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• Transcriptomics for the ALTTO study

  Transcriptomics for the ALTTO study by high-throughput sequencing. 386 HER2+ breast cancers treated by trastuzumab were sequenced. Two fastq files are given for each sample.

  Dataset EGAD50000000746

• 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

• Exome sequencing data for LMS tumor and control samples

  The data set contains paired end fastq files for whole exome sequencing data for Leiomyosarcoma tumor and control samples

  Dataset EGAD00001003829

• Bacterial SNPs in the human gut microbiome associate with host BMI

  Genome-wide association studies (GWAS) have revolutionized the field of genetics, providing numerous associations between human SNPs and health traits. Likewise, metagenome-wide association studies (MWAS) between bacterial SNPs and human traits can suggest mechanistic links between the microbiota and its host. However, very few such studies have been done to date, in part due to the large number of samples required to address the variable coverage of bacteria across samples and the fact that most bacteria are present in only a subset of the population. Here, we devised an MWAS framework to detect SNPs and associate them with host phenotypes systematically. We recruited and obtained gut metagenomic samples from a cohort of 7,190 healthy individuals and discovered 1,358 statistically significant associations between a bacterial SNP and host body mass index (BMI). To address the possible effects of population structure and linkage disequilibrium, we applied a clumping procedure, and found 40 independent associations between SNPs and host BMI. We uncovered BMI-associated SNPs in the genomes of 27 bacterial species, even though the relative abundance of 12 of these species was not associated with the phenotype. We separated genome-wide sub-species variations from local associations in individual SNPs, and demonstrated how this framework can highlight specific bacterial functions of interest. Our results demonstrate the importance of considering nucleotide-level diversity in microbiome studies and pave the way toward a better understanding of interpersonal gut microbiome differences and their health implications.

  Study EGAS00001007204

• RNA-Seq data for Academic and For-Profit researchers.

  RNA-Seq data for both Academic and For-profit use

  Dataset EGAD00001009676

• Stitched BAM files for manuscript titled Discrepancies in Tumour Mutation Burden (TMB) reporting from sequential Endobronchial ultrasound trans bronchial needle aspiration (EBUS TBNA) samples within single lymph node stations for SNP and INDEL Variant Calling.

  Stitched BAM files for manuscript titled Discrepancies in Tumour Mutation Burden (TMB) reporting from sequential Endobronchial ultrasound trans bronchial needle aspiration (EBUS TBNA) samples within single lymph node stations for SNP and INDEL Variant Calling.

  Dataset EGAD00001012639

• Human tumor scMultiome

  We profile 10 high-grade gliomas patient brain tumor samples by single-cell multiome ATAC + gene expression, using the 10X Chromium technology. 3 sets of fastq are provided for each samples: R1 and R2 for gene expression, R1 and R2 for ATAC-seq as well as index1 and index2 for ATAC-seq.

  Dataset EGAD00001008349

• Re-aligned BAM files for manuscript titled Discrepancies in Tumour Mutation Burden (TMB) reporting from sequential Endobronchial ultrasound trans bronchial needle aspiration (EBUS TBNA) samples within single lymph node stations for Copy Number Variant Calling.

  Re-aligned BAM files for manuscript titled Discrepancies in Tumour Mutation Burden (TMB) reporting from sequential Endobronchial ultrasound trans bronchial needle aspiration (EBUS TBNA) samples within single lymph node stations for Copy Number Variant Calling.

  Dataset EGAD00001012638

• ChIP-Seq (H3K4me3, H3K4me1, H3K9me3, H3K27ac, H3K27me3, H3K36me3, Input) data for HL60 cell line generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency.

  ChIP-Seq (H3K4me3, H3K4me1, H3K9me3, H3K27ac, H3K27me3, H3K36me3, Input) data for HL60 cell line generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency.

  Dataset EGAD00001002238

• DNA Whole Exome Sequence for manuscript titled: Evaluation of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration (EBUS-TBNA) Samples from Advanced Non-Small Cell Lung Cancer for Whole Genome, Whole Exome and Comprehensive Panel Sequencing

  DNA Whole Exome Sequence for manuscript titled: Evaluation of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration (EBUS-TBNA) Samples from Advanced Non-Small Cell Lung Cancer for Whole Genome, Whole Exome and Comprehensive Panel Sequencing

  Dataset EGAD00001015395

• Whole exome sequence in EGFR-TKI resistant non-small cell lung cancer

  Whole exome analysis to clear molecular basis and mutation spectrum in EGFR-TKI resistant non-small cell lung cancer

  Study JGAS000102

• Shallow dataset

  Associated with Molecular biomarkers in progression from refractory celiac disease to the lethal cancer variety enteropathy associated T cell lymphoma (EATL) Study. shallow Whole Genome Sequencing (sWGS) of 63 samples. sWGS was done to analyze copy number aberration.

  Dataset EGAD50000001165

• Investigating genomic intratumor heterogeneity in colorectal carcinoma

  To investigateintertumor heterogeneity of colorecatal carcinoma, we profiled the genome and epigenome in multiple regions within each of nine colorectal tumors.

  Study JGAS000060

• Whole exome sequencing of solid tumors which received PD-1 blockade therapy

  We performed whole exome sequencing of solid tumors which received PD-1 blockade therapy to evaluate tumor mutation burden.

  Study JGAS000244

• Single-cell genotype-to-phenotype (scG2P) of normal esophageal epithelium

  Single-cell genotype-to-phenotype (scG2P) of normal esophageal epithelium, based on targeted DNA genotyping of mutation hot spots and targeted RNA capture.

  Dataset EGAD50000002066

• Genetic_factors_underlying_premature_coronary_heart_disease_in_patients_with_normal_coronary_arteries

  The study will analyse by exome sequencing 42 Greek patients with premature MI and no vessel disease to identify genetic factors underlying this condition.

  Study EGAS00001000133

• RNAseq in blood CD34+ cells

  The aim of the project was to perform expression quantitative trait locus (eQTL) analysis in blood CD34+ cells from random blood donors.

  Study EGAS00001005655

• Whole exome genome sequencing data to study "A biobank of patient-derived pediatric brain tumor models"

  Whole exome sequencing data to 30 PDOX models (28 early passages, 3 late passages (1 overlap)), 3 cell lines, and 20 matching human tumors

  Dataset EGAD00001003544

• 5WGS and 35WES sample pairs belongs to COCA-CN

  There are 5WGS and 35WES sample pairs from the first affiliated hospital of kunming medical university, which belongs to ICGC projects COCA-CN.

  Dataset EGAD00001003456

• MP-WGS and WES from CCND1-negative MCL

  BAM files from 5 CCND1-negative MCL cases. 4 BAM files corresponded to long insert size Mate Pair-WGS and 3 to WES. In 2 of the cases both technologies were performed.

  Dataset EGAD00001004161

• Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress

  Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress

  Dataset EGAD00001001210

• IMCISION RNAseq

  RNA sequencing could be performed on all 32 baseline and 30 on-treatment primary tumor biopsies. Based on gene-set enrichment analysis, the epithelial to mesenchymal transition signature was enriched in baseline tumors of patients without MPR, though its expression was insufficient to predict ICB response. Baseline and on-treatment IFNγ and T-cell signature expression (Z-score) were not significantly higher in patients with an MPR.­­­ Baseline primary tumor hypoxia-associated gene expression in IMCISION did not predict ICB response. However, on-treatment biopsies of MPR tumor samples showed significantly lower hypoxia gene expression when compared to non-MPR samples. Moreover, in a paired analysis of baseline and corresponding on-treatment samples, a significant decrease of hypoxia-related gene expression was observed in MPR biopsies, while this decrease was absent in non-MPR biopsies.

  Study EGAS00001005454

• Neoadjuvant immune checkpoint blockade in high-risk resectable melanoma

  We conducted a randomized phase II study of neoadjuvant nivolumab versus combined ipilimumab with nivolumab in 23 patients with high-risk resectable melanoma (NCT02519322) and assessed clinical responses and immune correlates. Treatment with combined ipilimumab and nivolumab yielded high response rates (RECIST overall response rate 73%, pathologic complete response rate 45%) but substantial toxicity (73% grade 3 treatment related adverse events), whereas treatment with nivolumab monotherapy yielded modest responses (RECIST overall response rate 25%, pathologic complete response rate 25%) and low toxicity (8% grade 3 treatment related adverse events). Immune correlates of response were identified, demonstrating higher lymphoid infiltrates in responders to both therapies and a more clonal and diverse T cell infiltrate in responders to nivolumab monotherapy. Mutational load was also higher in responders to therapy.

  Study EGAS00001003178

• Neuroblastoma tumor heterogeneity and cell plasticity (from PDX and cell lines)

  Two cell identities, noradrenergic and mesenchymal, have been characterized in neuroblastoma cell lines according to their epigenetic landscapes relying on specific core regulatory circuitries of transcription factors. Yet, their relationship and relative contribution in patient tumors remain to be defined. Here, we document a spontaneous plasticity between the noradrenergic and mesenchymal identities in a subset of cell lines. Strikingly, mesenchymal neuroblastoma cells revert to a noradrenergic phenotype in vivo. Consistently, tumor cells with a mesenchymal identity are detected in single-cell transcriptomic analyses of neuroblastoma tumors and PDX models. Our data also highlight neuroblastoma intra-tumor heterogeneity with the co-existence of distinct tumor populations, including sympathoblast-like and chromaffin-like cells suggesting that neuroblastoma cells arise from a common sympatho-adrenal progenitor.

  Study EGAS00001004781

• The Iberian Roma genetic variant server

  The Roma are the most numerous ethnic minority in Europe. The Iberian Roma arrived in the Iberian Peninsula five centuries ago and still today, they keep a strong group identity. Demographic and cultural reasons lie behind a high rate of Mendelian disease often related to founder variants. We have analysed exome data from 119 Iberian Roma individuals collected from 2018 to 2020. A database of variant frequency has been implemented (IRPVS) and made available online. We have analysed the carrier rate of founder private alleles as well as pathogenic variants present in the general population. Significant enrichment in structural variants involving gene clusters related to keratinization and epidermal growth suggest that evolutive mechanisms have developed towards climate and environmental adaptation. IRPVS can be accessed at http://irpvs.clinbioinfosspa.es/

  Study EGAS00001006758