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• ICR96 exon CNV validation series

  A resource for assessment of exon CNV calling methods in targeted NGS data, we here present the ICR96 exon CNV validation series. The dataset includes high-quality sequencing data from a targeted NGS assay (the TruSight Cancer Panel) together with Multiplex Ligation-dependent Probe Amplification (MLPA) results for 96 independent samples. 66 samples contain at least one validated exon CNV and 30 samples have validated negative results for exon CNVs in 26 genes. The dataset includes 46 exon CNVs in BRCA1, BRCA2, TP53, MLH1, MSH2, MSH6, PMS2, EPCAM and PTEN, giving excellent representation of the cancer predisposition genes most frequently tested in clinical practice. Moreover, the validated exon CNVs include 25 single exon CNVs the most difficult exon CNV to detect.

  Dataset EGAD00001003335

• Exome sequencing of a Novel Primary T Cell Immunodeficiency Kindred (2019-08-19)

  Primary T cell immunodeficiency disorders have a heterogeneous genetic basis. This study will focus on one case characterised by severe T cell lymphopenia in the index case. We aim to sequence the complete exomes of this individual, her three unaffected siblings and parents in an effort to identify the causative genetic mutation responsible for this disorder. We will perform exome capture using Agilent SureSelect system, followed by sequencing on the HiSeq platform. Our study has the potential to uncover genes important for T cell development and novel therapeutic strategies to treat T cell immunodeficiencies. . This dataset contains all the data available for this study on 2019-08-19.

  Dataset EGAD00001005263

• A Tumour Organoid Biobank for Mapping Cancer Cell Vulnerabilities - RNA

  RNA sequencing data from cancer patient-derived organoids. Part of a study to include genomic and transcriptomic sequencing data, along with CRISPR screening data from cancer patient-derived organoids and matched tumour tissues. Some organoids were developed as part of the Human Cancer Models Initiative (HCMI) in collaboration with Cancer Research UK (CRUK). The study includes organoids derived from colorectal, oesophageal, ovarian, pancreatic, and stomach cancer samples.

  Dataset EGAD00001015470

• Germline and somatic variants in myelodysplastic syndrome and therapy-related myeloid neoplasms

  Somatic mutation frequencies in patients with therapy-related myeloid neoplasms (129 patients, 181 samples including bone marrow, mesenchymal stromal cells and hair DNA) and primary myelodysplastic syndrome (108 patients, 215 samples including bone marrow, mesenchymal stromal cells and hair DNA) is assessed by deep sequencing of selected genes, using a Fluidigm Access Array, a Nimblegen capture panel and an Ion AmpliSeq panel. The dataset consists of paired fastq files obtained by either Hiseq (2x101bp) or Nextseq (2x150bp) Illumina sequencing. The mutational burden is found to be similar in both, however the distribution of variants is different. Correlation of the mutational spectrum with prognosis is also observed.

  Dataset EGAD00001004861

• Spatial whole exome sequencing of metastatic melanoma

  We performed whole exome sequencing of 8 samples derived from a patient with metastatic melanoma. These represent six different regions of a metastatic melanoma biopsy that was treated with anti-PD-1 inhibitor, one pre-treatment biopsy that was treatment naive and one post-PD-1 inhibitor treated lesion. Exome sequencing data was generated using methods as previously described, including library preparation using the Agilent SureSelect XT Target Enrichment protocol (#5190-8646) prior to sequencing on an Illumina HiSeq 2000/2500 v3 system using 76bp paired-end reads. Raw sequencing data was then processed using Saturn V, the next generation sequencing data processing and analysis pipeline developed by the Department of Genomic Medicine at the UT MD Anderson Cancer Center.

  Dataset EGAD00001005819

• MYOSEQ

  The MYOSEQ project focuses on the application of next generation sequencing, in particular whole exome sequencing (WES), in a large cohort of patients with unexplained limb‐girdle weakness (LGW). Focusing on undiagnosed patients with a clearly defined clinical phenotype enables increased diagnostic rates for known genes (in particular Pompe disease, GNE related pathologies and other known LGMD subtypes) in this cohort, while the use of WES provides scope both for new gene discovery and for additional research into disease modifiers and genotype‐phenotype correlation with substantial cost effectiveness. The LGW patient cohort was collated by Newcastle University in collaboration with clinical centers across Europe. The sequencing was performed at the Broad Institute and jointly analyzed with Newcastle University.

  Dataset EGAD00001006158

• LCM_WGS__Thyroid_

  Whole genome sequencing through the low-input DNA pipeline in thyroid samples. Tissue will be processed either from laser capture microdissection or directly from bulk frozen/fixed/paraffin-embedded tissue. Insights will be gained here directly from the sequencing but also from using the data as a matched normal in Exome Nanoseq. Thyroid samples will be obtained from patients with and without thyroid disease.

  Study EGAS00001007913

• Whole exome sequencing Data from a child with ALPI deficiency and parents

  This dataset contains raw sequences (BAM files) of P1 trio: mother, father and affected child (P1). Whole exome sequencing (WES).

  Dataset EGAD00001004048

• PromethION (and Illumina) WGS and MinION transcriptome for a patient with diffuse large B-cell lymphoma.

  Dataset EGAD00001006204

• Dataset for CD8-Positive lymphocyte samples

  This dataset contains scRNA sequencing data for CD8-Positive lymphocytes samples. Sequencing was performed on a Illumina NextSeq 550. The sequencing was always paired.

  Dataset EGAD50000000092

• Whole Genome Sequencing of 2 expanded clones from rhabdoid tumor case 3

  Whole Genome Sequencing of 2 expanded clones from a cell line derived from the rhabdoid tumor case 3 (2 WGS 20X)

  Dataset EGAD50000000240

• WGS

  Our cohort represents infants with ALL in whom KMT2Ar was not detected by FISH or by standard cytogenetics. Whole-genome sequencing (WGS) was performed using Illumina’s HiSeqX to a depth of >30X.

  Dataset EGAD50000000594

• UniKilinikum Wuerzburg MSNZ AGRasche/AG Riedel EMD DAC

  This is a Data access committee for the Data presented in the paper tilted "Spatially resolved transcriptomics reveals profound subclonal heterogeneity and T cell dysfunction in extramedullary myeloma"

  Dac EGAC50000000173

• Systematic dissection of tumor-normal single-cell ecosystems across a thousand tumors of 30 cancer types

  Raw bam file for bulk RNA-seq of checkpoint-blockade treated lung cancer cohorts

  Dataset EGAD50000000469

• Adaptive long-read and transcriptome sequencing detail a submicroscopic inv(15)(q14q15), generating two fusion transcripts and MEIS2 and NUSAP1 haploinsufficiency

  Study an inversion affecting MEIS2 using ONT adaptive sequencing.

  Study EGAS50000000632

• Methylation profiling of CDS and ES tumor samples

  Methylation profiling of 9 CDS and ES tumor samples, using the approach described in "Patient-derived tumoroids from CIC::DUX4 rearranged sarcoma identify MCL1 as a therapeutic target

  Dataset EGAD00010002760

• WES of Multiple myeloma/MGUS cases (germline) - Fastq files

  WXS - Exome capture using the Twist Human Core Exome Kit on germline DNA, paired-end (2x100bp) sequencing on a NovaSeq system. Number of samples: 295

  Dataset EGAD50000001799

• Legal Notice EGA is a joint effort by the EBI and CRG. Please, check their terms of use and legal notice in order to follow them in the usage of the EGA website. EBI terms of use CRG terms of use

  Documentation legal-notice

• Single-cell RNA-sequencing of a multi-region pleural mesothelioma case

  Single-cell RNA-sequencing from three distant regions of an epithelioid pleural mesothelioma case.

  Study EGAS00001008062

• Polyomavirus-positive Merkel cell carcinoma derived from a trichoblastoma suggests an epithelial origin of Merkel cell carcinoma

  Tricholastoma (TB): Exome Merkel cell carcinoma (MCC): Genome and Exome Healthy tissue (HT): Exome

  Dataset EGAD00001005223

• Illumina_RNA_T-XEN_Validation_Cohort

  RNAseq on Illumina HiSeq2000/2500 of Patient-derived xenograft derived from colorectal cancer sample of a validation cohort of 60 PDX

  Dataset EGAD00001002883

• Whole genome sequencing of a breast cancer cohort with known functional homologous recombination status

  41 breast cancer patients with known functional homologous recombination status (matched normal and tumor genomes, n=82)

  Dataset EGAD00001008027

• Single-cell RNA sequencing for metastatic gastric adenocarcinoma

  Single-cell RNA sequencing was performed on a total of 20 PC specimens.

  Dataset EGAD00001006172

• Berlin Neuroblastoma Patient Genomic Data from Targeted Sequencing

  Targeted DNA sequencing data of paired primary and relapse tumor material taken from a pediatric patient with neuroblastoma.

  Dataset EGAD00001008564

• Genomic Analysis of Focal Nodular Hyperplasia with Associated Hepatocellular Carcinoma Unveils its Malignant Potential

  Whole exome sequencing of FNH and two HCC compartments from a single patient, along with matched germline.

  Dataset EGAD00001007702

• Exome sequencing of osteosarcoma, blood and saliva

  We profiled 31 osteosarcoma tumor patient samples, 18 blood and 1 saliva control samples by exome sequencing, for a total of 50 samples. The raw fastqs are provided.

  Dataset EGAD00001011370

• Single-cell dissection of the immune response after a myocardial infarction

  38 STEMI patients at hospital admission, 24 hours (acute phase) and 6-8 weeks (chronic phase) after STEMI

  Dataset EGAD00001010064

• NiCOL Study Target-seq dataset

  10 samples sequenced in Target-sequencing of a panel of 571 genes (Illumina NovaSeq 6000) - Raw FASTQ data - Annotated VCF

  Dataset EGAD00001010911

• Prostate cancer datasets RNA Seq

  Total RNA Seq: 15 Samples (2 patients (MF1 and MF3)) (HiSeq) and Poly A RNA Seq: 27 Samples (4 patients Normal and Tumour ) (HiSeq)

  Dataset EGAD00001004468

• Neoadjuvant Breast Cancer Validations

  This study aims to re-sequence findings from whole genome studies using a bespoke pulldown method to validate mutations in those genomes sequenced.

  Dataset EGAD00001000663

• Angiosarcoma follow-up 2 validation study

  A bespoke targeted pulldown experiment will be performed on patients with Angiosarcoma. the resulting products will be sequenced to determine the prevalence of previously found mutations in these patients.

  Dataset EGAD00001000679

• Bone Cancer - Rare Types Whole Genome

  We propose to definitively characterise the somatic genetics of a selection of rare bone cancers through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing.

  Dataset EGAD00001000785

• NKI PRECSION Mutations

  38 samples with DCIS and matched recurrences sequenced with a targeted mutation panel on IonTorrent.

  Dataset EGAD00001008338

• ChIP sequencing from a collection of PFA tumors

  ChIP data from PFA (n = 10). Raw data provided as FASTQ. Data generated on Illumina NovaSeq 6000 PE50.

  Dataset EGAD00001009045

• Transcriptomic Profiling of Peripheral Immune Cells in a Trial of Ruxolitinib with Nivolumab for Anti-PD1 Non-Responsive cHL

  Treatment with checkpoint inhibitors is effective in multiple cancer types. However, even in cancers with high response rates such as Hodgkin lymphoma, some patients fail to respond or relapse following an initial response to checkpoint inhibitors. In this study, we examined patients enrolled in a clinical trial of ruxolitinib with nivolumab in relapsed or refractory Hodgkin lymphoma (NCT03681561). Patients relapsed or refractory to anti-PD1 therapy received ruxolitinib for 8 days followed by nivolumab every 4 weeks and continued ruxolitinib twice daily. For this transcriptomic study, peripheral blood mononuclear cells (PBMCs) were collected at baseline and 8 days of ruxolitinib therapy and analyzed by single-cell and bulk RNA-sequencing.

  Study phs003601

• A Genomics-Driven Artificial Intelligence-Based Model Classifies Breast Invasive Lobular Carcinoma and Discovers CDH1 Inactivating Mechanisms

  We developed an artificial intelligence (AI)-model applied to histological images using CDH1 biallelic mutations, pathognomonic for breast invasive lobular carcinoma (ILC), as ground truth. We evaluated the performance of the AI-model to predict the presence of CDH1 biallelic mutations and to diagnose ILC. Subsequently, we investigated the molecular underpinning cases of predicted by the model to harbor a CDH1 biallelic mutations but lacking these alterations according to targeted sequencing. Among this analyses, we subjected to whole genome sequencing (WGS) one ILC case lacking CDH1 biallelic mutations by targeted sequencing and lacking CDH1 promoter methylation to determine the molecular basis of its lobular phenotype.

  Study EGAS50000000485

• RNA-seq of longitudinal human blood and nose swab samples from a controlled human infection experiment with SARS-CoV-2 virus

  Controlled human infection experiments enable longitudinal profiling of immune responses to a pathogen. 36 healthy volunteers aged 18-29 years, with no evidence of previous infection or vaccination, were inoculated with SARS-CoV-2 virus and quarantined for 14 days. Blood samples (n=374) for RNA sequencing were collected into PAXgene tubes before virus challenge, 6 hours after challenge, daily thereafter for 14 days and on day 28. Mid-turbinate nose swabs (n=96) for RNA sequencing were collected before virus challenge, and on days 1, 3, 5, 7, 10 and 14 after challenge, preserved in RNAprotect. 18 of 36 participants developed a replicative SARS-CoV-2 infection as evidenced by consecutive PCR-positive swabs for the virus. For every participant, blood RNA from selected days were extracted and depleted for genomic DNA and globin mRNA, before cDNA libraries were constructed using KAPA RNA HyperPrep with RiboErase kits. Libraries were sequenced on the Illumina NovaSeq 6000 platform using NovaSeq 6000 S4 Reagent Kits (200 cycles). Nose swab RNA samples were extracted and depleted for genomic DNA before cDNA libraries were constructed using KAPA mRNA HyperPrep Kits. Libraries were sequenced on the Illumina NextSeq platform the using the NextSeq 500/550 High Output Kit (75 cycles).

  Dataset EGAD50000000942

• A Combined Omics and Tissue Biobank for Paediatric Cancers

  The Swedish Childhood Tumour Biobank (BTB) is a nonprofit national infrastructure for samples and genomic data collection from pediatric patients diagnosed with central nervous system and other solid tumours in Sweden. Fresh frozen tumour tissue and patient’s matched blood are collected from affected patients and genomic data is continuously generated and made available for approved medical research projects. We expect that the accessibility of biological samples and/or data to the research community will contribute to further advances in the understanding of tumour biology, which in turn will impact many aspects of clinical care of children with cancer, by refining diagnosis and/or identifying oncogenic drivers and therapeutic targets.

  Study EGAS50000000209

• A human induced pluripotent stem cell toolbox for studying sex chromosome effects -transcriptional landscape

  We use state of the art reprogramming methods to generate panels of isogenic XXY, XX and XY iPSCs from XXY patient fibroblasts. We use CRISPR/Cas9 system to evict Y chromosome from XY cells and generate XO iPSCs. The generation and characterisation of panels of isogenic XXY, XX, XY and XO iPSCs will provide a foundational toolkit to study sex differences in vitro. As iPSCs can be differentiated into any somatic cell type, we can apply the model to any human disease. We have generated bulk RNA-Seq from 12 autosomally isogenic hiPSCs to investigate transcriptional landscape and any differences in those cells in pluripotent state.

  Study EGAS50000000931

• Star2xml: metadata converter into XML

  Star2xml: metadata converter into XML Welcome to the landing page for star2xml - a tool developed by the European Genome-phenome Archive (EGA) that enables users to convert metadata into XML format that is compliant with EGA's programmatic submission system. For starters, if you are not sure what metadata is in this context, you may want to explore our brief metadata introduction. . Star2xml is useful for users who have already submitted their data to the EGA and want to also submit their metadata programmatically without having to create the XML files manually. The need for these XMLs containing metadata is explained in the EGA's metadata schemas and programmatic submission guidelines. In summary, star2xml allows for users to deposit metadata in a tabular format (e.g. excel spreadsheet) and transform it into a compliant XML format. This saves time in large submissions, where the sheer size of metadata makes it difficult to manage. For smaller submissions, it is recommended to use EGA's Submitter Portal (SP) instead. The installation of the tool is straightforward, and it contains detailed documentation on how to use it in its GitHub repository . While star2xml can help users convert metadata formats, it does not validate the resulting metadata against EGA's schemas. Therefore, after creating your XMLs, you should still validate your metadata before submitting it to EGA, as described in the documentation for programmatic metadata validation.

  Documentation tools/star2xml

• A whole genome analysis of single fetal human stem cells from the liver and the intestine

  Mutations of embryonic and fetal origin have the potential to affect a large proportion of adult cells and may alter cancer predisposition or lead to genetic disease syndromes. We have recently shown that human adult-stem cells progressively acquire approximately 40 novel tissue-specific mutations per year throughout postnatal life. Prenatal mutation rates are as yet unknown. Here we determined genome-wide mutation patterns of single stem cells in human development by sequencing of clonally expanded intestinal and liver organoid cultures of 2nd trimester human foetuses. Our results show that mutation rates in fetal stem cells are significantly higher than in adult stem cells.

  Study EGAS00001002886

• A standardised framework for robust fragmentomic feature extraction from cell-free DNA sequencing data

  Fragmentomic features of cell-free DNA represent promising non-invasive biomarkers for cancer diagnosis. However, a lack of systematic evaluation of biases in feature quantification has hindered the adoption of such applications. We compared features derived from whole-genome sequencing of ten healthy donors using nine library kits and ten data-processing routes, and validated them in 1,182 plasma samples from published studies. Our results clarify the variations resulting from library preparation and feature quantification methods. We designed the Trim Align Pipeline and the cfDNAPro R package as unified interfaces for data pre-processing, feature extraction, and visualisation, aiming to standardise multimodal feature engineering and integration for machine learning.

  Study EGAS00001008051

• Characterization of mutational signatures in human cancer cell lines reveals episodic APOBEC mutagenesis

  Multiple signatures of somatic mutations have been identified in human cancer genomes. To investigate whether mutational signatures continue to be generated, and if so their temporal patterns of activity, subsets of cell lines were cultured in vitro for extended periods and subjected to single cell cloning and whole genome or exome sequencing or directly to single cell whole genome sequencing. As expected, signatures of past exogenous exposures, such as tobacco smoke and ultraviolet light, were not generated in vitro. In contrast, signatures of normal and defective DNA repair and replication continued to be generated at essentially constant mutation rates. Signatures of APOBEC cytidine deaminase DNA-editing activity exhibited a distinctive pattern with substantial fluctuations in mutation rate over time and episodic bursts of mutations. The initiating factors for these bursts are unclear although retrotransposon mobilisation may play a role. This cell line set now constitutes a comprehensive resource of live experimental models of mutational processes of both known and unknown aetiologies potentially retaining the patterns of activity and regulatory influences operative in human cells in vivo.

  Dataset EGAD00001004201

• TCR- and BCR-sequencing data for The interface of malignant and immunologic clonal dynamics in high-grade serous ovarian cancer

  Each tumor sample was cut into three pieces, yielding two end-pieces for cryovials and a middle portion placed in 10% buffered formalin. End pieces were homogenized manually and with a paddle blender (Stomacher). All paraffin-embedded blocks, including formalin-fixed tumor samples and molecular-fixed fallopian tubes, were sectioned and stained with hematoxylin and eosin prior to expert histopathological review to confirm the presence of high grade serous carcinoma. Homogenized end pieces were then flash frozen, and RNA was extracted using the miRNeasy Mini kit. Nanodrop was used to assess quality (260/280) and quantity. Total RNA samples were also QC checked using the Caliper HT RNA HiSens assay. Samples ranging from 60-255ng RNA were re-arrayed into a 96-well plate. 5'-RACE PCR was carried out as described in "The interface of malignant and immunologic clonal dynamics in high-grade serous ovarian cancer" (Zhang et al.). Briefly, this involved first round and nested PCR with TRB (TCR beta chain) and IGH (immunoglobulin heavy chain) gene-specific primers. The indexed libraries were sequenced on the Illumina HiSeq platform with paired-end 250bp reads using v2 chemistry reagents.

  Dataset EGAD00001003985

• Clonal haematopoiesis in patients with AAA (2019-04-03)

  Recent advances in genomics have demonstrated that clonal haemopoiesis driven by leukaemia associated somatic mutations is a relatively common phenomenon that increases in frequency with advancing age. Whilst individuals with clonal haemopoiesis have an increased risk of developing haematological malignancies, they also have an increased mortality from other causes. Additionally, certain mutations are almost exclusively seen in individuals aged 70 years or older, whilst others are seen in individuals with non-haematological cancers including breast and ovarian. Recently, clonal haemopoiesis was found to be associated with a significantly increased risk of atherosclerotic cardiovascular disease. This association is thought to be causative with clonally-derived macrophages showing elevated expression of several chemokine and cytokine genes that contribute to atherosclerosis. Another vascular pathology, abdominal aortic aneurysm (AAA), increases with age and shares risk factors with atherosclerosis (including smoking, male sex, high cholesterol). However, the impact of these risk factors and the overlap between AAA and atherosclerosis is poorly understood. To investigate a possible link between clonal haemopoiesis and AAA, we will study DNA samples from 300 patients with AAA and up to 200 controls for evidence of clonal haemopoiesis. This will be done using target DNA enrichment with biotinylated RNA baits followed by high throughput sequencing. . This dataset contains all the data available for this study on 2019-04-03.

  Dataset EGAD00001004895

• Dataset for RNA sequencing of Glioblastoma samples

  This dataset contains 10x scRNA sequencing of glioblastoma samples. Sequencing was performed on a Illumina HiSeq 4000. The sequencing was always paired.

  Dataset EGAD50000000081

• Cancer Registry of Norway - NIPH Data Access Committee for CRCbiome datasets

  The Cancer Registry of Norway - NIPH appointed Data Access Committee for the CRCbiome datasets - The microbiome as a colorectal cancer screening biomarker. https://www.mn.uio.no/sbi/english/groups/rounge-group/crcbiome/.

  Dac EGAC50000000121

• Lifelines NEXT 16S-ITS-23S long read sequencing

  16S-ITS-23S amplicon long read PacBio sequencing of milk, fecal and oral cavity samples, along with sequencing controls, of a subset of newborn infants from Lifelines NEXT cohort

  Dataset EGAD50000000181

• Nanopore sequencing of brain tumor tissue obtained by cavitating ultrasonic aspiration

  This dataset contains 21 pediatric brain tumor cases which where obtained during surgery using a cavitating ultrasonic aspiration and submitted to nanopore whole genome sequencing.

  Dataset EGAD50000000269

• Targeted capture sequencing for LySeqST

  Targeted capture sequencing of 445 lymphoma samples and 13 normal samples for LySeqST: A targeted sequencing assay for robust genomic classification of diffuse large B-cell lymphoma.

  Dataset EGAD50000002290