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• Assessment_of_genetic_and_epigenetic_variation_in_human_IPS_cells

  In order to progress human induced pluripotent stem cells (hiPSCs) towards the clinic, several outstanding questions must be addressed. It is possible to reprogram different somatic cell types into hiPSCs but it is unlcear whether some cell types carry through fewer mutations through reprogramming (either due to mutations present in the primary cells, or mutations accumulated during reprogramming). Through in depth analysis of hiPSCs generated from different somatic cells, it will be possible to assess the variation in genetic stability of different cell types.

  Study EGAS00001000492

• Genomic_landscape_of_liver_cirrhosis

  We are interested in the genomic landscape of liver cirrhosis and its potential manifestations for liver physiology and risk for hepatocellular carcinoma. Previous work in CASM has shown that there is a strong element of clonality within cirrhotic nodules and that some recurring mutations have been identified. However how this relates to the overall liver is not known and therefore by taking geographically disparate biospies, we aim to correlate our findings and make conclusions as to the characteristics of the overall genomic landscape.

  Study EGAS00001004329

• Whole genome sequencing of primary and metastatic Melanoma cases in an Australian cohort.

  Melanoma is the fourth most common cancer in Australia and the leading cause of cancer death in young adults. The Australian Melanoma Genome Project (AMGP) is analysing whole genomes from melanomas. We include the results of whole genome sequencing (WGS) for a number of datasets that include cutaneous, acral and mucosal melanoma subtypes.

  Study EGAS00001001552

• Whole Exome Sequencing of 15 Tumor/Normal pairs of inflammatory hepatocellular adenomas

  The French ICGC project on liver tumors is coordinated by Pr Jessica Zucman-Rossi and funded by Inca (French Institute for Cancer). The aim of the present project is to identify the catalog of somatic and germline mutations in liver tumors. The present series corresponds to 15 Tumor/Normal pairs of Whole Exome Sequencing (WES) of IHCA samples. Aligned bam files can be both in hg19 (CHC750T/CHC750N; CHC2189T/CHC2189N; CHC2615T/CHC2614N) or hg38 (other samples).

  Study EGAS00001003686

• Boson HCV infected liver bulk RNASeq study

  ACE2 is a receptor for the SARS-CoV-2 and differences in its expression may affect susceptibility to infection. In a genome-wide eQTL analysis using hepatitis C virus-infected liver tissue, we discovered that polymorphism in a type III interferon gene (IFNL4), which eliminates IFN-lambda-4 production, is associated with a two-fold increase in ACE2 RNA expression. Conversely, among genes negatively correlated with ACE2 expression, IFN-signalling pathways were highly enriched and ACE2 was downregulated after IFN-alpha treatment.

  Study EGAS00001004996

• Knee_OA_Functional_Genomics

  The aim of this work is to apply an integrated systems approach to understand the biological underpinnings of knee osteoarthritis that culminates in the need for total joint replacement (TJR). This study is a feasibility pilot that integrates functional genomics data from diseased and non-diseased tissues of OA patients who have undergone TJR. For each tissue, we characterised epigenetic marks (methylation), gene transcription (RNASeq) and expression (quantitative proteomics). We also generated genotype data on the HumanCoreExome array for each individual.

  Study EGAS00001001899

• Systematic evaluation of NIPT aneuploidy detection software tools with clinically validated NIPT samples

  Non-invasive prenatal testing (NIPT) is a powerful screening method for fetal aneuploidy detection, relying on laboratory and computational analysis of cell-free DNA. Although several published computational NIPT analysis tools are available, no comprehensive and direct accuracy evaluations of these tools is published. Here, we evaluate and determine the precision of five commonly used computational NIPT aneuploidy analysis tools, considering diverse sequencing depth (coverage), arbitrary sequencing read placement, and fetal DNA fraction on clinically validated NIPT samples.

  Study EGAS00001005323

• 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

• Multiomic profiling of pleomorphic rhabdomyosarcoma

  Rhabdomyosarcoma (RMS) describes rare soft-tissue tumors that exhibit features of skeletal muscle differentiation. The most common subtypes in children are alveolar and embryonal rhabdomyosarcoma, with the alveolar subtype characterized by PAX3/7 fusions. A lesser known and rarer subtype, pleomorphic rhabdomyosarcoma (PRMS), occurs most frequently in adults vetween the ages of 40 and 50. This pleomorphic subtype is often misdiagnosed and little is known about its molecular characterization. Here, we conducted comprehensive genomic, transcriptomic, and methylation profiling of these tumors.

  Study EGAS00001007230

• Exome sequencing of early and late passage Patient Derived Xenogratf Tumoroids with matched Patient Derived Xenogratfs and matched normal liver

  The breadth and depth at which cancer models are interrogated contribute to successful translation of drug discovery efforts to the clinic. In colorectal cancer (CRC), model availability is limited by a dearth of large-scale collections of patient-derived xenografts (PDXs) and paired tumoroids from metastatic disease, the setting where experimental therapies are typically tested. XENTURION is a unique open-science resource that combines a platform of 129 PDX models and a sister platform of 129 matched PDX-derived tumoroids (PDXTs) from patients with metastatic CRC, with accompanying multidimensional molecular and therapeutic characterization. This specific dataset is focused on a comparison of early and late passage tumoroids transcriptomes. In this study we focused our attention on early (passage 3) and late (passage 8-12) PDXTs with their matched PDXs and normal liver

  Study EGAS50000000185