA sequencing of CD11b cells from a primary GBM - SF 10345i

  We collected fresh tissue from an untreated GBM directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine after selection of CD11b+ cells using magnetic beads.

  Dataset EGAD00001003107

• Single cell mRNA sequencing of CD11b cells from a primary GBM - SF 10360i

  We collected fresh tissue from an untreated GBM directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine after selection of CD11b+ cells using magnetic beads.

  Dataset EGAD00001003108

• Single cell mRNA sequencing of CD11b cells from a primary GBM - SF 10592i

  We collected fresh tissue from an untreated GBM directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine after selection of CD11b+ cells using magnetic beads.

  Dataset EGAD00001003109

• Single cell mRNA sequencing of CD11b cells from a primary GBM - SF 10679iA

  We collected fresh tissue from an untreated GBM directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine after selection of CD11b+ cells using magnetic beads.

  Dataset EGAD00001003110

• Single cell mRNA sequencing of CD11b cells from a primary GBM - SF 10360i

  We collected fresh tissue from an untreated GBM directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine after selection of CD11b+ cells using magnetic beads.

  Dataset EGAD00001003111

• Chromosomally integrated HHV6 data of parent-infant pairs

  Raw data used in the analysis of chromosomally integrated HHV6 genomes in parent-infant pairs, generated by means of full viral genome sequencing by SureSelect target enrichment, in the context of a larger study investigating the relationship between HHV6 and adverse pregnancy outcome.

  Dataset EGAD00001004592

• Single cell mRNA sequencing of primary GBM - SF 10282

  We collected fresh tissue from an untreated GBM (SF10282) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells.

  Dataset EGAD00001002270

• Single cell mRNA sequencing of primary GBM - SF 10360

  We collected fresh tissue from an untreated GBM (SF10360) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells.

  Dataset EGAD00001002272

• Single cell mRNA sequencing of primary GBM - SF 10345

  We collected fresh tissue from an untreated GBM (SF10345) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells.

  Dataset EGAD00001002271

• Tumor evolutionary trajectories during the acquisition of invasiveness in early stage lung adenocarcinoma

  Genomic analysis between pre-invasive and invasive components of malignant pulmonary nodule (MPN) facilitates the description of lung adenocarcinoma (LUAD) evolutionary patterns. We conduct an analysis of gene-panel sequencing on 53 T1 stage LUAD cases, which extend the understanding of evolutionary trajectories during invasiveness acquisition in early LUAD.

  Dataset EGAD00001006457

• CCA Visium spatial transcriptomics data (4 CCA)

  Visium spatial transcriptomics (10X Genomics) performed on 4 CCA samples. Each sample has two paired-end sequencing runs: the first (I1 & I2) are a pair reading indexes; the second (R1 & R2) are a pair reading inserts, with R1 additionally reading 10X barcodes. For histology images, please contact authors.

  Dataset EGAD00001011997

• RNASeq of Calcoco2 in beta and fat cell lines

  Investigation of the function of Calcoco2 by knocking it down in beta and fat cell lines.

  Dataset EGAD00001008654

• Observational study on the immune responses acquired by COVID-19 convalescent individuals

  We performed whole exome sequencing and microarray genotyping analysis of rare disease A two patients. .....

  Study JGAS000563