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• ENU_LS_411N_TripleTherapy

  BRAF V600E colorectal cancers do not respond to the only currently FDA approved targeted therapy for CRC. There is currently a trial underway in the UK recruiting V600E CRC patients for treatment with a triple therapy combination of Cetuximab, Trametinib and Dabrafenib. We have mutagenized a pool of V600E CRC cell lines and treated with this triple therapy to select out drug resistant clones. We will now sequence these drug resistant clones with the aim of identifying common point mutations engendering resistance to this new therapy.

  Study EGAS00001001777

• Single-cell RNA sequencing reveals cell-type specific eQTLs in peripheral blood mononuclear cells

  This proof-of-concept study shows that single-cell RNA sequencing in ~25,000 peripheral blood mononuclear cells (PBMCs) of 45 donors allows for the identification of cell type-specific cis expression quantitative trait loci effects (cis-eQTLs). Moreover, the significant top-eQTL effects show consistent allelic direction (94%) with previously published whole blood deepSAGE data. These cell type-specific eQTLs may give us additional insight into the downstream consequences of genetic risk factors for immune-mediated diseases.

  Study EGAS00001002560

• Solve-RD Solving the Unsolved Rare Dieseases

  Solve-RD – solving the unsolved rare diseases is a research project funded by the European Union’s Horizon 2020 research and innovation programme under grant agreement No 779257 from 1 January 2018 to 31 March 2024. Six European Reference Networks (ERNs; ERN-RND, -ITHACA, -EuroNMD, -GENTURIS, -RITA and -EpiCare) contributed data and samples to one or more of the four cohorts for data re-analysis and novel omics. For more information see https://solve-rd.eu/results/solve-rd-data/.

  Study EGAS00001003851

• Platelet response in aspirin adherent pregnant women

  We conducted an unbiased genome-wide assessment of genomic factors that may influence response to low-dose aspirin in pregnant women at high risk of pre-eclampsia in two pregnancy cohorts: Liverpool (n=91) and Dublin (n=91). We applied UK Axiom microarray technology for GWAS investigations. We specified tight phenotyping with COX-selective urinary 11-dehydrothromboxane B2 (pg/mg creatinine) and accounted for adherence/platelet exposure to aspirin by detection of aspirin’s principal urinary metabolite, SUA, with nuclear magnetic resonance (NMR).

  Study EGAS00001005188

• Acquiring and sequencing of all 24 single human chromosomes

  Haplotype phased whole genome sequencing of individuals is a technical challenge when family members are unavailable for determining chromosome of origin and variant linkage. Completely phasing genome sequences with single chromosomes has been shown to be feasible however amplifying all the single chromosomes for subsequent whole genome sequencing has been proposed but not performed to date. We acquired single chromosome of one of each of the autosomes and sex chromosomes to assess the feasibility of this sequencing library template preparation process.

  Study EGAS00001003300

• Characterization of MCSP+ melanoma DCC and MelDCC lines

  To dissect the sequence of genotypic and phenotypic progression during early metastatic colonization, we searched for the earliest detectable disseminated cancer cells (DCC) and identified MCSP+ melanoma cells as strong candidates for metastasis founder cells (MFC) in lymph nodes. We isolated MCSP+ DCC from various stages of metastatic colony-formation, performed scRNA-seq and unravelled their phenotypic progression. Further we performed bulk sequencing on patient-derived DCC models (MelDCC) and showed that they exhibit an immunosuppressive activity on CD8 T cells.

  Study EGAS00001006702

• Molecular analysis of cancer genomes in children with Lynch syndrome: exploring causal associations

  Lynch syndrome (LS) predisposes to cancer in adulthood and is caused by heterozygous germline variants in a mismatch repair (MMR) gene. Recent studies show an increased prevalence of LS among children with cancer, suggesting a causal relationship. For LS-spectrum (LSS) cancers, including high-grade gliomas and colorectal cancer, causality has been supported by typical MMR-related tumor characteristics, but for non-LSS cancers, causality is unclear. This dataset contains 5 patients with Lynch Syndrome from the INFORM registry.

  Study EGAS00001007146

• WGBS data of solid liver tumor DNA, and WGBS data of cell-free DNA derived from human blood, for CancerDetector study

  The blood samples of four liver cancer patients and four healthy people, and the solid liver tumor samples of two liver cancer patients are collected for this dataset. Blood samples were centrifuged first at 1,600 × g for 10 minutes, and then the plasma was transferred into new micro tubes and centrifuged at 16,000 × g for another 10 minutes. The plasma was collected and stored at -80⁰C. CfDNA was extracted from 5 ml plasma using the Qiagen QIAamp Circulating Nucleic Acids Kit and quantified by Qubit 3.0 Fluoromter (Thermo Fisher Scientific). Bisulfite conversion of cfDNA was performed by using EZ-DNA-Methylation-GOLD kit (Zymo Research). After that, Accel-NGS Methy-Seq DNA library kit (Swift Bioscience) was used to prepare the sequencing libraries. The DNA libraries were then sequenced with 150bp paired-end reads.

  Dataset EGAD00001004317

• 160 WES and 25 WGS for HBV related HCC, and 15 WES for ICC belongs LICA-CN

  160 WES and 25 WGS for HBV related HCC, and 15 WES for ICC belongs LICA-CN

  Dataset EGAD00001003205

• Strand-specific mRNA-Seq assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, as part of the International Human Epigenome Consortium.

  Strand-specific mRNA-Seq assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001227