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• Integration of metabolomics, genomics and immune phenotypes reveals the causal roles of metabolites in disease

  Study EGAS00001005348

• Analysis of circulating miRNAs for the identification of new prognostic and predictive markers in gastro-entero-pancreatic neuroendocrine tumour (GEP-NET)

  Study EGAS00001007227

• Multi-omics integration reveals only minor long-term molecular and functional sequelae in immune cells of individuals recovered from COVID-19

  Dac EGAC00001002267

• Liquid biopsy-based minimal residual disease monitoring for early risk stratification and decision-making in advanced non-small cell lung cancer

  Dac EGAC50000000832

• Biomarker data

  Biomarker data including the time point of sample collection, tumor content and ERBB2 gene expression.

  Dataset EGAD00001009415

• Melanoma multi site metastases

  These are caveman, pindel and sequenza calls for the metastatic melanoma exomes within this study.

  Dataset EGAD00001005487

• Expression profiles and genetic makeup of agnospheres.

  WES performed on 15 CUP-derived samples

  Dataset EGAD00001006668

• Genetic mechanisms of resistance to chemotherapy in breast cancer

  Resistance towards chemotherapy is one of the main causes of treatment failure and deathamong breast cancer patients.The main objective of this project is toidentify genetic mechanisms causing some breast cancer patients not torespond to a particluar type of chemotherapy (epirubicin) while otherpatients respond very well to the same treatment. In the project wewill perform genome / exome sequencing of a selection of breast cancerpatients (n=30). These patients are drawn from a cohort where allpatients have recieved treatment with epirubicin monotherapy before surgical removal of alocally advanced breast tumour, and where all patients have beensubjected to objective evaluation of the response to thetherapy. Subsequent to sequencing, we will analyse the data andcompare with the clinical data for each patient (object response totherapy). The main aim being to identify mutations that are associatedwith resistance to epirubicin. Identification of mutations with strongpredictive value, may have a direct impact on cancer treatment sinceit opens the possibility for genetic testing of a tumour, and desicionon which drug is likely to work best, prior to treatment start.

  Dataset EGAD00001000264

• Shallow Whole Genome Sequencing of Patient Derived Xenografts

  Chemotherapy is the standard-of-care treatment for metastatic colorectal cancer (mCRC) and benefits some patients, but what distinguishes responders from non-responders is unclear. In this study, we leveraged a comprehensive collection of 27 molecularly annotated patient-derived xenografts to uncover functional predictors of response to 5-FU and irinotecan combination therapy (FOLFIRI) in mCRC. Genetic analyses revealed that treatment sensitivity was marked by genomic scars indicative of BRCAness, suggesting homologous recombination (HR) deficiency as a key determinant. Accordingly, we surveyed a manually curated panel of 44 genes with a documented role in HR for the potential presence of pathogenic mutations. We did not observe a specific enrichment of HR gene mutations based on response to FOLFIRI. This result, combined with the absence of widespread biallelic inactivation of the analyzed genes and the predominance of mutations categorized as variants of unknown significance, suggests that FOLFIRI sensitivity is not primarily governed by underlying mutations in HR genes responsible for mitigating the genotoxic effects of this therapeutic regimen.

  Dataset EGAD50000000277

• Metagenomic Deep Sequencing in Meningitis and Encephalitis

  This is a prospective observational study seeking to identify pathogens in cases of unexplained neurological disease, particularly those in which there is a presumed infectious cause. This next generation analytical approach will hopefully allow for rapid identification of foreign genomic material, and through a sophisticated bioinformatics pipeline developed in the DeRisi lab, these foreign genomic sequences can be aligned to all known sequences in publicly available databases (i.e. GenBank) which may allow for identification of novel pathogens or known pathogens that are not frequently tested for as part of standard diagnostic work-ups.

  Study phs001067

• Novel Approach to High-Throughput Identification and Characterization of Neoantigens

  This study focuses on the development of novel approach for the screening, identification and characterization of neoantigen-specific T-cell receptors (TCRs). The developed method consists of collecting targeted RNA-Seq from a T-cell specific gene panel via 3' end Illumina sequencing combined to Oxford Nanopore based full-length TCR sequencing post T-cell activation. The data generated during this study demonstrates feasibility of the approach on a Jurkat control cell line as well as T-cells isolated from the blood of 3 independent healthy donors.

  Study phs002372

• Single-cell Analysis of Neoplastic Plasma Cells Identifies Novel Myeloma Pathobiology Mediators and Potential Targets

  Newly diagnosed symptomatic and relapsed/refractory myeloma is a clonal plasma cell (PC) dyscrasia that arises from precursors which have been studied utilizing bulk or single-cell (sc) techniques. By combining scRNA-sequencing with scB-cell receptor (BCR)-sequencing, we found more dysregulated genes in monoclonal PCs compared with analyses of the entire CD138+ population, which includes non-neoplastic/polyclonal PCs. We identified a panel of genes that were over- or under-expressed in symptomatic states that could be putative oncogenic drivers or tumor suppressors, respectively.

  Study EGAS50000000803

• Characterization of a New Case of XMLV (Bxv1) Contamination in the Human Cell Line Hep2 (Clone 2B) Using High-Throughput DNA- and RNA-Seq

  We have sequenced DNA and RNA from the Hep2 (clone 2B) cell line (Sigma-Aldrich catalog number: 85011412-1VL) using short read Illumina sequencing. We show that this cell line is indistinguishable from the HeLa cell line (as mentioned on the Sigma-Aldrich website) by mapping integrations of the human papillomavirus 18. We also show that the cell line is contaminated by the Bxv1 xenotropic murine leukemia virus. This contamination has to be taken into account when using the cell line in future experiments.

  Study phs001944

• Pyoderma Gangrenosum Caused by Molecular Uncoupling of OTULIN Catalytic Activity and LUBAC Binding

  This is a single-cell RNA sequencing (scRNA-seq) study using peripheral blood mononuclear cells (PBMC) from 3 healthy donors and 2 patients with OTULIN-related Pyoderma Gangrenosum (ORP). Samples were not hashed or multiplexed. The 10X Genomics Platform was used for sequencing. Principal findings include transcriptome changes due to a mutation in OTULIN that causes OTULIN-Related Pyoderma gangrenosum (ORP), without affecting OTULIN function but abrogating its binding ability to the linear ubiquitin assembly complex (LUBAC). FASTA files will be available through dbGaP.

  Study phs004114

• Lenalidomide Resistance in del(5q) Myelodysplastic Syndrome Follows Loss of RUNX1/TP53-mediated Megakaryocytic Differentiation

  Interstitial deletion of the long arm of chromosome 5 (del(5q)) is the commonest structural genomic variant in myelodysplastic syndromes (MDS). Lenalidomide (LEN) is the treatment of choice for patients with del(5q) MDS, but half of the responding patients become resistant within two years. TP53 mutations are detected in ~20% of patients who become resistant to LEN. Our data show that patients who become resistant to LEN harbor either TP53 or RUNX1 mutations or loss of RUNX1 expression. Here we show that LEN-induced degradation of IKZF1 permits a RUNX1/GATA2 complex to drive megakaryocytic differentiation and consequent del(5q) MDS progenitor cell death via CRBN-mediated CSNK1A1 degradation. Overexpression of GATA2 is able to restore LEN sensitivity in the context of RUNX1 or TP53 mutations by enhancing LEN-induced megakaryocytic differentiation. Screening for TP53 and RUNX1 mutations or downregulation should identify patients resistant to LEN, and strategies to activate GATA2 may resensitize del(5q) MDS cells to LEN.

  Dataset EGAD00001005769

• The landscape of somatic mutation in normal colorectal epithelial cells

  The colorectal adenoma-carcinoma sequence has provided a paradigmatic framework for understanding the successive somatic genetic events and consequent clonal expansions leading to cancer. As for most cancer types, however, understanding of the earliest phases of colorectal neoplastic change, which may occur in morphologically normal tissue, is comparatively limited because of the difficulty of detecting somatic mutations in normal cells. Each colorectal crypt is a small clone of cells derived from a single recently-existing stem cell. Here, we sequenced hundreds of normal crypts from 42 individuals. Signatures of multiple mutational processes were revealed, some ubiquitous and continuous, others only found in some individuals, in some crypts or during some phases of the cell lineage from zygote to adult cell. Likely driver mutations were present in ~1% of normal colorectal crypts in middle-aged individuals, indicating that adenomas and carcinomas are rare outcomes of a pervasive process of neoplastic change across morphologically normal colorectal epithelium.

  Dataset EGAD00001004192

• Autozygosity pilot - Born in Bradford (2017-05-11)

  The offspring of first cousin marriages have ~6% of their genome autozygous, i.e. homozygous identical by descent, or even more if there was further consanguinity in their ancestry. In the UK there are large populations with very high first cousin marriage rates of 20-50%. Sequencing the exomes of a sample of these individuals has the potential both to support genetic health programmes in these populations, and to provide genetic research information about rare loss of function mutations. This pilot study based on existing cohort samples from the Born In Bradford study will identify homozygous individuals for almost all variants down to an allele frequency around 1%, plus individuals carrying hundreds of new homozygous rare loss-of-function variants, and will support development of community relations and ethics for a wider study currently being designed. The data deposited in the EGA consist of low coverage whole exome sequencing on these samples. This dataset contains all the data available for this study on 2017-05-11.

  Dataset EGAD00001003329

• Raw DNA and RNA data from breast cancer organoids, control samples and biopsies

  Whole genome sequencing data for primary tumors, matching control material from blood and their corresponding organoid. Whole transcriptome data for organoids.

  Dataset EGAD00001003751

• UCSF Pediatric Bithalamic Glioma Genome Project

  Targeted next-generation sequencing of 13 pediatric bithalamic diffuse gliomas. BAM files of targeted next-generation DNA sequencing data of 13 pediatric gliomas, with multi-region sequencing data from 2 of these cases (17 total tumor samples). Genomic DNA was extracted from formalin-fixed, paraffin-embedded blocks of tumor tissue from using the QIAamp DNA FFPE Tissue Kit (Qiagen). Capture-based next-generation DNA sequencing was performed at the University of California, San Francisco Clinical Cancer Genomics Laboratory, using an assay that targets all coding exons of 480 cancer-related genes, select introns of 47 genes, and TERT promoter with a total sequencing footprint of 2.8 Mb (UCSF500 Cancer Panel). Sequencing libraries were prepared from genomic DNA, and target enrichment was performed by hybrid capture using a custom oligonucleotide library (Nimblegen SeqCap EZ Choice). Captured libraries were sequenced as paired-end 100 bp reads on an Illumina HiSeq 2500 instrument. Duplicate sequencing reads were removed computationally to allow for accurate allele frequency determination and copy number calling.

  Dataset EGAD00001005499

• Direct transcriptional consequences of somatic mutation in breast cancer

  The disordered transcriptomes of cancer encompass direct effects of somatic mutation on transcription; co-ordinated secondary alterations in transcriptional pathways; and increased transcriptional noise. To catalogue the rules governing how somatic mutation Overall, 59% of 6980 exonic substitutions were expressed. Compared to other classes, nonsense mutations showed lower expression levels than expected with patterns characteristic of nonsense-mediated decay. 14% of 4234 genomic rearrangements caused transcriptional abnormalities, including exon skips, exon reusage, fusion transcripts and premature poly-adenylation. We found productive, stable transcription from sense-to-antisense gene fusions and gene-to-intergenic rearrangements, suggesting that these mutation classes may drive more transcriptional disruption than previously suspected. Systematic integration of transcriptome with genome data therefore reveals the rules by which transcriptional machinery interprets somatic mutation.

  Dataset EGAD00001002237

• Next gen seq of eye cancers (2019-08-14)

  Retinoblastoma (RB), the commonest eye cancer in children was the first cancer for which a genetic cause was identified: the Rb1 gene is a tumour suppressor gene that is mutated in RB. The Rb1 gene defect alone does not predict the clinical outcome. We propose to study other possible mechanisms: 1. Stepwise further mutations occur in RB, increasing its carcinogenesis. We will sequence the whole genome in RB tissue, and relate the different genes expressed to the treatments used. 2. Extracellular matric proteins contribute to a tumour permissive environment for RB to continue to grow. This includes Samll Leucine Rich Proteoglycans (SLRP), a family of 15 secreted extracellular matrix proteins involved in eye development. 3. Cancer stem cells (CSC), a subpopulation of treatment resistant cells, drive RB tumours, and whether these stem cells can be manipulated for new therapies. The aim of this study is to assist finding targeted diagnostic techniques and treatments for RB. . This dataset contains all the data available for this study on 2019-08-14.

  Dataset EGAD00001005251

• Exome-seq data of two non-obstructive azoospermia patients

  Azoospermia, characterized by the absence of spermatozoa in the ejaculate is a common cause of male infertility with a poorly characterized etiology. Exome sequencing analysis of two azoospermic brothers allowed the identification of a homozygous splice mutation in SPINK2, encoding a serine protease inhibitor believed to target acrosin, the main sperm acrosomal protease. In accord with these findings we observed that homozygous Spink2 KO male mice had azoospermia. Moreover, despite normal fertility, heterozygous male mice had a high rate of morphologically abnormal spermatozoa and a reduced sperm motility. Further analysis demonstrated that in the absence of Spink2, protease-induced stress initiates Golgi fragmentation and prevents acrosome biogenesis leading to spermatid differentiation arrest. We also observed a deleterious effect of acrosin overexpression in HEK cells, effect that was alleviated by SPINK2 coexpression confirming its role as acrosin inhibitor. These results demonstrate that SPINK2 is necessary to neutralize proteases during their cellular transit towards the acrosome and that its deficiency induces a pathological continuum ranging from oligoasthenoteratozoospermia in heterozygotes to azoospermia in homozygotes.

  Dataset EGAD00001003326

• Metastatic Adult Pancreatoblastoma: Multimodal Treatment and Molecular Characterization of a Very Rare Disease (NCT MASTER)

  Pancreatoblastoma is a rare malignant tumor that occurs predominantly in children. We identified four adult patients with metastasizing pancreatoblastoma at a high-volume German university cancer center which were treated with multimodal therapies between 2013 and 2018. In three cases, we performed a comprehensive molecular analysis that included whole-genome sequencing (WGS) or whole-exome sequencing (WES); transcriptome sequencing was performed in two cases, respectively. Subsequent recommendations of molecularly stratified treatment options were discussed within a dedicated molecular tumor board (MTB) embedded in a precision oncology program (NCT MASTER).

  Study EGAS00001004157

• Sequencing Study in COPD cases and controls

  Since smokers with COPD have a higher risk of developing lung cancer than those without, we hypothesized that they carry more mutations in affected tissue. We called somatic mutations in airway brush samples from medium-coverage whole genome sequencing data from healthy never and ex-smokers (n=8), as well as from ex-smokers with variable degrees of COPD (n=4). Owing to the limited concordance of resulting calls between the applied tools we built a consensus, a strategy that was validated with high accuracy for cancer data.

  Study EGAS00001003406

• Genomic profiling of Follicular thyroid adenomas and carcinomas using exome-sequencing analyses

  While thyroid nodules per se are frequent (4%–50%), thyroid cancer is rare (∼5% of all thyroid nodules). The minimally invasive Fine Needle Aspiration Cytology (FNAC) is the current gold standard for the diagnosis thyroid nodule malignancy. However, proper discrimination of follicular neoplasias often require more invasive diagnostic techniques. To develop a novel molecular classification system for thyroid cancer malignancy, we performed an genomic profiling of 54 fresh frozen Follicular like thyroid samples using a whole exome sequencing approach (SureSelect V6 Target enrichment protocol and the Illumina Novaseq 6000 platform)

  Study EGAS00001005561