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• Deep exome sequencing

  Bam files from deep exome sequencing of blood DNA samples from five TET2 mutation carriers (Ly1, Ly2, Ly9, Ly11, Ly14) and three wild-type family members (Ly8, Ly10, Ly13) extracted at multiple time points. Library preparations were performed with SeqCap EZ Exome v3 (Roche, Switzerland) using six different index primers per sample for which paired-end Illumina sequencing was done with 75bp read length and HiSeq4000 sequencer. After alignment (bwa version 0.7.12), base recalibration (GATK 3.5), realignment around indels (GATK 3.5) and duplicate removal (MarkDuplicates; Picard Tools version 1.79), data from libraries with six different indexes were merged.

  Dataset EGAD00001004780

• Vumc_organoids

  Organoid cultures derived from normal colon and/or colorectal adenomas and/or colorectal carcinomas. RNA and DNA was isolated from these cultures for genome wide profiling.

  Dataset EGAD00001008479

• Whole Genome Sequencing Data of High Grade Serous Ovarian Cancer

  Longitudinal whole genome sequencing data to study chemoresponse in ovarian cancer. These samples belong to an ongoing sample collection and the data already includes hundreds of samples from over 200 patients. Samples are from primary and metastatic tissues and ascites. All patients have been treated with platinum-taxane based chemotherapy and majority of them are diagnosed with high-grade serous ovarian cancer.

  Study EGAS00001006775

• Genomics analysis of mucinous tumours of the ovary and related neoplasms

  To perform genetic and gene expression analyses on mucinous ovarian tumours to determine a progression model, cell of origin and novel therapeutic targets.

  Study EGAS00001003545

• Spatial transcriptomics of hepatoblastoma

  10X Genomics Visium Spatial transcriptomics analysis of hepatoblastoma and adjacent normal liver. Spatial data of normal liver and PT2 (fastq files), and and PT13, PT14 and PT16 (bam files) using the Visium Spatial Gene Expression Solution. All samples, except PT13, were collected post-chemotherapy.

  Dataset EGAD50000000797

• WES and RNA-Seq of HCC biopsies and HCC derived Organoids

  We aimed to identify somatic mutations and transcriptional differences that could explain the resistance to Doxorubicin. This dataset includes RNA-Seq of HCC biopsies and Organoids and WES of Organoids.

  Dataset EGAD50000000060

• Xeroderma Pigmentosum, Complementation Group C, (XPC) and Non-XPC Cutaneous Squamous Cell Carcinoma (cSCC) Mutation Rate Study

  Base mutations occur at higher frequencies within heterochromatin and late-replicating DNA. In this study, we show that regional differences in mutation frequency are absent in portions of the genome that are not transcribed within cutaneous squamous cell carcinomas (cSCCs) with an XPC-\- genetic background. The XPC-\- genetic background predicates a loss of global genome nucleotide excision repair (GG-NER), thus our data shows that regional differences in mutation frequency are a result of differential access of DNA repair protein. Unexpectedly, we also note that greater transcription reduces mutations on both strands of genes in heterochromatin, and only to those levels observed in euchromatin, in a XPC-dependent fashion. Therefore, transcription likely reduces mutation prevalence by increasing access to DNA repair proteins. This tripartite relationship between DNA repair, transcription, and chromatin state shows a new cancer risk factor in human populations.

  Study phs000830

• MYC Inhibition By Omomyc Causes DNA Damage And Overcomes PARPi Resistance In Breast Cancer.

  This study investigates the role of MYC dysregulation in DNA damage response (DDR) and PARP inhibitor (PARPi) resistance in breast cancer. Using Omomyc, a direct MYC inhibitor, we demonstrate that MYC inhibition shuts down DDR genes in triple-negative breast cancer (TNBC), causing DNA repair defects and inducing DNA damage that synergizes with PARPi treatment. Through patient-derived models and clinical samples from metastatic HR-altered breast cancer patients treated with PARPi, we identify MYC transcriptional activity as a predictive biomarker of PARPi resistance. Digital spatial profiling (DSP) analysis of pre-treatment tumor biopsies reveals that patients with progressive disease have significantly elevated MYC signatures compared to responders. These findings support the therapeutic strategy of combining MYC inhibition with PARPi in PARPi-resistant breast cancers where high MYC activity predicts poor response to therapy.

  Study EGAS50000001347

• Whole exome sequencing of SU- DIPG-XIII from different sites

  Whole exome sequencing of diffuse intrinsic pontine glioma (DIPG) cells isolated from the pons and from a sub-ventricular zone site of spread within the frontal lobe from the same individual (SU- DIPG-XIII)

  Dataset EGAD00001003563

• Rapid multiplex small DNA sequencing on the MinION nanopore sequencing platform

  Ultra low coverage sequencing results from the project 'Rapid multiplex small DNA sequencing on the MinION nanopore sequencing platform'. Sequencing data of sample NA12877 and NA12878 generated from 3 nanopore sequencing runs are included in this dataset.

  Dataset EGAD00001004052

• 2 paired WGS samples of peritumour regions of colorectal cancer

  2 paired WGS samples of peritumour regions of colorectal cancer (2 patients). The library was prepared using the Illumina TruSeq Nano FFPE kit and the sequencing was done on NovaSeq6000.

  Dataset EGAD00001009714

• Epigenetic Moderators of Naltrexone Efficacy for Alcohol Use Disorder

  This study was a 16-week randomized controlled trial of oral naltrexone (50 mg daily) vs. placebo among adults with Alcohol Use Disorder. DNA was extracted from peripheral mononuclear cells isolated from a blood sample collected at baseline, prior to study medication ingestion. The Illumina MethylationEPIC BeadChip was subsequently used to analyze these extracted DNA samples.

  Study phs002424

• CCMA-WGSraw

  This dataset has the mapped bam files from WGS for the cancer models in CCMA.

  Dataset EGAD00001010035

• Whole-exome sequencing of glioblastomas with long-term relapse interval

  Whole-exome sequencing data (Agilent SureSelectXT Human All Exon V7). Retrospective study of matched pairs of initial and post-therapeutic GBM cases treated with temozolomide+radiotherapy with a recurrence period greater than one year. Matched normal, initial and post-therapeutic samples for 27 patients and 1 patient (GBM046) with a matched normal and two post-therapeutic samples.

  Dataset EGAD00001008568

• Genomic analysis of HPV positive versus HPV negative esophageal adenocarcinoma

  High-risk human papillomavirus (hr-HPV) has been implicated in a subset of patients with esophageal adenocarcinoma (EAC). We therefore hypothesized that HPV associated EAC may have distinct genomic aberrations compared with viral negative esophageal cancer as shown in Head and Neck cancer and cervical cancer. Whole exome sequencing (WES) was performed to explore the mutational landscape and potential molecular signature of HPV positive versus HPV negative EAC, which includes four hr-HPV-positive and 8 HPV-negative treatment naive fresh-frozen EAC tissue specimens and matched normal tissues.

  Study EGAS00001001340

• Human adipose tissue immune cells

  We describe a novel and conserved Trem2+ lipid-associated macrophage (LAM) subset and identify markers, spatial localization, origin, and functional pathways associated with these cells. Genetic ablation of Trem2 in mice globally inhibits the downstream molecular LAM program, leading to adipocyte hypertrophy as well as systemic hypercholesterolemia, body fat accumulation, and glucose intolerance. These findings identify Trem2 signaling as a major pathway by which macrophages respond to loss of tissue-level lipid homeostasis, highlighting Trem2 as a key sensor of metabolic pathologies across multiple tissues and a potential therapeutic target in metabolic diseases.

  Study EGAS00001003725

• Structural variant analysis of homologous recombination-deficient genomes

  Homologous recombination (HR) deficiency causes DNA breaks and cytogenetic aberrations. Paradoxically, the types of DNA rearrangements specifically associated with HR-deficient cancers only minimally impact chromosomal structure. Addressing this, we combined a genome graph analysis of short-read whole genome sequencing (WGS) profiles across thousands of tumors with deep linked-read (LR) WGS of 46 BRCA1 or BRCA2 mutant breast cancers to discover a distinct class of HR deficiency-enriched rearrangements called reciprocal pairs. LR WGS showed that reciprocal pairs with identical rearrangement orientations gave rise to one of two distinct chromosomal outcomes, distinguishable only with long molecule data. While one (cis) outcome corresponded to the copy and pasting of a small segment to a distant site, a second (trans) outcome was a quasi-balanced translocation or multi-megabase inversion with substantial (10kb) duplications at each junction. The full spectrum of reciprocal pair outcomes could be explained by an HR-independent replication restart repair mechanism. LR WGS additionally identified single-strand annealing (SSA) as a BRCA2-deficiency specific repair pathway in human cancers. Replication restart- and SSA-associated SVs improved BRCA1- vs. BRCA2- deficiency classification and identified metastatic cancer cases with favorable chemotherapy responses. Our data reveal classes of BRCA1- and BRCA2-deficiency specific rearrangements as drivers of cytogenetic aberrations in HR deficient cells.

  Study EGAS00001007186

• POT1 splice site mutant analysis

  We are interested in the contribution mutations in the Shelterin complex protein POT1 may have to the development of melanoma. We have identified a patient who carries a splice site mutation in POT1 and as part of our analysis of this gene we aim to sequence the transcriptome of this patient to see how this mutation influences splicing. RNA has been obtained from lymphocytes collected from the patient.

  Dataset EGAD00001000786

• McGill Sperm Methylome Capture Sequencing Data

  The study includes methylC-capture sequencing (MCC-Seq) on 94 sperm DNA samples derived from both fertile and infertile individuals who were recruited from the Men’s Health Clinic at the Royal Victoria Hospital, Montreal, Quebec. All the data were generated with 100bp paired-end reads using the Illumina NovaSeq 6000 systems.

  Dataset EGAD00001005795

• Exome sequencing to identify predisposition to Wilms tumour

  To identify new Wilms tumor predisposition genes, we performed whole-exome paired-end sequencing of lymphocyte DNA from 12 affected individuals from six unrelated, non-syndromic Wilms tumor families in which known causes had been excluded.We prepared DNA libraries from 1.5 mg blood-derived genomic DNA using the Paired-End DNA Sample Preparation Kit (Ilumina). DNAwas fragmented using Covaris technology and the libraries were prepared without gel size selection. We performed target enrichment using the TruSeq Exome Enrichment Kit (Illumina) by targeting 62 mb of the human genome. The captured DNA libraries were PCR amplified using the supplied paired-end PCR primers.Sequencing was performed with an Illumina HiSeq2000 generating 2?101 bp reads.

  Study EGAS00001000904

• Metagenomic characterization of tracheal aspirates from non-pulmonary sepsis patients

  Our previous studies in mechanically ventilated Intensive Care Unit (ICU) patients with extrapulmonary sepsis revealed that pulmonary dysbiosis within 8 h from sepsis diagnosis was associated with ICU mortality. These observations offer promising options that could be technologically adapted to rapidly identify those patients at higher risk of death. However, they relied on 16S rRNA sequencing experiments which impedes deep characterization of the bacterial communities that could help to further substantiate the association. To further discern this association, here we assessed the pulmonary bacterial communities in these patients by leveraging metagenomics and evaluated if the presence of antibiotic resistance genes could explain the higher mortality of the patients.

  Study EGAS50000000384

• CD4 auto-antigens

  The CD4 auto-antigen Access Committee (DAC) manages and oversees data access, ensuring compliance with ethical and regulatory guidelines while facilitating secure sharing with authorized researchers.

  Dac EGAC50000000864

• Human omentum cell atlas

  This dataset contains single-cell RNA sequencing data derived from freshly dissociated human omental tissue. The study investigates the transcriptomic landscape of the omentum by comparing samples from patients with benign conditions against those with ovarian cancer metastasis. To capture the heterogeneity of the metastatic niche, sampling was performed across distinct anatomical sites, including non-metastasized tissue, distant omental regions, peritumoral zones, and the tumor core. This comprehensive profiling aims to define the cellular remodeling associated with malignant transformation

  Dataset EGAD50000002110

• 762 whole exome sequencing samples from the Singapore Living Biobank

  The dataset includes a subset of 762 individuals that were found to be closely related (≤3rd degree), including 263 Chinese and 499 Malays from the Singapore Living Biobank. There samples are whole-exome sequenced on Illumina HiSeq2000 platform (125bp paired end) with the exonic regions being captured using the Nimblegen SeqCap EZ Exome v3 kits.All the files are in the BAM format.

  Dataset EGAD00001003819

• Small Genomic Insertions Form Enhancers that Misregulate Oncogenes

  ChIP-Seq data from 102 cell lines were processed to identify insertions relative to the human reference genome. To confirm the ability of a computational pipeline to identify insertions that are actually present in these genomes, we PCR-amplified and deeply sequenced regions where insertions were predicted to exist in MOLT4 T-cell acute lymphoblastic leukemia cells. The current study release makes available sequences of amplicons from a tumor cell genome (MOLT4) where a computational pipeline predicted small insertions from orthogonal data.

  Study phs001242

• BE_screens_of_WRN_gene_in_MSI_models

  We will take advantage of a base-editing screening strategy to engineer mutations in the WRN gene by deep mutagenesis. Two MSI-H cell lines sensitive to WRNi will be genetically modified to express doxycycline-inducible ABE and CBE base editors through a knock-in strategy. Moreover, we will design a pooled library of ~4000 gRNAs targeting the WRN gene plus appropriate controls gRNAs. Library-transduced cells will be selected with WRNi to identify WRN mutations able to interfere with the activity of WRNi.

  Study EGAS00001006872

• AML_targeted_resequencing_study

  Genomic libraries will be generated from whole genome amplified genomic DNA derived from 3,000 myeloid neoplasms. Targeted capture will be performed by multiplexing 16 barcoded samples in each library. Pools of 96 DNA samples will be subjected to 1-2 lanes of HiSeq 75bp sequencing. Reads will be mapped to the current build of the human reference genome to facilitate the generation of a comprehensive catalog of somatic mutations associated with 116 known myeloid and cancer driver genes.

  Study EGAS00001000275

• The University of Hong Kong Intestinal Metaplasia Organoids Study scCNV Data

  Single cell encapsulation and DNA libraries were prepared by Chromium™ Single Cell DNA Reagent Kits and Chromium™ Single Cell C and D Chip Kits.

  Dataset EGAD00001015423

• Genetic architecture of male infertility in India

  The dataset consists of whole exome and genome sequencing data from infertile males and his parent(s) and/or sibling(s)

  Dataset EGAD00001015606

• Data distribution Statistics

  EGA Statistics Bibliography Growth Community Archive Distribution Catalogue Here, we show the amount of data distributed by the EGA. Data Distributed / Live EGA Data Distribution / Live SFTP Aspera HTSGET lineChartLive("svg#ega-dist-live", document.querySelector("#ega-figure-dist-live figcaption")); Data Distributed The below figure represents the cumulative EGA data distribution via the download clients(v2 and v3.x api versions) using HTTPS, FTP, and download boxes using ASPERA. You can see cumulative values by clicking "Cumulative". EGA Data Distribution //lineChart('#ega-data-distribution svg.stats', 'https://stats.ega-archive.org/distribution', // ['Amount of Distributed Data', ['Aspera', 'Download Clients', 'Total']]) curveChart('#ega-data-distribution', [ { domId: 'stats-aspera', label: 'Aspera', url: 'https://stats.ega-archive.org/distribution/aspera' }, { domId: 'stats-sftp' , label: 'SFTP', url: 'https://stats.ega-archive.org/distribution/sftp' }, //{ domId: 'stats-htsget', label: 'HTSGET', url: 'https://stats.ega-archive.org/distribution/htsget' }, { domId: 'stats-streamer' , label: 'Download Client', url: 'https://stats.ega-archive.org/distribution/streamer' }, { domId: 'stats-total' , label: 'Total', url: 'https://stats.ega-archive.org/distribution/total' } ] );

  Documentation about/statistics/distribution

• Genomic characterisation of SDH deficient renal cell carcinoma - WGS

  SDH deficient renal cell carcinomas are a rare and recently defined subtype of kidney cancer, often associated with an inherited mutation in one of the SDH gene subunits. This dataset sought to understand the genomic events that underpin tumour formation, from putative cell of origin, characterisation of the tumour microenvironment, to the genomic evolution of these rare tumours. We performed whole genome and RNA sequencing of 4 patients with SDH deficient renal cell carcinomas, including one patient who had an additional paraganglioma. An addition patient in this cohort had the initial diagnosis revised to a clear cell renal cell carcinoma.

  Dataset EGAD00001008469

• Blood Transcriptome Profiling Links Immunity to Disease Severity in Myotonic Dystrophy Type 1 (DM1)

  Here, we explore the molecular signatures in RNA sequencing data from blood associated with disease severity as measured in Myotonic dystrophy type 1 (DM1) patients with less than 400 CTG-repeat length size in the DMPK gene in blood. These DM1 patients participated in the OPTIMISTIC study. This approach involved stratifying those within the OPTIMISTIC study into different patient groups with different degrees of disease severity (as measured by the muscle-impairment rating scale (MIRS)) and assessed at baseline. Patients were divided into groups with mild (MIRS 1–2) and severe (MIRS 3–5) neuromuscular symptoms with different DMPK repeat length characteristics. Therefore these .Bam files are baseline samples from this study.

  Dataset EGAD00001010010

• Mutational landscape of renal cell carcinoma with venous tumor thrombus

  Renal cell carcinoma with venous tumor thrombus opens the unique opportunity to investigate the clonal evolution of a tumor in two fundamentally different compartments i.e., within the confinement of an organ and inside a large blood vessel. We performed multiregion whole exome sequencing of a total of 37 samples from five consecutive patients (normal tissue, n=5; primary tumors, n=16; tumor thrombi, n=16) to >35-fold target coverage. Four patients had a clear cell RCC, one patient had a poorly differentiated type II papillary RCC (RCC-VTT-04). The latter patient had a friable thrombus, the others were of solid consistency.

  Study EGAS00001001950

• Target gene sequencing for human normal endometrial glands

  The raw fastq files target sequencing of 112 genes for 1,298 endometrial glands and matched blood samples. The paired-end sequencing data sets (R1 and R2) are deposited. ABCC1, ACRC, ANK3, ARHGAP35, ARID1A, ARID5B, ATCAY, ATM, ATR, BARD1, BCOR, BRCA1, BRCA2, BRD4, BRIP1, CAMTA1, CDC23, CDYL, CFAP54, CHD4, CHEK1, CHEK2, CTCF, CTNNB1, CUX1, DGKA, DISP2, DYNC2H1, EMSY, FAAP24, FAM135B, FAM175A, FAM65C, FANCA, FANCB, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCL, FANCM, FAT1, FAT3, FBN2, FBXW7, FGFR2, FRG1, GPR50, HEATR1, HIST1H4B, HNRNPCL1, HOOK3, KIAA1109, KIF26A, KMT2B, KMT2C, KRAS, LAMA2, LRP1B, MLH1, MON2, MRE11A, MSH2, MSH6, MTOR, NBN, PALB2, PHEX, PIK3CA, PIK3R1, PLXNB2, PLXND1, PMS2, POLE, POLR3B, PPP2R1A, PTEN, PTPN13, RAD50, RAD51, RAD51B, RAD51C, RAD51D, RAD52, RAD54B, RAD54L, RICTOR, SACS, SIGLEC9, SLC19A1, SLX4, SPEG, STT3A, TAF1, TAF2, TAS2R31, TFAP2C, TNC, TONSL, TP53, TTC6, UBA7, VNN1, WT1, XIRP2, ZBED6, ZC3H13, ZFHX3, ZFHX4, ZMYM4.

  Dataset EGAD00001008465

• single-cell RNA sequencing and RNA sequencing of normal uterine cervix

  We designed this study to identify molecular markers of HPV18 early promoter. In this study, we developed patient-derived organoids from squamous-columular junction of normal uterine cervix and infected HPV18 into those organoids to elucidate the molecular biological characteristics of HPV18-activated cells.

  Study JGAS000640

• Fibroblast heterogeneity and immunosuppressive environment in Human breast cancer

  Carcinoma-associated fibroblasts (CAF) are key players in the tumor microenvironment. Here, by combining 6 well-known stromal markers, we identify four CAF subsets (CAF-S1 to CAF-S4) in human breast cancer (BC) that exhibit distinct activation patterns and accumulate differently in BC subtypes.

  Study EGAS00001002508

• RNA-Seq of Myeloid Cells in Dendritic Cell Therapy Response

  RNA libraries were prepared from 100 ng of total RNA using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit, then sequenced (2×150 bp) on the Illumina NextSeq550. Transcript-level quantification was done with kallisto, followed by gene-level summarization (tximport) and differential expression analysis (DESeq2). Quality control included PCA, hierarchical clustering, and deconvolution with CIBERSORTx to exclude non-myeloid genes. Final analyses identified transcriptomic differences among healthy donors and three patient subgroups based on response to dendritic cell therapy.

  Dataset EGAD50000001681

• WES data from tumors and matching controls collected from 11 UTSW translocation renal cell carcinoma (tRCC) patients.

  This study investigates translocation renal cell carcinoma (tRCC) to identify mutations contributing to tRCC progression. The analysis relies on Whole Exome Sequencing (WES) data obtained from 11 patients treated at University of Texas Southwestern Medical Center (UTSW) affiliated hospitals, including Parkland Hospital and Children’s Medical Center. Tumor samples and their corresponding normal DNA were sequenced using the Illumina platform.

  Dataset EGAD50000000171

• Breast Cancer Histology Images

  Fresh frozen breast cancer H&E tissue images collected and annotated by the International Cancer Genome Consortium (ICGC), that included the BASIS collaboration. Associated with whole genome sequence data as originally described by Nik-Zainal et al, Nature, 2016 (DOI: 10.1038/nature17676) and deposited with ID EGAS00001001178

  Dataset EGAD00010001911

• Whole genome sequencing data of normal/tumors pairs from 9 patients with uterine or ovarian carcinosarcoma.

  This dataset provides whole genome sequencing data of normal/tumors pairs from 9 patients with uterine or ovarian carcinosarcoma using the HiSeq 2000 sequencing system. It includes 27 samples (9 normals, 16 uterine tumors and 2 ovarian tumors). Through separate whole genome sequencing of carcinomatous and sarcomatoid components, we analyse and compare the genomic alterations of these components.

  Dataset EGAD00001003755

• Next Generation Sequencing Characterization of Hematopoietic Stem and Progenitors Cells in Human Systemic Lupus Eryhtematosus

  This dataset contains RNA-sequencing of Bone marrow-derived CD34+ cells from Healthy Controls (n=2) and SLE patients (n=8). SLE patients are divided into two categories based on severity: patients with moderate/mild disease (n=3) and patients with severe disease (n=5). Libraries were generated using the Illumina TruSeq Sample Preparation kit v2. Single-end 75-bp mRNA sequencing was performed on Illumina NextSeq 500. The raw fastq files are uploaded.

  Dataset EGAD00001005052

• PBMC gene expression profiles in diet treated celiac disease upon oral gluten challenge

  This dataset contains PBMC genome-wide RNAseq reads from 21 samples and one expression matrix file after alignment and aggregation of the 21 samples. The samples are case-control drawn on day 6 from long-term GFD treated CD patients after 3 day oral gluten challenge, on day 0 from patient controls on long-term GFD treatment, and on day 6 from 4 week GFD treated healthy controls after 3 day oral gluten challenge.

  Dataset EGAD00001006655

• Next Generation Sequencing Characterization of Hematopoietic Stem and Progenitors Cells in Human Systemic Lupus Eryhtematosus (2)

  This dataset contains RNA-sequencing of Bone marrow-derived CD34+ cells from Healthy Controls (n=2) and SLE patients (n=10). SLE patients are divided into two categories based on severity: patients with moderate/mild disease (n=4) and patients with severe disease (n=6). Libraries were generated using the Illumina TruSeq Sample Preparation kit v2. Single-end 75-bp mRNA sequencing was performed on Illumina NextSeq 500. The raw fastq files are uploaded.

  Dataset EGAD00001009744

• Single Nuclei RNA sequencing batch 1

  This dataset includes the first 9 PTC samples and 6 ATC samples profiled on the same sequencing flowcell.

  Dataset EGAD00001011366

• Landscape of somatic mutations and DNA copy number alterations and transcriptomic profiling identifies metabolic reprogramming as a hallmark of ibrutinib resistance

  Whole-exome sequencing (WES) was conducted on the clinical specimens of 14 cases that had sufficient isolated tumor DNA, including 7 ibrutinib-sensitive cases and 7 ibrutinib-resistant cases. Whole transcriptome sequencing (RNA-seq) was performed on clinical specimens isolated from 14 ibrutinib-sensitive and 7 ibrutinib-resistant cases. Unsupervised hierarchical clustering of MCL tumors using RNA-seq gene expression data showed a response-specific gene expression signature.

  Study EGAS00001003418

• NEC

  This multi-centre, non-randomized, open-label, phase II trial (NCT03016338), assessed niraparib monotherapy (cohort 1, C1), or niraparib and dostarlimab (cohort 2, C2) in patients with recurrent serous or endometrioid endometrial carcinoma. The primary endpoint was clinical benefit rate (CBR). Secondary outcomes were safety and objective response rate (ORR). Translational research was an exploratory outcome. Potential biomarkers were evaluated in archival tissue by immunohistochemistry and next generation sequencing panel. Feasibility of liquid biopsy by ctDNA was assessed.

  Study EGAS00001007013

• TRACERx NSCLC - whole genome sequencing for ctDNA study

  Data used in "An ultra-sensitive and specific ctDNA assay provides novel pre-operative disease stratification in early stage lung adenocarcinoma"

  Dataset EGAD50000000452

• Genomic Landscape of Chordoid Glioma

  This data set consist genomic information of 10 Chordoid Glioma samples: - Exome sequencing: 10 tumors and matched normal DNA for four of them (BAM files) - RNAseq : 10 tumors (fastq files) - CNV array: 9 tumors (IDAT files)

  Dataset EGAD00001004112

• CRISPR screen M14, NCI-H3122

  Genome wide CRISPR screen was performed to find resistance to targeted drugs for melanoma and lung

  Dataset EGAD00001001389

• Epigentic sequence data of monocytes and macrophages

  Data for paper: Epigenetic dynamics of monocyte to macrophage differentiation with Chip Seq, NOMe, mRNA, total RNA, noncoding RNA, whole genome bisulfite seq,

  Dataset EGAD00001002201