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• WES of breast cancer patients and controls

  Investigation of post-zygotic and germline variants using whole exome and ultra-deep duplex sequencing in paired uninvolved margin and primary tumor samples from 126 breast cancer patients with differing survival outcomes, with skin or blood samples as reference. Pairs of uninvolved margin and blood samples were also collected for 15 reduction mammoplasty patients without personal or familial history of cancer, serving as controls.

  Dataset EGAD50000000770

• Dataset on keratinocytic gene expression pattern in Hidradenitis suppurativa

  Human skin samples were obtained from HS patients after informed consent (Ethical vote, University of Würzburg; No. 306/12). Lesional and perilesional were taken and epidermis and dermis separated. Isolated epidermal keratinocytes were further processed for RNA isolation. mRNA was extracted from five pairwise-matched lesional and perilesional epidermal HS pellets and RNA sequencing was performed.

  Dataset EGAD00001008005

• Genomics from LCCC1525: A Priming Dose of Cyclophosphamide Prior to Pembrolizumab to Treat mTNBC

  This phase II, single-arm, multicenter study will evaluate pembrolizumab therapy, 200 mg IV, given every 3 weeks (Q3W), following a single priming dose of cyclophosphamide, 300 mg/m2 IV, in patients with advanced triple-negative breast cancer (TNBC) who have received at least one prior line of therapy. Data uploaded consists of FASTQ sequencing data from tumor RNASeq (pre-pembrolizumab), tumor and normal tissue WES, and sequencing for targeted T and B cell chains (TRB, IGK, IGL, IGH) from peripheral blood at various timepoints: pre-, post-, and during pembrolizumab therapy.

  Study phs002659

• Epigenomics of Prostate Cancer from Cell Free Plasma

  We sought to perform epigenomic characterization of prostate cancers by profiling circulating nucleosomes isolated from patient plasma using cell free chromatin immunoprecipitation followed by sequencing (cfChIP-seq). Our major findings include identification of prostate-cancer specific regulatory elements using a novel statistical method accounting for variable tumor DNA fraction in plasma, inferring transcription factor activity based on binding motif enrichment within regulatory elements, and epigenetically phenotyping patients based on clinical and genomic features. Data available in dbGaP will include cfChIP-seq and targeted sequencing from approximately 50 patients with a known diagnosis of cancer and healthy patient controls.

  Study phs003482

• colorectal_epigenome

  Three different types of samples were used: 19 normal adjacent, 17 adenoma and 19 colorectal tumor tissue samples. This included 10 pairs of colorectal cancer and normal samples and 1 pair of adenoma-normal samples of the same patient. Tissue specimens were formalin-fixed paraffin-embedded (FFPE). DNA was isolated using the QIAamp FFPE Tissue kit (Qiagen, Hilden, DE) according to the manufacturer’s instructions. The processed DNA was run on the Illumina Human MethylEPIC® v1.0 BeadChip array.

  Dataset EGAD00010002726

• SG Peranakan Project dataset

  This dataset contains the genotypes jointly-called from whole genome sequencing data of 177 self-reported Peranakans in Singapore. Reads were aligned to GRCh37 reference genome and jointly-called with other WGS samples. Basic quality control measures and population phasing without reference were performed on the called genotypes. The data are stored in VCF v 4.3 format, and one .vcf.gz file stored the genotypes from one of the 23 chromosomes (22 autosomes+X chromosome).

  Dataset EGAD00001007786

• Peripheral blood RNA-sequencing in 4,732 participants of the INTERVAL cohort

  We performed bulk RNA-sequencing on peripheral blood collected from 4,732 blood donors recruited as part of the INTERVAL study. Using these data, we mapped gene expression and splicing quantitative trait loci (QTLs). Then, we integrated these data with protein, metabolite and lipid QTLs in the same individuals. The study aimed to identify the shared genetic etiology across transcriptional phenotypes, molecular traits and health outcomes in humans.

  Dataset EGAD00001008015

• 10xchromium 3' v3 sequencing from cerebellum, lung, and heart aligned to GRCh38 genome

  Each run contains single cell RNA-seq data from unbiased sampling of single cells from the indicated human tissue. Single cell suspensions were prepared using enzymatic dissociation followed by tituration. The samples were processed using the 10XChromium 3' v3 sequencing pipeline, sequenced on an Illumina NovaSeq 6000, and analyzed using the cellranger software and aligned to the human GRCh38 genome version 93.

  Dataset EGAD00001006110

• Enhancer profiling to identify identifies epigenetic markers of endocrine resistance in metastatic castration resistant prostate cancer patients

  ChIP-seq and matched input data of AR, FOXA1 and H3K27ac for mCRPC patient samples taken prior to and after treatment with AR targeted therapy

  Dataset EGAD00001008688

• Vγ9Vδ2-T cells in chronic lymphocytic leukemia patients and healthy controls

  RNA sequencing data from Vγ9Vδ2-T cells from chronic lymphocytic leukemia patients and age-mnatched healthy controls. Matched Vγ9Vδ2-T cell samples before and after expansion with autologous monocyte-derived dendritic cells for each donor are included.

  Dataset EGAD00001004325

• Whole-exome sequencing and microRNA profiling predicted relapse risk of stage I lung adenocarcinomas

  This dataset contains BAM files for whole exome-sequencing of stage I lung adenocarcinomas from Asian patients. In total, there are 113 patients and 262 samples, including 113 tumor samples, 113 adjacent normal samples and 36 buffy coat samples.

  Dataset EGAD00001006188

• Genome-wide DNA Methylation Analysis Reveals a Unique Methylation Pattern for Pleural Mesothelioma Compared to Healthy Pleura and Other Lung Diseases

  Study EGAS00001007783

• PDX WES for #87, #95, #32, #217, #86

  Exome sequencing of tumour PDX and matched patient blood

  Dataset EGAD50000000215

• EGAD00010000538

  28 unlinked autosomal microsatellite loci for 20 African and 4 philippine populations

  Dataset EGAD00010000538

• Biomarker Data Subset

  This dataset contains data for CBC counts and absolute protein abundance measurements from ELISA experiments.

  Dataset EGAD00001011163

• RNAseq data

  RNAseq data for 10 patients: 10 tumors and 10 cell lines

  Dataset EGAD00001002691

• Malignant pheochromocytomas/paragangliomas harbor mutations in transport and cell adhesion genes

  One out of ten patients with pheochromocytoma (PCC) and paraganglioma (PGL) develop malignant disease. Today there are no reliable pathological methods to predict malignancy at the time of diagnosis. Tumors harboring mutations in the succinate dehydrogenase subunit B (SDHB) gene often metastasize but the sequential genetic events resulting in malignant progression are not fully understood. The aim of this study was to identify somatic mutations that contribute to the malignant transformation of PCC/PGL. We performed pair-wise (tumor-normal) whole-exome sequencing to analyze the somatic mutational landscape in five malignant and four benign primary PCC/sympathetic PGL (sPGL), including two biological replicates from each specimen. In total, 225 unique somatic mutations were identified in 215 genes, with an average mutation rate of 0.54 mutations/megabase. Malignant tumors had a significantly higher number of mutations compared to benign tumors (p<0.001). Three novel genes were identified as recurrently mutated; MYCN, MYO5B and VCL, and mutations in these genes were exclusively found in malignant sPGL tumors. Mutations in the MYO5B gene could be verified in two publicly available data sets. A gene ontology analysis of mutated genes showed enrichment of cellular functions related to cytoskeletal protein binding, myosin complex, and motor activity, many of which had functions in Rab and Rac/Rho GTPase pathways. Conclusively, we have identified recurrent mutations in genes related to intracellular transport and cell adhesion, and we have confirmed recurrent mutations of MYO5B in PCC/PGL cases with malignant potential. Our study suggests that deregulated Rab and Rac/Rho pathways may be important in PCC/PGL tumorigenesis.

  Study EGAS00001001601

• Methylation sequencing dataset for "Molecular counting enables accurate and precise quantification of methylated ctDNA"

  Methylation sequencing dataset for "Molecular counting enables accurate and precise quantification of methylated ctDNA." This dataset was created by running samples through Northstar Response, where bisulfite converted samples are amplified in a multiplex PCR targeting more than 500 genomic regions. Samples in this dataset include contrived samples made from 84 different tumors DNA, each mixed with their matched buffy coat DNA at varying ratios, as well as cfDNA and buffy coat DNA samples collected from 67 cancer patients undergoing treatment. All samples were sequenced on Illumina NextSeq 2000 with single end 100 cycle sequencing; files are in fastq.gz format.

  Dataset EGAD50000001015

• A Model of Human Asthma Exacerbation Identifies Mechanisms That Drive Allergic Asthma

  In this study, we will enroll allergic adults to undergo bronchoscopic segmental allergen challenge, in order to identify differences in the airway immune response to allergen in those with asthma compared to those without asthma. After a discussion about the study and potential risks, subjects giving written informed consent will undergo two bronchoscopies. During the first procedure, samples will be collected from the left lung and allergen will be administered to a small segment of the right lung. The second procedure will be performed 24 hours later, with collection of samples from the allergen-challenged lung segment.

  Study phs003101

• Reference Epigenomes and Regulatory Landscape of CLL

  Analysis of the reference epigenomes and regulatory landscape of CLL as a whole and its major clinico-biological subtypes (with mutated and unmutated IGHV) in the light of the normal B-cell differentiation. We have extensively characterized the reference epigenomes of seven primary chronic lymphocytic leukemia samples (CLLs) with mutated (n=5) and unmutated IGHV (n=2) as well as several mature B-cell subpopulations (naive B cells from blood and tonsil, germinal center B cells, memory B cells and plasma cells from tonsil) using genome-wide maps of six histone marks (H3K4me3, H3K4me1, H3K27ac, H3K36me3, H3K9me3 and H3K27me3), DNA accessibility (ATAC-seq), DNA methylation (whole-genome bisulfite sequencing) and gene expression (RNA-seq). Furthermore, we have mapped the regulatory chromatin landscape of 100 additional CLL cases using chIP-seq of H3K27ac and ATAC-seq and linked these data to additional layers of information (whole-genome and/or whole-exome sequencing (WGS/WES), RNA-seq and DNA methylation microarrays) studied in the context of the International Cancer Genome Consortium (ICGC).

  Dataset EGAD00001004046

• DNA sequences from adolescent and young adult patients with melanoma treated with immunotherapy

  Sequencing libraries were prepared and barcoded using the unique molecular identifier and index tagging following the VariantPlex Somatic Protocol (ArcherDx). Pool-library was loaded at 1.2 pM concentration with 20% PhiX and paired-end sequencing was performed using the NextSeq 500 Illumina sequencer using 300 cycle high output reagent kit.

  Dataset EGAD50000000353

• 340 human whole genome sequences from Angola and Mozambique

  CRAM files of 340 human genomes from Angola and Mozambique. Paired-end reads were generated in an Illumina-X Ten and were mapped against the human reference genome build hg19/GRCh37. More details about the sequencing and the samples in Tallman et al. 2023. Nature Communications.

  Dataset EGAD00001011992

• Myocardial Infarction Genetics Exome Sequencing Consortium: Registre Gironi del Cor

  The Registre Gironi del Cor (REGICOR) study developed a nested case-control cohort from the Girona province in Spain in order to study genetic factors associated with the development of coronary heart disease. All exome sequencing was performed at the Broad Institute of Harvard and MIT; samples sequence capture was performed using Agilent SureSelect Human All Exon Kit v2 and sequencing was performed on an Illumina HiSeq 2000 or 2500.

  Study phs000902

• sWGS of Pap test smears from healthy donors and HGSOC patients and matched tumor tissue

  Shallow whole genome sequencing was performed on Pap test smears considering at least 10 M reads per sample. The cohort consists of 77 samples from healthy women, i.e. no tumor diagnosis, and 65 samples from women with a diagnosis of high-grade serous ovarian cancer (HGSOC) taken months or years before diagnosis. 44 primary tumor samples matched to the respective HGSOC patients were sequenced in the same manner as the Pap test smears.

  Study EGAS00001007084

• Correlative Genomic Analysis of Durvalumab plus Pazopanib Combination in Patients with Advanced Soft Tissue Sarcomas

  We conducted an open-label, phase 2 study to determine the activity of the anti-VEGF receptor tyrosine-kinase inhibitor, pazopanib, combined with the anti-PD-L1 immune checkpoint inhibitor, durvalumab, in unselected advanced sarcomas. In addition, we conducted whole exome and transcriptomic sequencing with pre-treatment tissue biopsy to correlate clinical outcomes with molecular and genomic biomarkers to identify patients who would most likely benefit from the combination treatment.

  Study EGAS50000000082