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• miRNA

  miRNA Sequencing of olfactory mucosa (OM) cells derived from cognitively healthy and individuals with AD exposed to traffic-related ultrafine particles (UFPs) for 72h in submerged cultures. The UFPs used for exposures were: A0 and A20. Exposures were compared to the corresponding blank samples.

  Dataset EGAD50000001532

• WTCCC2 Bacteraemia Susceptibility (BS) samples

  A WTCCC2 project genome-wide association study for bacteraemia susceptibility in 4924 individuals from Kenya, genotyped on the Affymetrix 6.0 array.

  Study EGAS00001001756

• Whole Genome Sequencing for the paper titled "Orthotopic Patient-Derived Xenografts of Pediatric Solid Tumors"

  Whole Genome Sequencing for the paper titled "Orthotopic Patient-Derived Xenografts of Pediatric Solid Tumors"

  Dataset EGAD00001003435

• Glioblastoma stem cell lines WGS data

  WGS data for 20 Glioblastoma stem cell (GSC) lines and matched blood samples. Fastq files are available. For 10 GSC samples and the 10 matched blood samples the reads are on 3 fastq files per sample

  Dataset EGAD00001006488

• Reference exome data for a Northern Brazilian population

  Here we provide a catalogue of variants called after sequencing the exomes of 45 babies from the State of Rio Grande do Nord in Brazil. Our data set provides a useful reference point for diagnosis of rare diseases in Brazil.

  Dataset EGAD00001006407

• Reconstructing the dispersals and adaptive history of Bantu-speaking populations in Africa and North America

  Bantu languages are spoken by ~310 million Africans, yet the genetic history of Bantu-speaking populations remains largely unexplored. We generated genomic data for 1,318 individuals from 35 populations in western central Africa, where Bantu languages originated. We found that early Bantu speakers first moved southward, through the equatorial rainforest, before spreading toward eastern and southern Africa. We also found that genetic adaptation of Bantu speakers was facilitated by admixture with autochthonous populations, particularly for the HLA and LCT loci. Finally, we identified a major contribution of western central African Bantu speakers to the ancestry of African Americans, whose genomes present no strong signals of natural selection. Together, these results highlight the contribution of Bantu-speaking peoples to the complex genetic history of Africans and African Americans.

  Study EGAS00001002078

• Integrated Analysis of Multimodal Single-Cell Datasets for SARS-CoV-2 Vaccination

  The study aimed to explore immune responses during a time course of BNT162b2 mRNA vaccination. To better characterize these responses, we utilize a suite of multi-modal single-cell sequencing technologies to identify and characterize antigen-specific CD8+ T cells. We leverage an integrative analysis strategy to characterize five molecular modalities in these cells. Our dataset enables the discovery of new subpopulations, molecular signatures, and developmental regulators of these cells. Moreover, we identify these cells in SARS-CoV-2 infected patients and demonstrate their positive predictive value for subsequent clinical recovery. The sequence data of CITE-seq, ASAP-seq and ECCITE-seq experiments are deposited in dbGaP. Peripheral blood mononuclear cell (PBMC) samples for CITE-seq and ASAP-seq were collected from six healthy donors at four time points: immediately before (Day 0) vaccination, after primary vaccination (Day 2, Day 10), and seven days after boost vaccination (Day 28). PBMC samples for ECCITE-seq were collected from eight healthy donors on Day 28.

  Study phs003322

• Ultra-sensitive ctDNA monitoring required for predicting response and resistance to immunotherapy in advanced melanoma

  Circulating tumor DNA (ctDNA) monitoring in peripheral blood has shown promise for disease surveillance and prognostication of ICI response. Yet even in the metastatic context, ctDNA signals can be missed, suggesting the need for increased assay sensitivity. We used a tumor-informed ctDNA assay capable of detection down to 1 part-per-million (PPM) ctDNA to profile 188 plasma samples from 23 melanoma patients receiving ICI over several years. Residual disease was detected in ctDNA over a broad range, from 130,000 PPM down to 2.3 PPM, with approximately a quarter of detections below 50 PPM. Early on-treatment increases in ctDNA level, and both ctDNA-based molecular clearance (mCR) and molecular progression (mPD) were all prognostic of both OS and PFS. Additionally, mCR consistently preceded radiographic imaging. Our results show the importance and utility of an ultra-sensitive ctDNA assay in advanced melanoma treated by ICI with potential implications for other cancers.

  Study EGAS50000000550

• WGS data of paediatric T-ALL acute lymphoblastic leukemia (set2)

  The dataset includes FASTQ and CRAM files from diagnostic and matched remission (control) samples of one T-ALL patient (ALLK-118), and relapse (from BM and tonsil) and matched remission (control) samples of another T-ALL sample (ALLT-317, tonsil relapse ALLT-3107L). Diagnostic sample of ALLT-317 in the first dataset in this submission. Sequencing library was made using PCR free-based WGS library preparation (PCR-), using NEBNext® Ultra™ II DNA Library Prep Kit (Cat No. E7645). Both diagnostic/relapse (90x) and remission (30x) samples were sequenced using Illumina Novaseq 6000.

  Dataset EGAD50000002014

• Poland WES - The Genomic Map of Poland in Open Access

  This project used NGS (next generation sequencing), using Illumina NOVASEQ 6000 and Illumina DRAGEN aligner. The dataset includes BAM and BAM.BAI files from Whole Exome Sequencing of 450 samples (227 female, 223 male, Poland from POPULOUS collection). Library Construction Protocol: Illumina DNA Prep with Enrichment. Reference Genome: GRCh37.

  Dataset EGAD50000000130

• Whole genome sequencing data of normal/tumors pairs from 4 patients with uterine or ovarian carcinosarcoma.

  This dataset provides whole genome sequencing data of normal/tumors pairs from 4 patients with uterine or ovarian carcinosarcoma using the HiSeq 2000 sequencing system. It includes 10 samples (4 normals, 4 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 EGAD00001003898

• scRNA-seq dataset of patient and healthy donors

  scRNA-seq dataset on a patient (P) presenting with defects of immunity and four healthy donors (C1, C2, C3, C4). This dataset contains raw and processed files from scRNA-seq performed on samples using the 10x Genomics Chromium Controller with the Chromium Single Cell 3′ Reagent Kit (v3 chemistry). There are 15 paired-end fastq files (3 per patient/donor - I1, R1, R2) and 15 processed files generated with 10x Genomics Cell Ranger v3.0.2 software against GRCh38 human reference transcriptome (3 per patient/donor - barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz).

  Dataset EGAD00001008372

• Transcriptome profiling of three giant cell tumour of bone (GCTB) cell lines

  This dataset contains RNA-seq data of giant cell tumour of bone (GCTB) cell lines (n=3). Cell lines consist of neoplastic "stromal" cells harboring a heterozygous H3F3A p.G34W mutation. RNA-seq was performed on the BGISEQ-500 platform (PE100) and uploaded data contains fastq files, vcf files, and gene expression values (TPM). Cell lines, data generation, and data analysis are described in the following publication: Venneker et al., Histone deacetylase inhibitors as a therapeutic strategy to eliminate neoplastic “stromal” cells from giant cell tumors of bone, 2022.

  Dataset EGAD00001009074

• Dataset for Direct Detection of Early-Stage Cancers using Circulating Tumor DNA

  The dataset for Direct Detection of Early-Stage Cancers using Circulating Tumor DNA includes 602 bam files from next-generation sequencing on the Illumina HiSeq2500 or MiSeq. The samples analyzed include cancer cell lines as well as plasma and tissue specimens from healthy individuals and patients with cancer.

  Dataset EGAD00001003601

• FACS sorting of ploidy populations in an undifferentiated soft tissue sarcoma for RRBS

  Groups of cells belonging to different ploidy populations (based on PI staining) were collected from an undifferentiated soft tissue sarcoma. The different ploidy populations underwent RRBS, after which copy number signatures for the ploidy-sorted populations and the bulk population were extracted.

  Dataset EGAD00001008667

• Whole-genome sequence 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 later used for WGS. For all tumor and matched normal (peripheral blood) samples, DNA was extracted with the Qiagen AllPrep DNA/RNA kit (tumor samples from patients 25,26,28-32) or the Qiagen Blood and Tissue Extraction Kit (tumor samples from patients 1-4,7,9-17, and all blood samples). For all tumor and normal samples, DNA extraction was followed by library construction and sequencing using Illumina HiSeq2500 whole genome shotgun v4 chemistry with paired-end 125bp reads.

  Dataset EGAD00001003984

• Annotated VCF Files for WGS of ASD Cohort with 68 Individuals from 22 families, enriched for recent shared ancestry

  We performed whole genome sequencing (WGS) in an ASD cohort of 68 individuals from 22 families enriched for recent shared ancestry. Samples were sequenced using Illumina HiSeq X platform, and Variants (single nucleotide variants (SNVs) and insertions or deletions (indels)) were detected using GATK with HaplotypeCaller. Quality control checks for (i) duplicate samples, (ii) samples per platform, (iii) genome call rate, (iv) missingness rate, (v) singleton rate, (vi) heterozygosity rate, (vii) homozygosity rate, (viii) Ti/Tv ratio, (ix) inbreeding coefficient, and (x) sex inference were performed as previously described. Variant call format (VCF) files for SNVs and indels were annotated with ANNOVAR using allele frequencies from the 1000 Genomes project (2015; 1000G), the Genome Aggregation Database (gnomAD), and the Greater Middle East Variome Project (GME).

  Dataset EGAD00001008634

• DCIS Whole Exome & Whole Genome Sequencing Data

  Primary DCIS and recurrent DCIS/IBC (total n=82, ipsilateral n=78 and contralateral n=4) as well as non-recurrent DCIS (n=32) cases were identified through hospital databases from Royal Melbourne Hospital (RMH), Nottingham City Hospital (UK), the LifePool cohort and Peter MacCallum Cancer Centre (PMCC). All cases were micro-dissected from haematoxylin stained sections (range 4-20 sections) by manual micro-dissection to achieve >50% tumour tissue purity. DNA was extracted using the FFPE AllPrep kit (Qiagen, MD, USA). Depending on the success and timing of DNA extraction (Figure 1), cases were analysed by a targeted sequencing panel (n=46, samples pre-2020), whole exome sequencing (WES, n=67), or low-coverage whole genome sequencing (LCWGS). WES: DNA was processed by the Australian Genome Research Facility (AGRF) using the Twist Bioscience Human Comprehensive Exome v1 or v2 (Twist Bioscience HQ, South San Francisco, CA, USA) according to the Twist Target Enrichment Standard Hybridisation Protocol. Sequencing was performed on the Illumina NovaSeq 6000 with 150 bp paired-end reads for a median depth of 101.29x, range: 20.39-247x. Whole Genome Sequencing (WGS): Libraries for four paired samples with matched stromal DNA were made, processed and sequenced by AGRF using the IDT xGen Kit (USA) according to the manufacturer’s protocol, aiming to achieve 60x depth for tumour DNA and 30x for matched normal. File type: Paired-end FASTQ.

  Dataset EGAD50000001846

• The analysis of mtDNA variability of the modern Polish population

  The aim of the present study was to define the mtDNA variability of Polish population. For the first time, the study of Polish population was conducted on such a large number of individuals (n=5800) representing administrative units of both levels of local administration in Poland (voivodeships and counties). Furthermore, the clusters were used as an additional form of population subdivision, corresponding to geographic regions of Poland.

  Study EGAS00001003309

• The data access committee for Single molecule genome-wide mutation profiles of cell-free DNA for non-invasive detection of cancer

  Dac EGAC00001003253

• GnRH Agonist-Induced Ovarian Suppression and Ovarian Steroids in PMDD and Controls

  In this study, lymphoblastoid cell line cultures (LCLs) from women with premenstrual dysphoric disorder (PMDD) and asymptomatic controls were compared via whole-transcriptome sequencing (RNA-seq) during untreated (ovarian steroid-free) conditions and after estradiol and progesterone treatment. In untreated LCLs, pathway analysis of the LCL transcriptome revealed, among others, over-expression of ESC/E(Z) complex genes (an ovarian steroid-regulated gene silencing complex) with significant overexpression of MTF2, PHF19, and SIRT1 (P<0.05) in cells from women with PMDD compared with controls. Finally, mRNA expression of several ESC/E(Z) complex genes were increased by progesterone in controls only, and decreased by estradiol in PMDD LCLs.

  Study phs001344

• Deciphering molecular mechanisms underlying hematological malignancies and development of novel therapeutic approaches

  We aim to identify epigenomic features dysregulated in hematological malignancies through epigenetic analyses of hematological malignant cells. We also perform RNA sequencing to profile tumor cell-specific transcriptomes and target gene sequencing to profile somatic gene mutations in tumor cells. Regarding identified epigenomic abnormalities, we perform further analysis to determine whether they could be good candidates to translate into therapy development. To this end, we will modulate the activity of targets by using their activators and inhibitors in vitro and establish xenograft mouse models of hematological malignancies and manipulate their activity in vivo. Through these studies, we aim to develop new therapeutic agents or modalities that lead to improved patients��� prognosis.

  Study JGAS000603

• IGH repertoire sequencing of GZMB+ and GZMB− B cells

  This dataset contains high-throughput sequencing data of immunoglobulin heavy chain (IGH) repertoires from sorted GZMB⁺ and GZMB⁻ B cell subsets. Samples were obtained from healthy donors (Healthy Volunteers, HVs) and drug-free tolerant kidney transplant recipients (TOLs). Libraries were generated from genomic DNA using targeted BIOMED-2 PCR amplification and sequenced on an Illumina MiSeq platform. The dataset enables comparative analysis of B cell clonality, diversity, and somatic hypermutation patterns.

  Dataset EGAD50000002452

• Sequencing data from the study "Somatic rearrangements causing oncogenic ectodomain deletions of FGFR1 in squamous cell lung cancer"

  This dataset consists of 71 whole-genome samples and 47 RNA-seq samples. All WGS samples are provided in .bam format and RNA-seq samples are provided as .fq.gz (paired-end). Next-generation sequencing data on whole genomes were processed by aligning sequencing reads to a reference genome (NCBI build 37/hg19) using bwa-mem (0.7.13-r1126).

  Dataset EGAD50000001978

• WGS data of pediatric T-ALL acute lymphoblastic leukemia (set1)

  The dataset includes FASTQ and BAM files from diagnostic and matched remission (control) samples of one T-ALL patient (ALLT-317). Relapsed (BM ALLT-317L and Tonsil ALLT-3107L) sample files are in dataset set2 of this submission. Sequencing library was made using PCR free-based WGS library preparation (PCR-), using TruSeq DNA PCRfree library preparation kit v1 (PE150). Both diagnostic (60x) and remission (30x) samples were sequenced using HiSeq X.

  Dataset EGAD50000002013

• mRNA profiling of CAFs and cancer cells in response to TGF-β and BMP signaling

  TGF-β and BMP signalings are important signaling pathways in the tumor microenvironment during cancer progression. This RNA-sequencing (62 fastq pairs) analysis explored how cancer-associated fibroblasts (CAFs) from human (19TT) and mice (Balbc A/B) respond to TGF-β, BMP2, or Gremlin antibody, as well as how cancer cells (66cl4) respond to Gremlin antibodies.

  Dataset EGAD50000001351

• single-cell RNA-seq profiling of 2 patient derived colorectal cancer organoids after treatment with a combination of different anticancer drugs

  This dataset consists of single-cell RNA-seq profiling of colorectal cancer organoids derived from two patients. The organoids were profiled both after 4 weeks of treatment and after a drug holiday of two weeks. There are 49 RNA sequence files generated using single cell RNA sequencing technology from 10X genomics.

  Dataset EGAD50000001495

• M116 Whole Genome Sequencing

  Whole Genome Sequencing (WGS) was performed using DNA extracted from M116’s blood, saliva, and urine samples. DNA was fragmented to 350 bp, followed by library preparation, paired-end 150 bp WGS, and variant calling, all conducted by Novogene®. Sequencing was carried out with a 10X coverage (approximately 60 Gb and 200 million reads per sample) using the NovaSeq X Plus platform (Illumina). Files types included in this dataset are raw Fastq files.

  Dataset EGAD50000001286

• Comparison clinical recommendation MASTER and panel sequencing: Genomic data

  This dataset contains 29 case/control samples of WES and WGS sequencing data. Sequencing was performed on Illumina HiSeq X using TruSeq Stranded DNA Kit. The sequencing was always paired.

  Dataset EGAD50000000624

• European Roma whole genomes sequences

  Pair end fastq file of 40 Roma whole genome sequence data. This dataset contains the fastq files obtained using illumina hiseq X generated reads, ~30X coverage. 10 Makedonian Roma - Balkan Roma 10 Spanish Roma - North/Western Roma 10 Hungarian Roma - Vlax and Romungro Roma 5 Lithuanian Roma - North/Western Roma 5 Ukranian Roma - Romungro Roma.

  Dataset EGAD00001006024

• Whole Genome Sequencing of Head and Neck Angiosarcoma

  This dataset contains 55 Whole Genome Sequencing of the study titled Spatial transcriptomics reveal topological immune landscapes of Asian head and neck angiosarcoma.

  Dataset EGAD00001010140

• 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.

  Dataset EGAD00001010056

• ATAC-seq and RNA-seq datasets of CD14+ monocytes from healthy donors

  This dataset consists of functional genomic data from 6 healthy donors taken from CD14+ monocytes upon different immune stimulations. It contains 150 paired end fastq files consisting of 30 total RNA-seq samples across 4 runs and 30 ATAC-seq samples. The samples were sequenced on Illumina HiSeq4000 platform.

  Dataset EGAD00001011113

• Genomic alterations in MM - BAM

  Tumor DNA was extracted from 100 bone marrow aspirate samples where CD138+ selection had been performed to enrich plasma cells from patients with multiple myeloma. Patient matched control DNA from either peripheral blood leukocytes or CD34+ stem cell harvests was also isolated. Both tumor and control DNA underwent library preparation using the Hyperplus kit (KAPA Biosystems) and were hybridized to baits for a targeted SeqCap myeloma panel (Nimblegen) encompassing 129 genes, regions for SNPs for copy number determination, and the IGH, IGK, IGL loci, as well as approximately 5 Mb surrounding the MYC locus. Samples were sequenced on a HiSeq2500 using 100 bp paired end reads. Resulting BAM files were returned along with annotations for somatic events including single nucleotide mutations, indels and structural rearrangements.

  Dataset EGAD00001004117

• singel cell RNAseq dataset for the study "Composition and functional status of T and NK cells in Extramedullary myeloma tumor microenvironment""

  Dataset contains all newly generated single cell RNAseq data generated for the study. It includes 5 EMM soft tissue samples, 5 EMM bone marrow samples (EMM_BM) and 6 RRMM BM samples without EMM (RRMM_BM). Samples that are sequenced twice are marked by _1 or _2 in the sample name. The sample name mentioned corresponds to the sample name used in the publication. The rest of the EMM single cell RNAseq samples mentioned int the publication, EMM_03_1, EMM_11, EMM_14_1, EMM_14_2, EMM_16, and EMM_15_1 are already uploaded in EGA archive – dataset id EGAD50000000053.

  Dataset EGAD50000001511

• Germline hypomorphic CARD11 mutations in severe atopic disease

  We described five patients from four unrelated families who had severe atopic dermatitis and susceptibility to mild skin viral infections. Some patients also exhibited other allergic symptoms such as asthma and food allergy. We performed targeted sequencing for affected patients A-I of family A and B-I of family B, whole exome sequencing for D-I, D-II.1 and healthy mother D-II.3 of family D, and whole genome sequencing for C-I and healthy mother C-II.2 of family C. We identified three different novel damaging missense mutations of CARD11 (GeneID:84433) in patients A-I (L194P), B-I (R975W), and C-I (E57D). In patients D-I and D-II.1, a dup183_196 (p.K196_V197insMKEERDSYNDELVK) mutation was found in the coil-coil domain of the protein. These mutations act as dominant negatives impeding the scaffolding function of the wild type protein, which leads to downstream NF-kB and mTORC1 signaling defects after TCR stimulation. Sanger sequencing later identified the corresponding CARD11 mutations in the affected family members (C-II.1, D-II.2) that are not included in the dbGaP submission. Hypomorphic CARD11 dominant negative mutants are novel causes of severe atopic disease.

  Study phs001369

• GRIDSS, PURPLE, LINX: Unscrambling the tumor genome via integrated analysis of structural variation and copy number

  We have developed a novel, integrated and comprehensive purity, ploidy, structural variant and copy number somatic analysis toolkit for whole genome sequencing data of paired tumor/normal samples. We show that the combination of using GRIDSS for somatic structural variant calling and PURPLE for somatic copy number alteration calling allows highly sensitive, precise and consistent copy number and structural variant determination, as well as providing novel insights for short structural variants and regions of complex local topology. LINX, an interpretation tool, leverages the integrated structural variant and copy number calling to cluster individual structural variants into higher order events and chains them together to predict local derivative chromosome structure. LINX classifies and extensively annotates genomic rearrangements including simple and reciprocal breaks, LINE, viral and pseudogene insertions, and complex events such as chromothripsis. LINX also comprehensively calls genic fusions including chained fusions. Finally, our toolkit provides novel visualisation methods providing insight into complex genomic rearrangements.

  Study EGAS00001004034

• Chondrosarcoma_Targeted_Sequencing_Study

  This Study uses a focused bait pull down library method to target findings of Chondrosarcoma whole genome and whole exome sequencing studies in order to validate findings. This method will also be used on a larger set of tumour only samples in order to find precedence of these finding in a larger set of patients.

  Study EGAS00001000277

• Facioscapulohumeral dystrophy transcriptome signatures correlate with different stages of disease and are marked by different MRI biomarkers

  This project includes RNA-sequencing data from human FSHD and control skeletal muscle biopsies. This project includes data from 28 FSHD patients (total 37 samples, including vastus lateralis and tibialis anterior muscles) and 12 control individuals (total 24 samples, including vastus lateralis and tibialis anterior muscles).

  Study EGAS00001005782

• Influence of culture media on airway differentiation at the Air-Liquid Interface

  Single-cell dataset of human airways after in vitro regeneration at the Air-Liquid Interface. Samples from 2 donors were used for the establishment of Human Bronchial Epithelial Cell cultures (HBECs) and were analyzed during proliferation, at the onset of differentiation (ALI0) and after full differentiation (ALI28), in 4 distinct culture media. Single-cell RNAseq was performed with 10x Genomics 3’ v2 RNA-seq using hashtag antibodies for multiplexing, and sequenced on a NextSeq 500. Samples from 3 additional donors were used for the establishment of Human Nasal Epithelial Cell cultures (HNECs) and were analyzed during proliferation in three distinct culture media. Single-cell RNAseq was performed with 10x Genomics 3’ v3 RNA-seq without multiplexing, and sequenced on a NextSeq 2000.

  Dataset EGAD00001011362

• NHLBI TOPMed: Recipient Epidemiology and Donor Evaluation Study-III Brazil Sickle Cell Disease Cohort (REDS-BSCDC)

  Establishing a Brazilian Sickle Cell Disease Cohort and Identifying Molecular Determinants of Response to Transfusions, Genetic Determinants of Alloimmunization, and Risk Factors Associated with HIV Infection. The REDS-III Brazil SCD Cohort study focused on transfusion practices and predictors of health outcomes in patients with Sickle Cell Disease (SCD) and began in the Fall of 2013. The four primary aims of this study are: 1) Aim A - Establish a cohort of SCD patients with a comprehensive centralized electronic database of detailed clinical, laboratory and transfusion information, as well as establish a repository of blood samples to support biological studies relevant to SCD pathogenesis and transfusion complications; 2) Aim B - Characterize changes in markers of inflammation in response to transfusion by analyzing chemokine/cytokine panels in serial post transfusion specimens; 3) Aim C - Identify single nucleotide polymorphisms (SNPs) that contribute to the risk of red blood cell alloimmunization in SCD by performing a genome-wide association (GWA) study in transfused SCD patients; and, 4) Aim D - Characterize risk of HIV and HIV outcomes in the Brazilian SCD population and compare SCD outcomes among HIV sero-positive and sero-negative SCD patients. Patients are enrolled from six hospitals affiliated with the participating four REDS-III Brazil hemocenters.

  Study phs001468

• Whole-exome and targeted sequencing of pediatric hyperdiploid B-cell precursor acute lymphoblastic leukemia

  High hyperdiploidy defines the largest genetic entity of childhood acute lymphoblastic leukemia (ALL). Despite its relatively low recurrence risk, this subgroup generates a high proportion of relapses. The cause and origin of these relapses remains obscure. We therefore explored the mutational landscape in high hyperdiploid (HD) ALL with whole-exome (n=19) and subsequent targeted deep sequencing of 60 genes in 100 relapsing and 51 non-relapsing cases. We identified multiple clones at diagnosis that were primarily defined by a variety of mutations in receptor tyrosine kinase (RTK)/Ras pathway and chromatin-modifying genes. The relapse clones consisted of reappearing as well as new mutations, and overall contained more mutations. Although RTK/Ras pathway mutations were similarly frequent between diagnosis and relapse, both intergenic and intragenic heterogeneity was essentially lost at relapse. CREBBP mutations, however, increased from initially 18-30% at relapse, then commonly co-occurred with KRAS mutations (P<0.001) and these relapses appeared primarily early (P=0.012). Our results confirm the exceptional susceptibility of HD ALL to RTK/Ras pathway and CREBBP mutations, but, more importantly, suggest that mutant KRAS and CREBBP might cooperate and equip cells with the necessary capacity to evolve into a relapse-generating clone.

  Study EGAS00001001113

• Whole genome, whole exome, and targeted sequencing of high-grade meningioma tumor samples.

  High-grade meningiomas frequently recur and are associated with high rates of morbidity and mortality. To determine the factors that promote the development and evolution of these tumors, we analyzed the genomes of 274 high-grade meningiomas and compared this information with data from 456 low-grade meningiomas. High-grade meningiomas had a higher mutation burden than low-grade meningiomas but did not harbor any statistically significant mutated genes aside from NF2. High-grade meningiomas also possessed significantly elevated rates of chromosomal gains and losses, especially among tumors with monosomy 22. Meningiomas previously treated with adjuvant radiation had significantly more copy number alterations than radiation-induced or radiation-naïve meningiomas. Across serial recurrences, genomic disruption preceded the emergence of nearly all mutations, remained largely uniform across time, and when present in low-grade meningiomas, correlated with subsequent progression to a higher grade. In contrast to the largely stable copy number alterations, mutations were strikingly heterogeneous across tumor recurrences, likely due to extensive geographic heterogeneity in the primary tumor. While high-grade meningiomas harbored significantly fewer overtly targetable alterations than low-grade meningiomas, they contained numerous mutations that are predicted to be neoantigens, suggesting that immunologic targeting may be of therapeutic value.

  Study EGAS00001002294

• Constructing database of magnetic resonance imaging of the brain and the ancillary clinical information for multisite collaboration studies: a dataset from Schizophrenia individuals

  Previously there was no neuroimaging database available for research community that incorporated a large Japanese sample of healthy people and patients with neuropsychiatric disorders. Establishing such a database will enable large-scale, neuroimaging-based investigations on pathophysiology of neuropsychiatric disorders by simply using the large data pool or by combining it with investigators' own data sets.

  Study JGAS000043

• Constructing database of magnetic resonance imaging of the brain and the ancillary clinical information for multisite collaboration studies: a dataset from normal individuals

  Previously there was no neuroimaging database available for research community that incorporated a large Japanese sample of healthy people and patients with neuropsychiatric disorders. Establishing such a database will enable large-scale, neuroimaging-based investigations on pathophysiology of neuropsychiatric disorders by simply using the large data pool or by combining it with investigators' own data sets.

  Study JGAS000042

• Constructing database of magnetic resonance imaging of the brain and the ancillary clinical information for multisite collaboration studies: a dataset from Bipolar disorder individuals

  Previously there was no neuroimaging database available for research community that incorporated a large Japanese sample of healthy people and patients with neuropsychiatric disorders. Establishing such a database will enable large-scale, neuroimaging-based investigations on pathophysiology of neuropsychiatric disorders by simply using the large data pool or by combining it with investigators' own data sets.

  Study JGAS000045

• Constructing database of magnetic resonance imaging of the brain and the ancillary clinical information for multisite collaboration studies: a dataset from Depression individuals

  Previously there was no neuroimaging database available for research community that incorporated a large Japanese sample of healthy people and patients with neuropsychiatric disorders. Establishing such a database will enable large-scale, neuroimaging-based investigations on pathophysiology of neuropsychiatric disorders by simply using the large data pool or by combining it with investigators' own data sets.

  Study JGAS000044

• 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

• Genetic Progression of Head and Neck Squamous Cell Carcinoma

  These data are tumor/normal-matched exome sequencing results on 45 participants (median age of 58.6 years) treated for squamous cell carcinoma of the oropharynx at Mass Eye and Ear (MEE; Boston, MA, USA). Some tumors had two portions sequenced separately. All research complied with all relevant ethical regulations. Human subject research on patients at MEE was approved by the MEE Human Studies Committee under protocol HSC 11-024H, with informed consent obtained from participants. Participants were not compensated. Clinical data, including HPV status, were abstracted from patient records. Sequencing and clinical data were combined with TCGA data on 486 cases of head and neck squamous cell carcinoma (HNSCC). The PhylogicNDT suite of genomic analysis tools was used to infer the relative timing of genetic events during tumor progression for major molecularly defined classes of HNSCC: HNSCC negative for human papillomavirus (HPV), HPV-associated HNSCC, and HPV-negative HNSCC involving mutations in CASP8, NSD1, and NOTCH1. The timing of the development of whole-genome somatic events leading to tetraploidy or triploidy and to increased measures of intratumor genetic heterogeneity was determined. Associations of heterogeneity measures with clinical outcomes were assessed. The analysis identified genes with early mutations that likely play roles in HPV-tumor initiation (FBXW7, NOTCH1, CASP8, FAT1, NSD1, HRAS, EP300, CREBBP, KMT2D). Genes with mutations at later median relative timing (PK3CA, NFE2L2, HLA-A, SPEN, and KMT2C) were more likely to be important for progressing to later stages of the disease. Gain of chromosome arm 3q and loss of arm 11q were found to occur more frequent in HPV+ HNSCC cases. A high prevalence of 3p and 17p loss were also observed in HPV+ HNSCC cases.

  Study phs003139

• CoV2 challenge data

  Repository containing the transcriptomic data for the CoV2 challenge study

  Dac EGAC50000000391

• H3N2 challenge data

  Repository containing the transcriptomic data for the H3N3 challenge study

  Dac EGAC50000000379

• Fastq data for smRNA-Seq assays for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  Fastq data for smRNA-Seq assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001401

• ChIP-seq bulk

  This dataset gather ChIP-seq data produced by immunoprecipitating CTCF factor in own laboratory in MM.1S cell line in EtOH and Dex conditions. It also gather ChIP-seq dataset produced by external laboratory (Active Motif) for H3K27ac mark and GR transcription factor in same cell line and conditions ( MM.1S ETOH/Dex)

  Dataset EGAD00001011136

• Conserved interferon-gamma signaling and decreased immune exclusion programs in responses to immune checkpoint blockade therapy_CM38-RNA

  We analyzed baseline and on-therapy tumor biopsies from 101 patients with advanced melanoma treated with nivolumab (anti-PD-1) alone or combined with ipilimumab (anti-CTLA-4). Analysis of whole transcriptome data showed that T cell infiltration and interferon-gamma signaling signatures corresponded most highly with clinical response to therapy, with a reciprocal decrease in cell cycle and WNT signaling pathways in responding biopsies. Clinical outcome differences were likely not due to differential melanoma cell responses to interferon-gamma, as 57 human melanoma cell lines exposed in vitro to this cytokine showed a conserved interferon-gamma transcriptome response unless they had mutations that precluded signaling from the interferon-gamma receptor. Therefore, the magnitude of the antitumor T cell response and the corresponding downstream interferon-gamma signaling are the main drivers of clinical response or resistance to immune checkpoint blockade therapy.

  Dataset EGAD00001006282

• Conserved interferon-gamma signaling and decreased immune exclusion programs in responses to immune checkpoint blockade therapy_CM38-DNA

  We analyzed baseline and on-therapy tumor biopsies from 101 patients with advanced melanoma treated with nivolumab (anti-PD-1) alone or combined with ipilimumab (anti-CTLA-4). Analysis of whole transcriptome data showed that T cell infiltration and interferon-gamma signaling signatures corresponded most highly with clinical response to therapy, with a reciprocal decrease in cell cycle and WNT signaling pathways in responding biopsies. Clinical outcome differences were likely not due to differential melanoma cell responses to interferon-gamma, as 57 human melanoma cell lines exposed in vitro to this cytokine showed a conserved interferon-gamma transcriptome response unless they had mutations that precluded signaling from the interferon-gamma receptor. Therefore, the magnitude of the antitumor T cell response and the corresponding downstream interferon-gamma signaling are the main drivers of clinical response or resistance to immune checkpoint blockade therapy.

  Dataset EGAD00001006284

• Mutational anysis of breast cancer stem cells

  Exome sequences of breast cancer have been investigated for many patients. Recently it has been shown that there are intra-heterogeneity in tumor tissues. When the tumor cells were sequenced in bulk condition, only the major populations��� (clones���) mutations will be detected. Based on cancer stem theory, each populations��� cells are derived from each cancer stem cells, which their numbers are not so different among different clones. Here, we separated cancer cells into cancer stem cells and non-cancer stem cells exploiting cancer stem cell specific surface markers. By comping two groups��� mutation, we identified mutations, which were only detected in stem cell population. These mutations could be the mutations in cells of small size populations, and maybe the important mutations to understand the heterogeneity of tumor tissues, progression, and/or prediction for the outcome to therapies.

  Study JGAS000304

• DAC for Breast Invasive Lobular Carcinoma CDH1 study

  We developed an artificial intelligence (AI)-model applied to histological images trained 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 of cases predicted by the model to harbor a CDH1 biallelic mutations but lacking these alterations according to targeted sequencing. We then subjected one ILC lacking CDH1 biallelic mutations and lacking CDH1 promoter methylation to whole genome sequencing (WGS) to determine the molecular basis of its lobular phenotype.

  Dac EGAC50000000333

• Study of biomarkers implicated in radio-immunotherapy response in metastatic cancer

  Immuno-radiotherapy may improve outcomes for patients with advanced solid tumors, although optimized combination modalities remain unclear. Here, we report the analysis from the SABR-PDL1 (NCT02992912) trial that evaluated the PD-L1 inhibitor atezolizumab in combination with stereotactic body radiation therapy (SBRT) in patients with advanced cancer.

  Study EGAS50000001149

• Study of biomarkers implicated in radio-immunotherapy response in metastatic cancer

  Immuno-radiotherapy may improve outcomes for patients with advanced solid tumors, although optimized combination modalities remain unclear. Here, we report the analysis from the SABR-PDL1 (NCT02992912) trial that evaluated the PD-L1 inhibitor atezolizumab in combination with stereotactic body radiation therapy (SBRT) in patients with advanced cancer.

  Study EGAS50000000681

• The dataset for "ctDNA residual disease analyses during perioperative nivolumab or nivolumab plus ipilimumab in resectable diffuse pleural mesothelioma”

  The dataset for the study “ctDNA residual disease analyses during perioperative nivolumab or nivolumab plus ipilimumab in resectable diffuse pleural mesothelioma” includes 169 bam files from whole genome sequencing on the Illumina NovaSeq6000 platform. The samples analyzed include tumor (n=28) and normal (n=28) DNA samples, and serial plasma cfDNA (n=113) samples from 28 individuals with resectable diffuse pleural mesothelioma, treated with nivolumab or nivolumab plus ipilimumab on the NCT03918252 trial.

  Dataset EGAD50000001701

• SATB1 KO Treg and Teff cells: ATAC-seq

  We expanded human Treg and CD4+ Teff cells for 9 days, re-activated the cells and performed CRISPR/Cas9 RNP-mediated KO at day 11. The cells were treated with a pro-inflammatory cytokine IL-12 on day 12. 4 days after editing, living cells were FACS-sorted, the cell nuclei were extracted and prepared for ATAC-seq. AAVS1 KO served as control. The transcription factors SATB1 and two other targets (included to increase the robustness of the dataset) were knocked-out. Three biological replicates have been applied.

  Dataset EGAD50000001276

• SATB1 KO Treg and Teff cells: RNA-seq

  We expanded human Treg and CD4+ Teff cells for 9 days, re-activated the cells and performed CRISPR/Cas9 RNP-mediated KO at day 11. The cells were treated with a pro-inflammatory cytokine IL-12 on day 12. 4 days after editing, living cells were FACS-sorted, the RNA was extracted and prepared for RNA-seq. AAVS1 KO served as control. The transcription factors SATB1 and two other targets (included to increase the robustness of the dataset) were knocked-out. Three biological replicates have been applied.

  Dataset EGAD50000001277

• 2014_AML_WES_51 samples

  2014 AML WES study contains 51 paired WES samples which were collected from SNUH. The study was designed to examine the molecular abnormalities from leukemic patients at initial diagnosis in comparison with corresponding germ line control (saliva samples). The results of WXS were analyzed by Mutect for ranking cancer variants and creating mutational matrix.

  Study EGAS00001002819

• Whole-genome sequencing of Tibetans from China

  Whole-genome sequencing of 27 Tibetan individuals from China using the Illumina-B HiSeq X platform. These data are part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/.

  Study EGAS00001003500

• Whole-genome sequencing of Himalayan populations

  Whole-genome sequencing of 60 individuals from 15 Himalayan populations using the Illumina-B HiSeq X platform. These data are part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/.

  Study EGAS00001007269

• Brain mets discovery cohort variant calls

  These are the variant calls for the 50 brain tumour samples in the discovery cohort.

  Dataset EGAD00001005982

• NHLBI TOPMed: Pathways to Immunologically Mediated Asthma (PIMA)

  Study designed to further our understanding of the pathogenesis of asthma exacerbations in children. Children enrolled in the study (n=217) were all asthmatic and primarily Hispanic white. The children were followed for 18 months until they experienced an asthma exacerbation or completed the follow-up without an exacerbation. The time to the first asthma exacerbation was considered the outcome. The acute and convalescent immune phenotype of each asthma exacerbation was documented.

  Study phs001727

• Genetic analyses in patients with T or NK cells-associated disorders

  We conduct somatic gene mutation analysis in various diseases involving T cells or NK cells and clarify the gene mutation profile. By comparing clinical information and the results of mutation analysis, we will identify gene groups that influence the onset and refractoriness of the disease. As the analysis continues, the results of mutation analysis may become part of diagnostic criteria in the future, or provide basic data for the development of new therapeutic agents.

  Study JGAS000658

• Genetic analyses in patients with T or NK cells-associated disorders

  We conduct somatic gene mutation analysis in various diseases involving T cells or NK cells and clarify the gene mutation profile. By comparing clinical information and the results of mutation analysis, we will identify gene groups that influence the onset and refractoriness of the disease. As the analysis continues, the results of mutation analysis may become part of diagnostic criteria in the future, or provide basic data for the development of new therapeutic agents.

  Study JGAS000709

• The Etiological Bases of Giftedness: Epidemiological Study of Cognitive Ability in Children in Saudi Arabia

  Recent studies of genetic foundations of cognitive ability rely on large samples (hundreds of thousands) of individuals from relatively outbred populations of mostly European ancestry. Hypothesizing that the genetic foundation of cognitive ability depends on the broader population-specific genetic context, we performed a genome-wide association study and homozygosity mapping of cognitive ability estimates obtained through latent variable modeling in a sample of 354 children from the consanguineous population of Saudi Arabia. Approximately half of the sample demonstrated significantly elevated homozygosity levels indicative of inbreeding, and among those with elevated homozygosity, it was negatively associated with cognitive ability. Further homozygosity mapping identified a specific run, inclusive of the GRIA4 gene, that survived corrections for multiple testing for association with cognitive ability. The results suggest that in a consanguineous population, a notable proportion of the variance in cognitive ability in the normal range in children might be regulated by population-specific mechanisms such as patterns of elevated autozygosity.

  Study phs001884

• Ultra-Low-Pass Whole Genome Sequencing of Cell-Free DNA for Large B-Cell Lymphoma

  While deep targeted DNA sequencing of liquid biopsies has shown prognostic utility in large B-cell lymphoma (LBCL), the routine clinical adoption of these assays remains limited due to their high costs. Here, leveraging a well-annotated cohort of encompassing both frontline and relapsed/refractory (R/R) LBCL, we profiled patient plasma samples with two complementary modalities – ultra-low-pass whole genome sequencing (ulpWGS) and deep targeted DNA sequencing, the former being a cost-effective method to profile large scale chromosomal abnormalities and estimate tumor burden. Our findings revealed a strong association of high cell-free tumor burden by both genomic profiling modalities with established measures of tumor burden and patient survival. Notably, the associations with survival remained statistically significant after accounting for international prognostic index scoring. Furthermore, we showed that del(17p) in circulating tumor DNA as detected by ulpWGS was strongly associated with TP53 mutation status and predicted for significantly inferior patient outcome in frontline but not R/R LBCL patients. Our study demonstrates that ulpWGS can provide robust prognostic biomarkers for both frontline and R/R LBCL, highlighting its broad applicability for risk stratification.

  Study EGAS50000001027

• Large Cancer Fingerprint Screening for Detection of Minimal Residual Disease.

  We describe an approach for large cancer fingerprint screening and its application to cell-free DNA from patients with cancer. Our approach involves tracking somatic mutations identified from patients' tumor biopsies, in the cell-free DNA from a blood draw.

  Study phs001977

• CSER: Incorporating Genomics into the Clinical Care of Diverse NYC Children (NYCKidSeq)

  The NYCKidSeq program will significantly advance the implementation of genomic medicine, particularly for children, young adults and their families in Harlem and the Bronx. The study will assess the clinical utility of genomic medicine in three broad areas of pediatric disorders, while engaging a range of providers and community advisors to overcome the well-documented barriers to inclusion of underserved and underrepresented populations in genomic research. The study will also include testing, analyzing, and implementing a novel communication tool, Genomic Understanding, Information and Awareness (GUÍA), to facilitate the return of genomic test results. The use of GUÍA will enhance the understanding of these genomic testing results by families, patients, and care providers at all levels of expertise, in two health systems. Healthcare system leadership will be engaged to provide insights into their readiness for genomic implementation. Overall, the NYCKidSeq program will inform the genomics and clinical communities about how to implement genomic medicine in a diverse population in a clinically useful, technologically savvy, culturally sensitive, and ethically sound manner.

  Study phs002337

• Integrated Methylation and Copy Number Analysis for Non-invasive Bladder Cancer Detection in Urine

  The molecular analysis of urine cell-free DNA (cfDNA) offers a non-invasive tool to advance bladder cancer (BC) management. Assessment of somatic copy number aberrations (SCNA) and DNA methylation, as singular or complementary analysis, have emerged as promising approaches for BC detection. Here, we developed an integrated analysis to assess both SCNA and targeted methylation changes from the same template molecules, named the iSECURE (integrated SEquencing-based Copy number and methylation analysis in URinE) method.

  Study EGAS50000001350

• The gut microbiota in prediabetes and diabetes: a population-based cross-sectional study

  The link between the gut microbiota and type 2 diabetes (T2D) warrants further investigation because of known confounding effects from antidiabetic treatment. Here we profiled the gut microbiome in a discovery (n=1011) and validation (n=484) cohort comprising Swedish subjects naive for diabetes treatment and grouped by glycemic status.

  Study EGAS00001004480

• Genotype data for The admixture histories of Cabo Verde - genotype data

  Datasets used in the article "The genetic and linguistic admixture histories of the islands of Cabo Verde" by Laurent R et al. eLife 2023 (DOI: https://doi.org/10.7554/eLife.79827 - URL: https://elifesciences.org/articles/79827) As per Materials and Methods herein, the genotype data corresponds to 2,118,722 autosomal SNPs genotyped from the IlluminaOmni 2.5 Million BeadChip for 233 Cabo Verdean volunteer participants, family unrelated at the 2nd degree based on population genetics analyses (see Material and Methods). SNP rsID, Chromosome position and genetic position in (bp) are in Build GRCh38. Cabo Verdean individuals are designated with an alphanumeric unique code

  Dataset EGAD00001008979

• Clonal Lineage Tracing of Primary Human Cortical Progenitors, Cell Type Profiles in the Brain Vasculature and Genotyping Data for 22q11DS and Control iPS Lines

  We sought to characterize the cell types produced by individual human cortical progenitors and describe their lineage relationships. We labeled individual human cortical cells with a massively complex lentivirus library encoding a GFP reporter gene and a molecular barcode that could be captured by standard 3' scRNA-seq methodologies. We then cultured the labeled human cells for 6 weeks in either a 1) mouse cortical astrocyte co-culture system or 2) in the mouse cortex as a xenograft. In a separate experiment, we maintained human cortical tissue slices in organotypic slice culture for 12 days. GFP+ cells were then isolated by FACS and then captured on the 10x chromium scRNA-seq platform. An additional sample was labeled by lentivirus and briefly cultured for 3 days prior to being mixed with mouse 3T3 cells in order to perform a cell mixing experiment ("barnyard") to benchmark our methodologies. We found that human individual cortical progenitors gave rise to both excitatory and inhibitory neurons as well as glia.We also sought to characterize the adult brain vasculature in both vascular malformations and non-malformed tissue. We use the 10x chromium scRNA-seq platform across 10 individuals (5 control and 5 arteriovenous malformations). We find broad disregulation across multiple cell types including the immune cells and find a specific monocyte subtype to contribute to a rupture phenotype. We also find a novel population of fibromyocytes in both conditions.Finally, we confirmed the genotype status of iPS lines that were derived from either karyotypically normal control individuals or from DiGeorge Syndrome patients carrying the 22q11.2 deletion using the Illumina Infinium Global Screening Array v3.0.

  Study phs002624

• European Prospective Investigation into Cancer and Nutrition BAMs

  516 DNA samples were collected from individuals upon enrollment into the European Prospective Investigation into Cancer and Nutrition study between 1993 and 1998 across 17 different centers. 126bp pair-end reads sequencing data from the Illumina platform were converted to fastq format, the 2bp molecular barcode information at each read of the pair was trimmed and was written in the reads name. The Thymine nucleotide required for ligation was removed from the sequences. Burroughs-Wheeler Aligner (BWA-mem) was used for alignment of the processed fastq files to the reference hg19 genome, following indel-re-alignment using GATK. An in-house algorithm was written to collapse read families that share the same molecular barcode sequence

  Dataset EGAD00001003583

• Whole exome sequencing of ATCWGS42 primary tumour and PDX

  Genomic DNA was isolated from snap-frozen tissue and subjected to whole genome sequencing at The Center for Applied Genomics (Hospital for Sick Children, Toronto, ON) or at Beijing Genomic Institute (BGI). High-coverage whole exome-sequencing was performed at GeneSeeq Inc. (Toronto, Ontario, Canada) using IDT xGen exome panel.

  Study EGAS50000001490

• BELLINI clinical trial single-cell RNA-Seq and TCR data: cohorts A & B

  Single-cell RNA-Seq data and TCR sequencing data (both by 10X Genomics) of 51 TNBC primary tumors obtained from 29 unique patients from BELLINI clinical trial. The data includes pre- and post-treatment samples. Patients in cohort A (16 patients, 28 samples) received nivolumab for 4 weeks, patients in cohort B (13 patients, 23 samples) received nivolumab + ipilimumab for 4 weeks. The included sequencing data was generated from frozen material for cohort A and from fresh material for cohort B.

  Dataset EGAD50000000807

• Bulk 3' mRNA-Seq of dome and suspension tubuloids

  Bulk 3' mRNA-sequencing of human kidney tubuloids grown in dome and suspension culture for the identification of transcriptional differences associated with culture method, passage, and donor. Tubuloids were generated from 4 separate donors and collected for sequencing at day 7 of passage 3, 4, and 5 in dome and suspension culture.

  Study EGAS50000001629

• ChIP-seq and 4C-seq datasets in megakaryocytes and granulocytes from individuals with QPD and unaffected controls

  ChIP-seq was performed for the following histone modifications in both megakaryocytes and granulocytes: H3K27ac, H3K4me2, and H3K36me3. ChIP-seq was performed for H3K27me3 and CTCF in megakaryocytes only. All ChIP experiments consist of n=3 replicates for each of QPD and Control, with the exception of control granulocyte H3K4me2 for which only n=2 replicates were performed. 4C-seq datasets consist of 2 viewpoints (PLAU promoter and an intergenic enhancer), profiled in megakaryocytes from n=2 controls and n=4 QPD.

  Dataset EGAD00001006048

• Glioblastoma epigenome profiling identifies SOX10 as a master regulator of molecular tumour subtype

  Glioblastoma in adult patients are classified into four subtypes, IDH, MES, RTK I, and RTK II, based on DNA methylation and RNA expression data. Tumour subtype transitions commonly occur during the treatment of glioblastoma patients, and transitions to the mesenchymal (MES) subtype have been associated with therapy resistance and adverse prognosis. Here, we generate DNA methylome and histone modification data of glioblastoma primary tumours and show that glioblastoma subtypes differ by their enhancer landscapes. Using Core Regulatory Circuitry analysis of H3K27ac data, and independent analysis of RNA-derived gene regulatory networks, we identified 38 subtype master regulators whose cell type-specific activities we mapped in single-cell RNA sequencing data. These analyses identified the chromatin modifier SRY-Box 10 (SOX10) as a master regulator in tumours of the RTK I subtype. In functional studies we demonstrate that SOX10 loss causes a transition of RTK I tumour cells to a mesenchymal cellular state by altering the accessibility of enhancer-rich chromatin regions and their occupancy by Bromodomain Containing 4 (BRD4), a dynamic constituent of super-enhancers. Treatment with the BRD4 inhibitor JQ1 blocked this transition. These data demonstrate the fundamental role of enhancer chromatin remodelling and master regulator activity in the establishment, maintenance and plasticity of glioblastoma cellular states. We also make our data publically browsable at https://dkfz-b060.github.io/gb_browse/

  Study EGAS00001003953

• HLA-A*3101 and Carbamazepine-Induced Hypersensitivity Reactions in Europeans

  Based on the prior knowledge of involvement of the human leukocyte antigen locus in Han Chinese patients with carbamazepine-induced Stevens-Johnson syndrome, we imputed the HLA types for each case and control subject from the array of SNPs in the Human610-Quad GWAS platform (NCBI Build 36.1). We then performed a genome-wide association test which included the imputed HLA alleles as markers.

  Study EGAS00000000036

• Y chromosome variability in Polish population

  The aim of the present study was to define the Y chromosome variability in Polish male population. For the first time, the study of Polish population was conducted on such a large number of individuals (n=2705) representing administrative units of both levels of local administration in Poland (voivodeships and counties). Furthermore, the clusters were used as an additional form of population subdivision, corresponding to geographic regions of Poland.

  Study EGAS00001004111

• Population whole-genome bisulfite sequencing across two tissues highlights environment as principal source of human methylome variation

  The study includes whole-genome bisulfite sequencing (WGBS) on 34 adipose(7 MZ pairs, 6 DZ pairs and 8 singletons) and 27 blood (7 MZ pairs, 6 DZpairs and 1 singleton) DNA samples derived from a total of 43 female twinsbelonging to the MuTHER/TwinsUK cohort. We generated 11.5 billion 100bppaired-end reads covering 2.3 Tera-basepairs (Tbp) ofsequence using the Illumina HiSeq2000 or 2500 systems. Applying standardalignment methods and filters we obtain a mean genome coverage of 6.3-fold(range: 1.0- to 12.9-fold) for adipose and 8.7-fold (range: 0.7- to29.0-fold) for blood.

  Study EGAS00001001569

• Whole Exome Sequences from Eivissan and Menorcan Individuals

  30 and 21 whole exome sequences for Eivissan and Menorcan healthy unrelated volunteers, respectively. The exomes were captured with the Agilent SureSelect Human All Exon V6 capture kit and pair-end sequenced in Illumina platforms. For each individual, a pair of ".fastq" files can be found containing the raw reads.

  Dataset EGAD50000000620

• SCLC study MGH - RNAseq dataset

  RNA-seq analyses were performed on cDNA libraries prepared from PolyA+ RNA using the Illumina TruSeq protocol for mRNA. The final libraries were sequenced with a paired-end 2×75 bp protocol aiming at 8.5 Gb per sample for a 30x mean coverage of the annotated transcriptome. All sequencing reactions were conducted on an Illumina HiSeq instrument (Illumina, San Diego, CA, USA).

  Dataset EGAD00001003969

• Fluctuating DNA methylation tracks cancer evolution at clinical scale

  Long-read Nanopore data of fCpGs from Gabbutt & Duran-Ferrer (2025) for developing the EVOFLUx method to study cancer evolution via DNA methylation fluctuations.

  Study EGAS50000001192

• FMT metagenomics triads and plasma metabolomics

  These are the metagenomic datasets of 29 FMT traids with corresponding plasma metabolomics. Data for each triad consists of metagenomics for baseline, post FMT and corresponding donor. Clinical data concerning the glucose rate of disappearance and blood pressure are available as phenotypes.

  Dataset EGAD50000000599

• Single-cell Transcriptomic and TCR Repertoire Profiling of DENV-specific CD8+ T Cells Across Dengue Disease Severities

  This dataset contains single-cell RNA sequencing (Smart-seq2) and paired TCR repertoire data of sorted dengue virus (DENV)-specific CD8⁺ T cells from individuals with differing clinical outcomes: asymptomatic dengue (AD), dengue fever (DF), and dengue hemorrhagic fever (DHF). Samples were obtained from HLA-A11⁺ and HLA-A24⁺ individuals during acute and convalescent phases, with antigen-specific CD8⁺ T cells isolated using HLA tetramers loaded with immunodominant DENV epitopes. The study identifies phenotypically distinct T cell subsets associated with disease severity, TCR avidity, and antigen reactivity to current or prior DENV serotypes. The dataset supports the understanding of CD8⁺ T cell heterogeneity, TCR features, and potential mechanisms of CD8⁺ T cell-mediated protection versus immunopathogenesis in dengue infection.

  Dataset EGAD00001015637

• Transcriptome analysis of kidney organoids lacking NPHP1gene

  To explore the molecular mechanisms of cyst formation in kidney organoids lacking NPHP1, we performed RNA-seq transcriptome experiments. Because the potential for cyst formation by suspension culture should already be derived from kidney organoids at the adherent culture, we compared the global gene expression pattern of kidney organoids on day 18 between healthy group and NPHP1-deficient group

  Study JGAS000683

• Dataset for ChIP-seq data for neuroblastoma tumor samples(NB,Neuroblastoma)

  Dataset for H3K27me3 ChIP-seq data of neuroblastoma tumor samples. The sequencing was performed on Illumina HiSeq 2000 and Illumina HiSeq 2500

  Dataset EGAD00001015813

• Comprehensive molecular profiling with whole-exome sequencing (WES) of PDX tumors

  To identify biomarkers for the antitumor effects of molecularly targeted therapy, we performed whole-exome sequencing on 795 patient-derived xenograft (PDX) samples established from 269 patients with solid tumors and 125 frozen tissue samples obtained at the time of surgery.

  Study JGAS000853

• single cell RNA sequencing and ATAC sequencing, and Whole Genome sequencing of ALS patients

  To investigate ALS pathology at the cellular level, we conducted a multiome (single-nucleus RNA sequencing and assay for transposase-accessible chromatin using sequencing) analysis using the motor cortex and spinal cord of patients with ALS and control individuals.

  Study JGAS000852

• shallow WGS of cell free DNA

  12.5 ng of cfDNA was used as input for shallow whole-genome sequencing (sWGS), aiming for a coverage of x0.2-0.4-fold. Library preparation was performed using the TruSeq Nano DNA High Throughput Library Prep Kit (Illumina, San Diego, CA, USA) on an automated Hamilton STAR liquid handling system (Hamilton, Germany GmbH, Robotics, Gräfeling, Germany) with dual indexing, and sequencing was performed on the NextSeq500/550 platform (Illumina). The fraction of tumor-derived DNA in cell-free DNA was estimated using the R package ichorCNA.

  Dataset EGAD00001009796

• WGS patient 130

  Whole genome sequencing on DNA from snap frozen tumour sample and matched whole blood of patient #130. Analysis used the QIAamp DNA Mini Kit. Libraries were prepared using the Illumina TruSeq Nano library method using 200ng of DNA. Extracted DNA was sheared using the Covaris M220 Focused-ultrasonicator with a target fragment length of 550bp through bead size selection. The libraries were sequenced at depth of 40x for germline DNA and 80-100x for tumour DNA using paired 150bp reads.

  Dataset EGAD00001011271

• The data access committee for High Grade Serous Ovarian Carcinomas Originate in the Fallopian Tube

  Dac EGAC00001000755

• Data Access Committee for the UCSF Chordoid Glioma of the Third Ventricle Genome Project Dataset

  Dac EGAC00001000776

• RNA sequencing of Notch inhibitor treated HCC PDX models across timepoints

  To study the effect of Notch inhibition on the transcriptional profiles our PDX models, we generated bulk RNA-seq data for two Notch inhibition sensitive and three Notch inhibition insensitive models across multiple timepoints (8h, 24h, 48h, 7d, 17d) using anti-JAG1, anti-Notch2, anti-Notch1 or anti-gD antibodies. 3-5 samples were collected for each treatment condition, resulting in a total of 96 samples. Isolated RNA was used as input for library preparation using TruSeq RNA Sample Preparation Kit v2 (Illumina). The libraries were multiplexed and sequenced on Illumina HiSeq 2500 (Illumina) to produce FASTQ files.

  Dataset EGAD50000000737