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• Screening_for_human_epigenetic_variation_at_CpG_islands

  Many human characteristics, including susceptibility to disease, are determined genetically. An unexplored alternative to such genetic determination concerns epigenetic mechanisms such as DNA methylation. CpG islands (CGIs) are generally constitutively hypomethylated, however there are circumstances in which they become heavily methylated and, when coincident with a gene promoter, this invariably causes transcriptional silencing. CGI methylation occurs in normal tissues during processes such as X-inactivation, but abnormal patterns of methylation have also been implicated in disease. The vast majority of evidence relates to cancer, where silencing of multiple genes in this way appears to be a causal contributor to the cancer state. To address the role and extent of CGI methylation in ‘normal’ and diseased cells we applied MBD-affinity purification in conjunction with next generation sequencing in a panel of human brain autopsy samples. These samples represent a panel of individuals as well as specific brain regions and neurological pathologies.

  Study EGAS00001000074

• 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

• Whole_Exome_sequencing_in_a_large_IBD_pedigree

  We perform whole exome sequencing on samples from a large IBD pedigree. The selected samples are from more distantly related family members (healthy and with IBD) and a set of matched population (Ashkenazy Jewish ancestry) samples.

  Study EGAS00001000240

• 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

• 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

• 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