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• Redefined indel taxonomy reveals insights into mutational signatures

  Despite their deleterious effects, small insertions and deletions (indels) have received far less attention than substitutions. Here we generated isogenic CRISPR-edited human cellular models of post-replicative repair dysfunction (PRRd), including individual and combined gene-edits of mismatch repair (MMR) and replicative polymerases (POLE and POLD1), enabling the study of mutational processes driving indel formation.

  Study EGAS50000000148

• HDAC3 mediates the inflammatory response and LPS tolerance in human monocytes and macrophages

  Study EGAS00001004218

• EXPRESSION OF ANTIBODY-DRUG CONJUGATE TARGETS IN BREAST CANCER METASTASES AND NORMAL TISSUE

  Using bulk mRNA sequencing, we investigated the expression of 72 ADC targets, which are clinically approved or under investigation, in 909 samples (64 primary untreated, 749 metastatic, 96 normal) from 30 female patients from our post-mortem tissue donation program UPTIDER (NCT04531696). The study explores changes in target expression across multiple samples to identify novel targets of clinical interest and validation

  Study EGAS50000001334

• The molecular landscape of colorectal cancer reveals genetic mutations - COCA-CN

  We collected tumor samples and adjacent nomal mucosae from 46 patients with colorectal cancer in surgical operation from 2014 to 2016 in the First Affiliated Hospital of Chongqing Medical University (Chongqing, China) and the Research Institute of Surgery, Third Military Medical University (Chongqing, China). the qualified captured library of each sample was then loaded on Illumina HiSeq 2000 (Illumina, San Diego, CA) platforms and subjected to high-throughput sequencing.

  Dataset EGAD00001003304

• Gene expression profiles of single disseminated breast cancer cells

  A set of 56 EpCAM-positive cells derived from bone marrow aspirates of breast cancer patients or patients without a cancererous disease (30 cells from 21 M0-stage and 11 cells from five M1-stage breast cancer patients, 15 cells from seven non-cancer patients serving as controls). EpCAM-positive cells from breast cancer patients were considered disseminated tumor cells as they harbored copy number alterations and showed high expression of the epithelial marker EpCAM and the mammary luminal progenitor marker KIT in comparison to EpCAM-positive bone marrow cells from non-cancer patients. Paired-end RNA-Sequencing of the samples was performed on Illumina NovaSeq6000, raw data are provided in the Fastq format.

  Dataset EGAD00001006359

• Transcriptional mechanisms of resistance to anti-PD-1 therapy

  Purpose: To explore factors associated with response and resistance to anti-PD-1 therapy, we analyzed multiple disease sites at autopsy in a patient with widely metastatic melanoma who had a heterogeneous response.Materials and Methods: Twenty-six melanoma specimens (four pre-mortem, 22 post-mortem) were subjected to whole-exome sequencing. Candidate immunologic markers and gene expression were assessed in ten cutaneous metastases showing response or progression during therapy.Results: The melanoma was driven by biallelic inactivation of NF1. All lesions had highly concordant mutational profiles and copy number alterations, indicating linear clonal evolution. Expression of candidate immunologic markers was similar in responding and progressing lesions. However, progressing cutaneous metastases were associated with over-expression of genes associated with extracellular matrix and neutrophil function.Conclusions: Although mutational and immunologic differences have been proposed as the primary determinants of heterogeneous response/resistance to targeted therapies and immunotherapies, respectively, differential lesional gene expression profiles may also dictate anti-PD-1 outcomes.

  Study EGAS00001002195

• SCLC MeDIP-seq

  Methylation profile of 33 patients with small cell lung cancer (SCLC) for both, tumour and normal lung samples using MeDIP-seq.

  Dataset EGAD50000000724

• OncoScan SNP data set for localized follicular lymphoma (lFL)

  149 unpaired initial tumor samples (133/149 FFPE and 16/149 fresh frozen samples) of lFL patients measured with OncoScan SNP microarrays, Affymetrix CEL intensity data file types (Thermo Fisher Scientific, Waltham, Massachusetts, USA)

  Dataset EGAD00010002593

• Identifying new diagnostic and treatment pathways for patients with unclassifiable sarcomas

  Whole genome sequencing of tumour normal pairs of human undifferentiated sarcomas.

  Dataset EGAD00001003216

• GCAT| PCAs GCATcoreSpain V2

  First 20 principal components of 4988 genotyped GCAT Cohort individuals with Infinium Multi-Ethnic Global (MEGAEX2) array, with data for Cr1-22. Plink files with QC and imputed (SHAPEIT+IMPUTE).

  Dataset EGAD00001007730

• Dataset for Stromal-induced epithelial-mesenchymal transition induces drug resistance in acute lymphoblastic leukemia

  RNA-seq was performed to compare gene expression profiles between 11 patient adherent ALL samples and nonadherent ALL samples.

  Dataset EGAD00001009056

• Clinical dataset (new)

  ctDNA guiding adjuvant immunotherapy in urothelial carcinoma (Nature 2021). ABACUS clinical data cut (2020) used in 2021 paper: Clinical data include PCR, RFS_months, RFS_event, and OUTCOME for 40 patients in ABACUS with ctDNA data.

  Dataset EGAD00001007578

• Whole-exome sequencing data from breast cancer recurrence, endometrial cancer, and colon tumor samples harboring a rare germline BARD1 variant

  This dataset comprises whole-exome sequencing data from tumor and matched blood samples of a patient with breast cancer recurrence and endometrial cancer carrying a germline BARD1 p.(Gly753Val) variant, as well as from the colon tumor of the proband's father

  Dataset EGAD50000002412

• Whole-genome sequencing data of metastatic salivary gland cancer

  This dataset contains whole-genome sequencing data of three patients with metastatic salivary gland cancer who underwent autopsy to harvest tumor biopsies from spatially separated metastatic sites and biopsies from healthy skin as a control. Two patients had the subtype adenoid cystic carcinoma (patients 1 and 4) and one patient had the subtype myoepithelial carcinoma.

  Dataset EGAD50000002056

• Targeted DNA sequencing of TTFields-treated glioblastoma, IDH wildtype

  This dataset contains raw paired-end FASTQ files from targeted DNA sequencing using the TruSight Oncology 500 panel in patients with glioblastoma, IDH wildtype, treated with surgery, standard chemoradiotherapy and Tumor Treating Fields at Charité – Universitätsmedizin Berlin. Tumour samples were collected at first surgery and are linked to pseudonymised clinical and molecular annotations described in the associated EGA study.

  Dataset EGAD50000002117

• Whole exome sequencing data of matched pairs of primary tumour and normal frozen tissue of seven osteosarcoma patients

  This dataset contains whole exome sequencing data of matched pairs of primary tumour and normal frozen tissue of seven osteosarcoma patients. Whole exome sequencing with a minimum coverage of 100x was performed using the Illumina Novaseq6000 platform and the Agilent SureSelect Human All Exon V7 kit.

  Dataset EGAD50000002264

• Spatial transcriptomics reveals immune and tissue remodeling, highlighting diverse host responses across mycobacterial granuloma types

  Granulomas are the hallmark of Mycobacterium infections, forming structured immune environments that drive disease persistence. However, their spatial and functional organization remains unclear. Using spatial RNA sequencing on 33 patient explants, we try to reveal the detailed gene expression and cell composition landscape of granulomas.

  Dataset EGAD50000001462

• MET amplification in gastric cancer

  WES sequencing of two cases of MET amplified gastric cancer. Six unfixed fresh frozen samples were obtained from the primary tumors (three samples from each) and three samples from corresponding non-neoplastic mucosa. In addition, formalin-fixed and paraffin-embedded (FFPE) samples were obtained from the primary tumors (n=2), lymph node metastases (n=7) and non-neoplastic mucosa (n=2).

  Dataset EGAD50000001099

• Transcriptomic consequences of complex rearrangements inv8p23.1 and inv17q21.31 associated with Autism Spectrum Disorders

  We have performed an RNAseq analysis in order to elucidate the transcriptomic consequences of two complex rearrangements associated with Autism Spectrum Disorder, including patients and controls (total n=24).

  Study EGAS00001005612

• Gene panel sequencing of paired samples from primary and relapsed IDH-wt glioblastomas

  This dataset contains gene panel sequencing data from 43 sample pairs of primary and relapsed IDH-wt glioblastomas. The gene panel covers 50 glioma-associated genes. 14 of the sequenced sample pairs were sequenced with whole genome sequencing also and are accessible under EGAD00001004563.

  Dataset EGAD00001004565

• TN

  In order to comprehensively investigate the genetic relationship between PTC tumors and benign nodules, we totally collected 127 fresh-frozen biopsies samples from 28 patients with concurrent thyroid benign nodule and PTC (n=20) or simple benign nodule (n=8). We carried out whole-exome sequencing on all the 127 biopsies samples and RNA-sequencing in total of 40 samples.

  Dataset EGAD00001003351

• Illumina 5'end RNA sequencing

  The dataset contains 200 fastq files of Illumina 5'end RNA sequencing data of 50 PBMC samples. The paired-end data includes 100 fastq files (R1 and R2) of 50 full-length cDNA sequencing libraries and 100 fastq files (R1 and R2) of 50 HLA amplicon sequencing libraries.

  Dataset EGAD00001006838

• Genomic insight into the origins and dispersal of the Brazilian Coastal Natives

  Study EGAS00001004036

• The dataset of Detection and characterization of lung cancer using cell-free DNA fragmentomes on NovaSeq 6000 at 1-2x coverage

  The dataset contains 364 CRAM files from whole-genome next-generation sequencing on the Illumina NovaSeq 6000 at 1- 2x coverage. These are plasma samples from healthy individuals and patients with cancer.

  Dataset EGAD50000001961

• A complex chromosomal rearrangement (CCR) was resolved at the nucleotide level by whole genome long read sequencing using PacBio sequencing platform.

  A complex chromosomal rearrangement (CCR) involving 7 chromosomes and 11 breakpoints was resolved at the nucleotide level by whole genome long read sequencing using PacBio sequencing platform.

  Study EGAS00001008133