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• DNA methylation array study for 7 pairs of primary NSCLCs and distant metastases

  This study is to compare DNA methylation profiles between primary NSCLCs and paired distant metastases.

  Study EGAS00001004079

• The HLA-DQβ1 insertion is a strong achalasia risk factor and displays a geospatial north-south gradient among Europeans

  Idiopathic achalasia is a severe motility disorder of the esophagus and is characterized by a failure of the lower esophageal sphincter to relax due to a loss of neurons in the myenteric plexus. Most recently, we identified an 8 amino acid insertion in the cytoplasmic tail of HLA-DQβ1 as strong achalasia risk factor in a sample set from Central Europe, Italy, and Spain. Here, we tested whether the HLA-DQβ1 insertion also confers achalasia risk in the Polish and Swedish population. We could replicate the initial findings and the insertion shows strong achalasia association in both samples (Poland P = 1.84×10-04, Sweden P = 7.44×10-05). Combining all five European data sets – Central Europe, Italy, Spain, Poland, and Sweden – the insertion is achalasia associated with Pcombined = 1.67×10-35. In addition, we observe that the frequency of the insertion shows a geospatial north-south gradient. The insertion is less common in northern (around 6-7% in patients and 2% in controls from Sweden and Poland) compared to southern Europeans (around 16% in patients and 8% in controls from Italy) and shows a stronger attributable risk (AR) in the southern European population. Our study provides evidence that the prevalence of achalasia may differ between populations.

  Study EGAS00001001515

• Myocardial Infarction Genetics Exome Sequencing Consortium: German Heart Center in Munich

  The Munich-MI study is a case-control cohort study recruited at the German Heart Center in Munich, Germany. It is focused on understanding the genetic contributors to early myocardial-infarction (MI) in the German population. All exome sequencing was performed at the Broad Institute of Harvard and MIT; samples sequence capture was performed using Illumina's ICE Capture reagent and sequencing was performed on an Illumina HiSeq 2000 or 2500.

  Study phs000916

• Mutational Landscape of MCPyV-Positive and MCPyV-Negative Merkel Cell Carcinomas

  Merkel cell carcinoma (MCC) is an aggressive neuroendocrine carcinoma of the skin most commonly found on the sun-exposed skin of older Caucasian adults. Roughly one-third of patients with MCCs die of the disease; therefore, MCC is the most lethal skin cancer on a case-by-case basis. 49 cases were studied, and putative cancer driver gene mutations and tumor antigens in both MCPyV-negative and MCPyV-positive MCCs were identified.

  Study phs002515

• Study of Cutaneous Biology of Cutaneous T Cell Lymphoma

  This study is designed to help us understand the biological factors that contribute to the development of Cutaneous T Cell Lymphoma (CTCL) through the use of single-cell -omics technologies. The data that will be available include single-cell RNAseq and paired single-cell TCRseq data from the primary lesions of CTCL patients.The number of consented subjects listed here is artificially inflated by one to account for the pooling of all subjects.

  Study phs002717

• OTOF mutation analysis with massively parallel DNA sequencing in 2,265 Japanese sensorineural hearing loss patients.

  The OTOF gene, encoding otoferlin, is reported to be one of the major causes of non-syndromic recessive sensorineural hearing loss, and is also reported to be the most common cause of non-syndromic recessive auditory neuropathy spectrum disorder (ANSD). In the present study, we performed OTOF mutation analysis using massively parallel DNA sequencing (MPS) to reveal the frequency and clinical characteristics of OTOF-related hearing loss in a large hearing loss population.

  Study JGAS000166

• Analytical study of protein function and RNA expression involved in predicting treatment efficacy and adverse event development in lung cancer radiotherapy.

  The purpose of this study is to elucidate the functions of DNA repair proteins and RNA expression that are involved in the therapeutic efficacy and adverse events of radiotherapy for lung cancer at our hospital. In particular, this is an exploratory study to identify proteins and RNAs involved in the expression of proteins that are likely to be involved in the prediction of radiotherapy response and adverse events.

  Study JGAS000545

• Development of blood-based biomarkers for precision medicine in castration-resistant prostate cancer

  Cell-free DNA (cfDNA) testing is emerging as a tool for cancer precision medicine. However, little is known about the clinical significance of low-frequency variants detected in circulating cell-free tumor DNA (ctDNA) from castration-resistant prostate cancer (CRPC) patients. We conducted targeted sequencing of cfDNA and paired leukocyte DNA from CRPC patients using molecular barcodes, and ctDNA variants with a variant allele frequency ??? 0.1% were detected using an in-house pipeline.

  Study JGAS000330

• Deciphering the aggressive nature of morphoeic basal cell carcinoma

  Morphoeic basal cell carcinoma (mBCC) has a high risk of local recurrence compared to the more indolent nodular subtype reflected by a different set of driver mutations including FLNB and HECTD4. Surrounding mBCC stroma is abnormal, containing mutations such as EPHA3. Hedgehog pathway over-expression is seen in both the tumour and stroma of morphoeic tissue with the latter potentially being partly responsible for its aggressive nature and risk of recurrence.

  Study EGAS00001001915

• Breast Cancer Follow Up Series

  This study's purpose is to use data generated in whole genome and exome Breast Cancer sequencing to target specific areas in multiple other Breast Cancer samples. These areas will then be subjected to PCR in multiple cases, tagged and then pool the resultant amplicons. These amplicons will then be sequenced on the Illumina GAII. This is hoped to show the prevalence of previous findings in multiple individuals in a high throughput method.

  Study EGAS00001000002

• Sequencing of heritable Bleeding and Platelet Disorders

  The BRIDGE-BPD study aims to discover new causal genes for Bleeding and Platelet Disorders (BPD) by high throughput sequencing using cluster analyses based on improved and standardized deep phenotyping of cases. BPD is one of the 13 Rare Disease projects under the NIHR BioResource Rare Diseases BRIDGE consortium, which is a collaboration aiming to discover the genetic sequence variants underlying unresolved inherited disorders and to improve identification of already identified high penetrance variants.

  Study EGAS00001001172

• TRACERx 100: RNAseq data from the first 100 TRACERx tumours

  TRACERx (TRAcking Cancer Evolution through therapy (Rx)) is a prospective cohort study designed to investigate intratumor heterogeneity (ITH) in relation to clinical outcome, and to determine the clonal nature of driver events and evolutionary processes in early stage non-small cell lung cancer (NSCLC). This study looks at the multi-region RNAseq data from the TRACERx100 cohort with high enough quality RNA available. There is RNAseq data from 164 regions (64 patients).

  Study EGAS00001003458

• Genomic landscape of poorly differentiated thyroid carcinoma

  Poorly differentiated thyroid carcinoma (PDTC) is a rare and aggressive subtype of thyroid cancer with limited molecular characterization. This study aims to define the somatic mutational landscape of PDTC using whole-genome sequencing. Paired tumour and matched normal blood samples were collected from six patients undergoing surgery. The overarching goal is to identify recurrent mutations, structural variants, and other genomic alterations associated with tumour aggressiveness and poor clinical outcomes.

  Study EGAS50000001134

• IMMUcan Lung NSCLC2 cohort

  The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes patients with non-small cell lung cancer who had surgical resection. This is a subcohort of the EORTC SPECTAlung study. Comprehensive profiling data are integrated with longitudinally collected clinical information. Cellular profiling of the same tumor samples was performed using multiplex immunofluorescence imaging, imaging mass cytometry, and H&E staining.

  Study EGAS50000001558

• Exome_sequencing_of_a_cohort_of_Rett_syndromelike_patients

  The aim of the project is the definition of the molecular defect in a cohort of Rett-like patients negative for mutations in known disease genes. To this aim, a number of unrelated trios (patients plus parents) will be analysed by exome sequencing. 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 EGAS00001002059

• Whole genome and RNA sequencing of paediatric glioblastoma in the ICGC PedBrain project

  Paediatric glioblastoma (pedGBM) is characterised by substantial intertumoural heterogeneity. In order to identify the genetic lesions underlying tumourigenesis, we analysed whole genomes and transcriptomes of pedGBMs and in vitro model systems by next generation sequencing. Novel fusions of the receptor tyrosine kinase MET lead us to investigate targeted therapy using MET inhibitors. This study is part of the International Cancer Genome Consortium PedBrain Tumor Project (ICGC PedBrain, http://www.pedbraintumor.org/).

  Study EGAS00001001139

• Sequencing of liver cancer cell lines

  Liver cancer is a dreadful disease with limited therapeutic options. How to translate genomic findings into biomarkers and precision treatment is challenging. A large cell line-based platform was established, termed as Liver Cancer Model Repository. Heterogeneities in patients were faithfully recapitulated by 81 liver cancer cell lines at genomic and transcriptomic levels. This platform provides a rich resource and models to study cancer drivers and drug responses in liver cancer.

  Study EGAS00001002237

• Molecular subtypes of malignant peritoneal mesothelioma

  Malignant Peritoneal Mesothelioma (PeM) is a rare but frequently fatal cancer that originates from the peritoneal lining of the abdomen. Standard treatment of PeM is limited to cytoreductive surgery and/or chemotherapy, and no targeted therapies for PeM yet exist. This study performs comprehensive integrative analysis of genome, transcriptome, and proteome of treatment-naive PeM tumors with the aim of identifying mesothelioma-related molecular alterations and potentially identifying novel treatment strategies.

  Study EGAS00001002820

• RNAseq of medulloblastoma data (MB_COMICS cohort)

  Medulloblastoma (MB) is the most common malignant brain tumor in children. It is a neuroectodermal tumor located in the cerebellum. International consensus recognizes four distinct subgroups of MBs including Wingless (WNT), Sonic Hedgehog (SHH), Group 3 (G3), and Group 4 (G4) with distinct molecular characteristics, prognoses, and mortality rates in patients. Here, we have compiled and evaluated a large international MB cohort for which we generated transcriptomic data (RNAseq) for 208 primary MB patient samples.

  Study EGAS50000000410

• MOSAIC - Multi-Omics Spatial Atlas In Cancer

  MOSAIC is a collaborative initiative founded by Owkin, Lausanne University Hospital (CHUV), Charité Universitätsmedizin Berlin, University Hospital Erlangen (UKER), Gustave Roussy Institute in Paris, and University of Pittsburgh. The goal of MOSAIC is to build the largest collection of spatial omics data in cancer. By integrating comprehensive high quality clinical annotations with advanced deep profiling techniques, MOSAIC aims to uncover novel cancer subtypes and identify key drug targets and biomarkers within them.

  Study EGAS50000000689

• Whole-exome sequencing profiling of patients with metastatic prostate cancer at VHIO

  Metastatic prostate cancer (mPC) is enriched for homologous recombination repair (HRR) gene alterations, which have prognostic and predictive value. Routine clinical implementation of next-generation sequencing (NGS) is still limited. We investigated the association between genomic and functional loss of HRR, using NGS and a RAD51 immunofluorescence (RAD51-IF) iprimary or metastatic biopsies from patients with stage IV prostate cancer. Whole-exome sequencing was pursued for paired tumor-normal samples.

  Study EGAS50000000736

• Whole genome sequencing of patients affected by acute intermittent porphyria

  Acute intermittent porphyria (AIP) is an hereditary rare metabolic disorder of incomplete penetrance, affecting the biosynthesis of heme. IAP is an autosomal dominant disorder, resulting in a substantial reduction of the activity of the hydroxymethylbilane synthase coding gene (HMBS). Most HMBS mutation carriers are asymptomatic and only between 10% and 20% of patients present acute attacks of the associated symptoms. Here, we sequenced whole genomes of 16 AIP patients.

  Study EGAS00001004999

• glioblastoma single cell RNAseq

  Understanding the cellular origin and differentiation status of glioblastoma is critical to resolve the etiology of the disease. we profile 18 patient glioblastomas by single cell RNA sequencing (scRNAseq). From this, we uncovered two principal cell-of-origin relations. Each lineage displays unique directional differentiation trajectories and transcriptional cores from the naïve cell populations. Thus, glioblastoma is defined by robust cell lineage features which may provide insights into the cell origin of the diseases.

  Study EGAS00001006236

• RNA sequencing of NK cells in human lung

  Human lung tissue-resident NK cells (trNK cells) are likely to play important roles in viral infections, inflammation and cancer. However, knowledge about lung trNK cells is lacking but is fundamental for exploiting these cells in therapeutic approaches. Here we analysed the transcriptome of CD69+CD49a+CD103+CD16-CD56bright, CD69+CD49a+CD103-CD16-CD56bright, CD69+CD49a-CD103-CD16-CD56bright, CD69-CD49a-CD103-CD16-CD56bright, and CD56dimCD16+NKG2A+CD57- NK cells isolated from human lung.

  Study EGAS00001003544

• RNA sequencing in primary human macrophages overexpressing ETS2

  We investigated an intergenic haplotype on chr21q22, linked to five different inflammatory diseases, and discovered a mechanism that orchestrates macrophage responses during chronic inflammation. We delineated how the risk haplotype increases expression of the causal gene, ETS2, and demonstrated that ETS2 is necessary for inflammatory macrophage effector functions. To establish whether ETS2 is sufficient to drive inflammatory responses, we overexpressed ETS2 in a dose-dependent manner and performed RNA-sequencing to characterise the transcriptional effects.

  Study EGAS00001007554