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• Nuclease deficiencies alter plasma cell-free DNA methylation profiles (Mouse samples)

  The dataset contains sequencing data in wildtype, Dnase1-deficient and Dnase1l3-deficient mice. We performed 2 x 75bp paired-end whole genome bisulfite sequencing of pooled plasma cell-free DNA (cfDNA) and buffy coat genomic DNA. The effects of DNASE1L3 or DNASE1 deficiency on cfDNA methylation was explored in plasma of mice deficient in these nucleases.

  Dataset EGAD00001007751

• GEL WGS Comparison

  These samples are to be analysed with the CGP Developed cancer panel and the results will be compared with WGS data from 4 different comercial providers.

  Dataset EGAD00001000872

• Transcriptional mechanisms of resistance to anti-PD-1 therapy

  Purpose: To explore factors associated with response and resistance to anti-PD-1 therapy, we analyzed multiple disease sites at autopsy in a patient with widely metastatic melanoma who had a heterogeneous response.Materials and Methods: Twenty-six melanoma specimens (four pre-mortem, 22 post-mortem) were subjected to whole-exome sequencing. Candidate immunologic markers and gene expression were assessed in ten cutaneous metastases showing response or progression during therapy.Results: The melanoma was driven by biallelic inactivation of NF1. All lesions had highly concordant mutational profiles and copy number alterations, indicating linear clonal evolution. Expression of candidate immunologic markers was similar in responding and progressing lesions. However, progressing cutaneous metastases were associated with over-expression of genes associated with extracellular matrix and neutrophil function.Conclusions: Although mutational and immunologic differences have been proposed as the primary determinants of heterogeneous response/resistance to targeted therapies and immunotherapies, respectively, differential lesional gene expression profiles may also dictate anti-PD-1 outcomes.

  Study EGAS00001002195

• Dissecting features of epigenetic variants underlying cardiometabolic risk using full-resolution epigenome profiling in regulatory elements

  Sparse profiling of CpG methylation in blood by microarrays have identified epigenetic links to common diseases. We apply methylC-capture sequencing (MCC-Seq) in a clinical population of ~200 adipose tissue and matched blood samples (Ntotal ~400), providing high-resolution methylation profiling (>1.3M CpGs) at regulatory elements. We link methylation to cardiometabolic risk through associations to circulating plasma lipid levels and identify lipid-associated CpGs with unique localization patterns in regulatory elements. We show distinct features of tissue-specific versus tissue-independent lipid-linked regulatory regions by contrasting with parallel assessments in ~800 independent adipose tissue and blood samples from the general population. We follow-up on adipose-specific regulatory regions under (1) genetic and (2) epigenetic (environmental) regulation via integrational studies. Overall, the comprehensive sequencing of regulatory element methylomes reveals a rich landscape of functional variants linked genetically as well as epigenetically to plasma lipid traits.

  Study EGAS00001003415

• RNA Fusion Panel

  RNA extracted from FFPE tumour samples 368, 455, 503, and 521, sequenced using the TruSight RNA Fusion Panel

  Dataset EGAD50000000272

• ParityImmune

  Blood transcriptome from women participating in the Norwegian Women and Cancer study (NOWAC)

  Dataset EGAD00010001412

• RNA-Seq Medulloblastoma data

  RNA-Seq data from 12 medulloblastoma samples, all group 4 medulloblastomas. The data consists of BAM files aligned using STAR

  Dataset EGAD00001010850

• Single cell RNA-Seq of Clear Cell Sarcoma of the Kidney

  Dataset EGAD00001007498

• Myeloma XI trial data

  The dataset contains WGS and RNA-seq from Myeloma XI trial

  Dataset EGAD00001005491

• Tumor-derived exosomes modulate PD-L1 expression in monocytes

  Small RNA expression profiles of the blood plasma-derived exosomes from B-cell chronic lymphocytic leukemia patients

  Dataset EGAD00001003230