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• Whole-genome bisulfite sequencing analysis of low-grade astrocytomas in the ICGC PedBrain Tumor Project

  Pilocytic Astrocytoma (PA) is the most common pediatric brain tumor. While genome and transcriptome landscapes are well-studied, data of the complete methylome, tumor cell composition and immune infiltration are scarce. We generated whole genome bisulfite sequence data (WGBS) of nine PAs to find evidence for a link of focal methylation differences and differential gene expression to immune infiltration.

  Study EGAS00001004019

• Exome sequencing of Fibromyalgia patients

  Fibromyalgia is a complex disorder characterized by increased sensitivity to pain and extreme tiredness. It affects mostly women, and its causes are unknown. In this study we have performed exome sequencing of 87 fibromyalgia cases, including some sibling pairs, to perform rare variant association analysis and identify fibromyalgia risk factors. A few of the included samples have been also included in a previous GWAS study.

  Study EGAS00001003826

• Transcriptional changes in GBM through therapy

  Primary glioblastoma (GBM) tumours recur following therapy, owing to treatment resistance mechanisms in unresectable cells. We have sequenced RNA from paired primary and locally recurrent GBM tumours to begin characterising therapy resistant cells and thereby infer the mechanisms by which they evaded treatment. Exome sequencing data from these samples were included in the first data release from the Glioma Longitudinal AnalySiS (GLASS) consortium

  Study EGAS00001003790

• PAH sequencing study

  The Cohort study of idiopathic and heritable PAH is an observational, prospective and longitudinal study of patients with idiopathic and heritable PAH. Follow-up information is collected as a part of routine clinical care every six months. The study allows recruitment of both incident and prevalent cases. Patients consented to the study agreed to have blood taken for next-generation sequencing and other omics studies.

  Study EGAS00001005532

• Molecular landscape of blastic plasmacytoid dendritic cell neoplasm

  Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is an aggressive malignancy assumed to originate from plasmacytoid dendritic cells (pDCs), which mostly affects the skin, bone marrow and lymph nodes and sequentially other organ systems. We applied paired WES/RNA-seq combined with genome-wide copy-number analysis to characterize 47 BPDCN patients regarding mutational drivers, cytogenetic aberrations and gene-expression profiles.

  Study EGAS00001006166

• Mutational signatures in normal tissues of patients treated with clinical stage G-quadruplex binder CX5461

  Drug induced photoreactions following exposure to UVA have been documented for several therapeutic compound classes, including psoralens and fluoroquinolones. We used deep (~80X) whole genome sequencing to examine the mutagenic spectrum of CX5461, quinolone-derived small molecule, in normal tissues of cancer patients undergoing treatment. We compared the distribution of somatic base substitutions and short indels from skin biopsies taken from non-sun exposed areas pre and post CX5461 exposure of patients. To further characterize the mutational pattern of CX5461 photoreactivity, we compared mutational profiles of human retinal pigment epithelial cells exposed to UVA, CX5461, or a combination of both UV and CX5461.

  Dataset EGAD50000001640

• Targeted DNA sequencing and mRNA sequencing data from patients with peritoneal metastasis from colorectal cancer

  Patients with peritoneal metastasis from colorectal cancer (PM-CRC) have inferior prognosis and respond particularly poorly to chemotherapy. This study aims to identify the molecular explanation for the observed clinical behavior and suggest novel treatment strategies in PM-CRC. Tumor samples (230) from a Norwegian national cohort undergoing surgery and hyperthermic intraperitoneal chemotherapy (HIPEC) with mitomycin C (MMC) for PM-CRC were subjected to targeted DNA sequencing, and associations with clinical data were analyzed. mRNA sequencing was conducted on a subset of 30 samples to compare gene expression in tumors harboring BRAF or KRAS mutations and wild-type tumors.

  Dataset EGAD50000000593

• RAF1 extrachromosomal DNA amplification confers acquired erlotinib resistance in NSCLC cell model

  Despite their clinical significance, EGFR-directed therapies inevitably encounter drug resistance. This study demonstrates that ecDNA-mediated RAF1 amplification reactivates MAPK signaling independently of mutant EGFR, contributing to erlotinib resistance in EGFR-mutant NSCLC cell models. This finding identifies oncogenic amplification by ecDNA as a novel mechanism leading to erlotinib resistance, opening new avenues for therapeutic strategies in NSCLC.

  Study EGAS50000001832

• Genetic regulation of gene expression in human brain cell types

  We leveraged single nuclei RNA-seq from 192 human brain samples to map cis-eQTLs in 8 brain cell types. We found extensive cell-type specific genetic effect on gene expression and integrated our results with GWAS to identify putative novel risk genes for brain disorders and the cell types in which the disease mechanisms are likely active.

  Study EGAS00001006345

• Transcriptomes_of_human_lymphocytes

  In this study we will compare the single cell transcriptomes of immune cells from asthmatics responding to steroids, those refractory to steroids, and a control population.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001001755