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• Patient WGS for #198

  Whole genome sequencing of patient tumour and blood

  Dataset EGAD50000000217

• PDX WGS for #264

  WGS of tumour PDX and matched patient blood

  Dataset EGAD50000000033

• PDX WES for #039 and #049

  Exome sequencing of PDX and matched patient blood

  Dataset EGAD50000000034

• DAC - organotypic co-cultures @IEO

  DAC for RNAseq data on patient-derived organotypic models (Battistini et al, CDDis 2024)

  Dac EGAC50000000238

• eQTL-CHiC DAC

  The Data Access Committee for eQTL-CHiC and related data from Ray-Jones et al., 2024.

  Dac EGAC50000000445

• DAC for Transcriptomic and genomic profiling of fragile X syndrome unmethylated full mutation carriers

  Dac EGAC50000000416

• DKFZ-HIPO DACO for "Patient-derived tumoroids from CIC::DUX4 rearranged sarcoma identify MCL1 as a therapeutic target"

  Dac EGAC00001003559

• Data Access Committee for Patient-derived tumoroids from CIC::DUX4 rearranged sarcoma identify MCL1 as a therapeutic target

  Dac EGAC00001003558

• DAC_Circadian_Neuroendocrinology

  DAC for projects of the group Circadian Neuroendocrinology at the Department of Endocrinology and Metabolism at Amsterdam UMC.

  Dac EGAC50000000692

• Cryopreservation of human cancers conserves tumour heterogeneity for single-cell multi-omics analysis

  Study EGAS00001005115

• Nimblegen SeqCap Custom Panel Sequencing

  Nimblegen SeqCap Custom Panel Sequencing for pNet

  Dataset EGAD00001005494

• Genomic Sequencing of Triple Negative Breast Cancer - Exome data

  Exome data for study EGAS00001008261

  Dataset EGAD00001015687

• WGS dataset

  4 WGS bam files for 4 cases with fusion

  Dataset EGAD00001004359

• PDAC

  ctDNA and protein markers for earlier detection of pancreatic cancers

  Dataset EGAD00001004399

• AML WGS bam

  WGS bam files for paired diagnostic and remission samples

  Dataset EGAD00001015515

• 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

• Identifying Novel Small RNA Biomarkers Unique to Patients with Gastric Cancer

  The biomarker development study consisted of two parts: discovery and validation. The first part was the discovery and verification phase of biomarkers using two different platforms: transcriptomic and miRNA. The salivary transcriptomes of 63 GC samples and 31 non-GC controls were profiled using Affymetrix HG U133+2.0 microarrays (Affymetrix, Santa Clara, CA). The identified exRNA candidates were verified by quantitative real-time PCR (RT-qPCR) using all 94 of the original samples. In the discovery phase for the miRNA biomarkers, 10 early-stage GC samples and 10 non-GC controls were selected. The salivary miRNAs of these samples (n=20) were profiled using the TaqMan MicroRNA Array (Applied Biosystems, Foster City, CA). MicroRNA candidates were verified using TaqMan miRNA Assay (Thermo Scientific, Grand Island, NY). The second part of the study was to validate these verified exRNA biomarker candidates with exRNA samples extracted from an independent cohort of 100 GC and 100 non-GC saliva samples. The cohort was not balanced for demographics on gender and smoking history but more accurately reflected the diagnostic setting where our proposed final model could be implemented. Reprinted from "Li F, Yoshizawa MJ, Kim K, Kanjanapangka J, Grogan T, Wang X, Elashoff D, Ishikawa S, Chia D, Liao W, Akin D, Yan X, Lee M, Choi R, Kim S, Kang S, Bae J, Sohn T, Lee J, Choi M, Min B, Lee J, Kim J, Kim Y, Kim S, Wong D. (2018) Development and Validation of Salivary Extracellular RNA Biomarkers for Noninvasive Detection of Gastric Cancer. Clin Chem. PMID: 30097497 DOI: 10.1373/clinchem.2018.290569", with permission from American Association for Clinical Chemistry (United States).

  Study phs001767

• The Role of Germline Mutation and Parental Age in Autism Spectrum Disorders

  <p>We will apply whole genome sequencing of trio families to determine how patterns of germline mutation throughout the genome determine risk for Autism Spectrum Disorder (ASD). We will investigate the nature intrinsic hypermutability and the extrinsic forces, such as paternal age, that influence rates of germline mutation. We will accomplish these goals through the following specific aims: Specific Aim 1 will characterize germline de novo mutations (DNMs) by whole genome sequencing in families. These studies will identify and validate ~8,000 de novo point mutations and structural variants in trios and controls to determine the parent of origin of DNMs. Specific Aim 2 will identify hot spots for germline mutation based on the regional density of DNMs in the genome, and determine the effects of DNA sequence features on rates of mutation. We will determine the association of mutation hotspots with ASD in the discovery sample and in genomic datasets from an independent sample of 2700 cases and 2700 controls. Specific Aim 3 will characterize the effects of extrinsic factors, including parental age and environment, on genome-wide rates of mutation. We will quantify the effect of paternal age on pathogenic and neutral alleles in sperm and investigate whether some DNMs confer a germline selective advantage. The findings of this study will provide fundamental insights into the genetic basis of autism risk and the genetic mechanism of the observed parental age effects in ASD. We will identify genes that confer significant risk for autism, and we will determine how intrinsic properties of the genome interact with extrinsic forces to determining risk for disease in offspring.

  Study phs001164

• A Missense SNP in the Tumor Suppressor SETD2 Reduces H3K36me3 and Mitotic Spindle Integrity in Drosophila

  While examining DNA from renal cell carcinoma (RCC) patients we observed a single nucleotide polymorphism (SNP; rs58906143,chr3:47163422 C→G (hg19); E902Q*) within SETD2 that was overrepresented in kidney cancer patients compared to control patients. This original study utilized directed sequencing of 14 genes. In an expanded study using a Taqman assay to study the specific SNP, a G allele was found in 72/493 cases (14.6%) and 24/356 (6.7%) controls. Analysis by ancestry revealed that there was there was a G allele in 50/119 (42.0%) cases and 21/71 (29.6%) controls in patients with African Ancestry while there was a G allele in 19/335 cases (5.7%) and 3/269 (1.1%) controls in patients with European Ancestry. These differences did not reach statistical significance. Concurrently, we studied the functional effect of this SNP in a Drosophila model. The homologous amino acid substitution at E741Q reduces H3K36me3 levels which could be rescued by wild type Set2. Additionally, the mutation resulted in significant defects in spindle morphogenesis, consistent with a role for SETD2 in alpha-tubulin methylation during mitosis. Data available through dbGAP include the 14 gene sequence files of 52 control and 128 RCC patients, the results of Taqman SNP (rs58906143) analysis in text files for 221 controls and 357 RCC patients, and compiled phenotype data including age and assigned race. Due to data use limitations, genotyping data for 8 RCC patients and 83 controls as well as GWAS data for ancestry determination will not be available on dbGaP, but will be made available on request.

  Study phs003474

• Clinical and Molecular Features of Acquired Resistance to Immunotherapy in Non-Small Cell Lung Cancer

  PD-(L)1 blockade has been shown to promote durable responses in non-small cell lung cancer (NSCLC) patients and has been rapidly incorporated into the treatment regimens for many with advanced disease. Despite this, mechanisms of acquired resistance (AR) to PD-(L)1 have not been well understood. To address the clinical and molecular landscape of AR to PD-(L)1 blockade in NSCLC patients, a large clinical cohort of AR to PD-(L)1 blockade in lung cancer was examined. In conjunction, a systematic genomic and transcriptomic analysis in a subset of patients (n = 29) with available tissue samples was conducted. To investigate the molecular mechanisms of AR to PD-1 blockade from pre- and/or post-treatment tumors, microarray-based whole transcriptome expression data for 29 tumor samples, and whole exome sequencing (WES) data from 34 tumor samples was generated from this subset. Microarray data was uploaded to the Gene Expression Omnibus (GEO) database. Most AR tumors showed retained or increased inflammatory characteristics with significant upregulation of IFNγ which was suggestive of persistent albeit insufficient anti-tumor immune response. This finding expounds upon the prior pre-clinical and translational data supporting the intricate role of IFNγ in sensitivity and resistance to immunotherapy. Whereas initial IFNγ exposure may be fundamental to T cell activation (a hallmark of immune response), persistent IFNγ related effects and upregulation may potentially signal immune dysfunction and IFNγ insensitivity in contrast. The inflammatory phenotypes identified have implications for future rational development of new immunotherapy strategies for patients with AR.

  Study phs002834

• Puerto Rico Heart Health Program (PRHHP-BioLINCC)

  Data Access NOTE: Please refer to the “Authorized Access” section below for information about how access to the data from this accession differs from many other dbGaP accessions. Objectives: To investigate morbidity and mortality from Coronary Heart Disease (CHD) in Puerto Rican rural and urban men. The objectives of the study were: (1) to identify factors related to the development of CHD, (2) compare the etiology of disease in rural versus urban men, and (3) determine the prevalence and incidence of CHD and other cardiovascular diseases in Puerto Rican males.Background: As Puerto Rico became more industrialized in the 1940s and 1950s, mortality rates for CHD increased. Since many factors related to CHD can be relatively homogenous within a population, two contrasting subgroups were selected for study in Puerto Rico: a rural population of men from a mountainous community and an urban population selected from San Juan. The NHLBI initiated the Puerto Rico Heart Health Program in May, 1965 as a prospective study of lifestyle, environmental and biological factors in the progression of cardiovascular disease in Puerto Rican men.Participants: A total of 9,824 (2,976 rural, 6,848 urban) men, age 45 to 64 were examined at the baseline exam.Design: The examination consisted of standardized questionnaires to determine education, occupation, smoking habits, and physical activity. Trained interviewers conducted a nutritional survey through a 24 hour diet recall. Subjects were also examined to determine prevalent cardiovascular, cerebrovascular and peripheral vascular abnormalities. The examination included vital capacity, a 12-lead ECG, and laboratory tests for hematocrit, glucose, serum cholesterol, serum glycercides and lipoprotein electrophoresis. A medical history was also obtained. Three additional exams, approximately three years apart, were conducted and morbidity and mortality follow-up concluded in 1980.

  Study phs003930

• High Frequency Ventilation in Premature Infants (HIFI-BioLINCC)

  Data Access NOTE: Please refer to the “Authorized Access” section below for information about how access to the data from this accession differs from many other dbGaP accessions. Objectives: To evaluate the hypothesis that high frequency oscillatory ventilation in preterm infants would reduce the incidence of mortality and pulmonary complications compared to conventional mechanical ventilation.Background: With the introduction of mechanical ventilation in preterm infants, mortality and morbidity significantly improved but remained high. The improvement in survival that accompanied the use of mechanical ventilation also brought about an increase in the incidence of pulmonary complications. The principal complication occurs in the form of bronchopulmonary dysplasia. Barotrauma and oxygen toxicity are considered to be in the pathogenesis for this disorder. Considerable interest in high frequency ventilation for preterm infants was generated when animal studies indicated high frequency ventilation to be effective in promoting gas exchange without apparent adverse effects. High Frequency Ventilation (HFV) delivers small tidal volumes at high frequencies of 4 to 15 Hz, and animal studies had indicated that HFV was associated with effective gas exchange, less barotrauma, and lower mean airway pressure. However, the efficacy and safety of HFV in preterm infants had not been studied. The HIFI Planning Phase was initiated in August 1984, and recruitment and intervention began in February, 1986. Follow-up studies continued thru September, 1988.Participants: A total of 673 infants were enrolled.Conclusions: Bronchopulmonary dysplasia incidence was similar in the two groups as was mortality and the need for ventilatory support during the first 28 days. There was a significantly greater rate of pneumoperitoneum of pulmonary origin in the high frequency group as was a greater incidence rate of intracranial hemorrhage. (HIFI Study Group, 1989, PMID: 2643039)

  Study phs004032

• Response to Hepatitis B vaccine

  Approximately 5-10% of individuals, who are vaccinated with a hepatitis B (HB) vaccine designed based on the HBV genotype C, fail to acquire protective levels of antibodies. Host genetic factors behind low immune response to the HB vaccine were investigated by GWAS and HLA association tests. GWAS and HLA association tests were carried out using a total of 1,193 Japanese individuals including 107 low responders (HBsAb ?10 mIU/mL), 351 intermediate responders (10 mIU/mL< HBsAb <100 mIU/mL), and 735 high responders (HBsAb ?100 mIU/mL). Classical HLA class II alleles were statistically imputed using the genome-wide SNP typing data. GWAS identified independent associations of HLA-DRB1-DQB1 haplotypes, HLA-DPB1 alleles and BTNL2 gene with immune response to the HB vaccine designed based on the HBV genotype C. Five HLA-DRB1-DQB1 haplotypes and two DPB1 alleles showed significant associations with response to the HB vaccine in a comparison of three groups of 1,193 HB vaccinated individuals. When frequencies of DRB1-DQB1 haplotypes and DPB1 alleles were compared between low immune responders and HBV patients, significant associations were identified for three DRB1-DQB1 haplotypes, and no association was identified for any of DPB1 alleles. In contrast, no association for DRB1-DQB1 haplotypes and DPB1 alleles was identified in a comparison between high immune responders and healthy individuals. The findings in this study clearly show the importance of HLA-DR-DQ (i.e. recognition of a HB vaccine related HBsAg by specific DR-DQ haplotypes) and BTNL2 molecules (i.e. high immune response to the HB vaccine) for response to a HB vaccine designed based on the HBV genotype C.

  Study JGAS000341

• DAC for high resolution genomic data generated by the Gisselsson Group at the Department of Clinical Genetics, Lund University.

  Dac EGAC00001000534

• The data access committee for Multimodal Genomic Features Predict Outcome of Immune Checkpoint Blockade in Non-small Cell Lung Cancer

  Dac EGAC00001001331

• Data Access Commitee for study Fine-Scale Genomic Analyses Of Admixed Individuals Reveal Unrecognized Genetic Ancestry Components In Argentina

  Dac EGAC00001001634

• Access to aligned sequencing data for study "Loss of SNAI2 in prostate cancer correlates with clinical response to androgen deprivation therapy".

  Dac EGAC00001001809

• B99

  Cardio-Metabochip genotypes for B99 cohort

  Dataset EGAD00010001427

• IHIT

  Cardio-Metabochip genotypes for IHIT cohort

  Dataset EGAD00010001428

• BreastCancer_Control_Micorarays

  Genotyping array data for normal mammary gland control samples

  Dataset EGAD00010002250

• CDK4 phosphorylation status and rational use for combining CDK4/6 and BRAF/MEK inhibition in advanced thyroid carcinomas

  Study EGAS00001007577

• Okayama University Hospital, CGM center, DAC

  Okayama University Hospital, Japan Centre for Comprehensive Genomic Medicine (CGM) Data Access Committee

  Dac EGAC50000000250

• Next generation sequencing of plasma cell neoplasms

  Includes raw data for genome sequencing studies performed at the University of Miami

  Dac EGAC50000000593

• An approach for evaluating the effects of dietary fiber polysaccharides on the human gut microbiome and plasma proteome

  Study EGAS00001005330

• GATCI exome sequencing fastqs

  Raw whole exome sequencing data (fastq) for the GATCI project

  Dataset EGAD00001005808

• Summary statistics for cervical cancer GWAS

  Summary statistics from GWAS meta-analysis of cervical cancer

  Dataset EGAD00001004361

• Metastatic Prostate Follow Up

  Validation/deeper sequencing for metastatic prostate cancer samples

  Dataset EGAD00001000988

• Global Anaplastic Thyroid Cancer Initiative

  Raw exome sequence data(fastq) for the GATCI project

  Dataset EGAD00001003235

• Spatial transcriptomic data of breast cancer

  Fastq files from spatial transcriptomic of breast cancer coming from 8 Breast cancer sections. Sample preparation: frozen BC samples were chosen based on tissue structure and RNA quality (RIN > 8). The “Visium Spatial Tissue Optimization Slide and Reagent Kit” (10X Genomics; #PN-1000193) was then used to optimize permeabilization conditions for BC tissues. Briefly, sections were fixed, stained and then permeabilized at different time points to capture mRNA, and the reverse transcription was performed to generate fluorescently labeled cDNA. The permeabilization time that resulted in the highest fluorescence signal with the lowest background diffusion was chosen. The best permeabilization time for BC tissue was 18 min. Cryostat sections of 10 μm of thickness were cut and placed on Visium Spatial Gene Expression slides (10X Genomics, PN-1000184). The slide was incubated for 1 min at 37°C, then fixed with methanol for 30 min at -20°C followed by Hematoxylin and Eosin (H&E) staining and images were taken under a high-resolution microscope. After imaging, the coverslip was detached by holding the slide in water and the slide was mounted in a plastic slide cassette. The spatial gene expression process, including tissue permeabilization, second strand synthesis and cDNA amplification, was performed according to the manufacturer’s instructions (10X Genomics; #CG000239). cDNA quality was next assessed using Agilent High sensitivity DNA Kit (Agilent, #5067-4626). The spatial gene libraries were constructed using Visium Spatial Library Construction Kit (10X Genomics, PN-1000184).

  Dataset EGAD50000000322

• Genetic Basis of Pulmonary Non-tuberculous Mycobacterial Infections

  This project aims at characterizing the human host susceptibility to pulmonary non-tuberculous mycobacterial (PNTM) infections. PNTM infections occur in patients with chronic lung disease, but also in a distinct group of elderly women without lung defects but who share a common body morphology: tall and lean with scoliosis, pectus excavatum, and mitral valve prolapse. We performed whole exome and genome sequencing in extended families of patients with active PNTM. This unique collection of familial cohorts in PNTM represents an important opportunity for a high yield search for genes that regulate mucosal immunity. We also sequenced the genome of mycobacterial isolates from PNTM patients to integrate host PNTM susceptibility with mycobacterial genotypes and gain insights into the key factors involved in this devastating disease.

  Study phs000719

• The mutational characterization of adenoid cystic carcinoma

  Adenoid cystic carcinoma (ACC) typically emanate from the major and minor salivary glands of the head and neck. ACCs have high rates of perineural invasion, locoregional recurrence, and distant metastasis. Here we report sequencing of 60 tumor/normal pairs and find substantial mutational diversity. On pathway analysis, a significant percentage of mutations involved chromatin remodeling, DNA damage, protein kinase A signaling, and FGF/IGF/PI3K signaling. Whole genome sequencing and FISH confirmed the MYB-NFIB translocation as the main structural variant in ACC. Evaluation of potential driver mutations KDM6A and PIK3CA reveal that specific, observed alterations impart functional consequences. Collectively, our data delineate the ACC mutational landscape and establish a molecular foundation for investigating new therapies for this disease.

  Study phs000612

• Natural Genetic Variation in the Human Genome

  In this study, we used existing whole genome sequencing data from the TOPMed Amish and Jackson Heart Study, as well as the GTEx study, to identify mobile element insertions in the genomes of these individuals.&#160; A total of 1112 TOPMed Amish, 3331 TOPMed Jackson Heart Study, and 698 GTEx individuals were examined.&#160; We used the Mobile Element Locator Tool (MELT) developed previously by our lab, along with a Cloud-based version of MELT (CloudMELT), to discover non-reference mobile element insertions (MEIs) in these genomes.&#160; We discovered Alu, L1, SVA, and HERV-K MEIs and produced genotypes in individual genomes.&#160; Build hg19 bams were used for the TOPMed samples, and build GRCh37 bams were used for the GTEx samples in this study.

  Study phs002463

• DirectHRD Enables Sensitive Scar-Based Classification of Homologous Recombination Deficiency (HRD)

  Homologous recombination deficiency (HRD)-induced genomic scars are an FDA-approved biomarker for identifying cancers likely to respond to PARP inhibitors. However, detecting HRD scars from blood biopsies has been challenging due to the low tumor content in blood samples. To address this limitation, we developed DirectHRD, a genomic scar-based HRD classifier leveraging whole-genome sequencing (WGS) data for non-invasive blood biopsy testing. DirectHRD was applied to 90 cell-free DNA (cfDNA) samples across four cancer types: breast, ovarian, prostate, and pancreatic. The method achieved an AUC of 0.87 and demonstrated the ability to detect HRD at tumor fractions as low as 1%, offering a tenfold increase in sensitivity compared to state-of-the-art methods.

  Study phs003760

• Ultrasensitive Detection and Monitoring of Circulating Tumor DNA using Structural Variants in Early-Stage Breast Cancer

  Circulating tumor DNA (ctDNA) detection has an emerging role in the management of breast cancer, offering a non-invasive means to monitor disease status and detect recurrence. This study demonstrates that longitudinal monitoring of tumor-specific structural variants - frequent alterations observed across many tumor types including all subtypes of breast cancer derived from Whole Genome Sequencing data - allows for ctDNA detection in nearly all participants in this cohort with untreated early breast cancer prior to starting neoadjuvant therapy. On-treatment ctDNA monitoring enabled the early identification of patients at high risk of recurrence and ctDNA was detected prior to relapse in participants across all receptor subtypes. These findings demonstrate the clinical validity of this assay approach for ultrasensitive ctDNA monitoring.

  Study EGAS50000000799

• 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

• Single cell transcriptomics to characterize the tumor microenvironment of prostate cancer fusion biopsies

  The primary objective of this study was to characterize the tumor microenvironment in fusion-guided transperineal biopsy samples from patients undergoing PC diagnosis. For each patient, one biopsy was taken from a suspected tumor region and another from a non-suspicious area, which were later classified as high- or low-tumorigenicity based on anatomopathological analysis. Using scRNA-seq data, we performed cancer-oriented cell annotation, differential expression analysis, and functional pathway enrichment studies across key cellular subpopulations. Additionally, differential abundance analysis was conducted to identify cell groups representative of different tumorigenicity levels. Finally, classification models were developed using gene expression data to differentiate high- vs. low-tumorigenicity samples, with the long-term goal of establishing a diagnostic classifier for PC stratification.

  Study EGAS50000000888

• Whole-exome sequencing identifies new pathogenic germline variants in patients with colorectal polyposis

  Adenomatous polyposis confers an increased risk of colorectal cancer development. Here, we investigated probably underlying predisposition variants in patients with suspected colorectal polyposis without variants in APC and MUTYH genes by whole exome sequencing (WES). Twenty-seven patients were included and subjected to germline WES. After filtering out variants for sequencing quality, variant allele fraction frequency, and population frequency, variants were manually prioritized by the ACMG criteria. Among the variants identified, 17 were classified as pathogenic or likely pathogenic (in 12 patients). This study gives information of probably associated polyposis variants in Brazilian patients without germline pathogenic variants in APC and MUTYH genes, supporting the utilization of next-generation sequencing for screening in these patients beyond these genes.

  Study EGAS50000000591

• GM adipose tissue study

  The Greek Metabolic (GM) adipose study was carried out in 106 individuals living in Greece and consists of genotyping data (chip), RNA-Seq and ATAC-Seq (for a subset of individuals) data from paired biopsies of Subcutaneous and Visceral adipose tissue. eQTL mapping was performed to study gene regulation and findings compared to those from adipose tissue GTEX data. The focus of this project was to study an underexplored population living in different environmental conditions in order to reveal novel regulatory effects for genes that shape complex traits and disease risk. Our results highlight the utility of modest-sized studies in adding to our understanding of the molecular basis of complex traits and to the identification of mechanisms that drive disease in specific tissues.

  Study EGAS00001007126

• Targeting PTPRK-RSPO3 colon tumours promotesdifferentiation and loss of stem-cell function

  Colorectal cancer remains a major unmet medical need, promptinglarge-scale genomics efforts in the field to identify moleculardrivers for which targeted therapies might be developed. Wepreviously reported the identification of recurrent translocationsin R-spondin proteins present in a subset of colorectal tumours.Here we show that targeting RSPO3 in PTPRK-RSPO3-fusion positivehuman tumour xenografts inhibits tumour growth andpromotes differentiation. Notably, genes expressed in the stem-cellcompartment of the intestine were among those most sensitive toanti-RSPO3 treatment. This observation, combined with functionalassays, suggests that a stem-cell compartment drives PTPRK-RSPO3colorectal tumour growth and indicates that the therapeutictargeting of stem-cell properties within tumours may be a clinicallyrelevant approach for the treatment of colorectal tumors.

  Study EGAS00001001462

• Integrative_Oncogenomics_of_multiple_myeloma

  We used targeted capture and massively parallel sequencing of exomes of CD138 purified plasma cells and matched somatic DNA from 17 patients with Multiple Myeloma. For each patient, an early tumor sample (at diagnosis) and a late one (at relapse) were available. For few of them, an additional late sample (2nd progression) was present. In total, the study has 52 samples. 1044 variants were validated by 454 sequencing. The present study will validate an additional 4630 variants by targeted pull-down and sequencing. All 52 samples will be indexed and then will be pre-pooled in groups of 5 or 6. The sequence capture will use 10 reactions. All samples will then be pooled and go thorugh one lane of HiSeq.

  Study EGAS00001000244

• May 2021 data update (fastq) 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.

  May 2021 data update (fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001008100

• RNA sequencing of periprostatic fat after a 6 month deep androgen deprivation therapy

  Androgen deprivation therapy treated patients (n=11) were recruited from an open label neoadjuvant phase II study in which patients with high-risk disease received a ‘supercastration’ regimen consisting of degarelix 240/80 mg subcutaneously every four weeks; abiraterone acetate 500 mg orally daily titrating upwards every two weeks by 250 mg to a final dose of 1000 mg daily; bicalutamide 50 mg orally daily; and prednisolone 5 mg orally twice daily for a total of 6 months (Australian New Zealand Clinical Trials Registry 12612000772842). Untreated patients with similar pre-treatment characteristics were obtained from a prospective prostatectomy biorepository22,23. Prior to ligation of the dorsal venous complex and prostate pedicles, the anterior prostate was defatted and the specimen was removed immediately, placed in a sterile container and transferred on ice for long-term storage in the vapour phase of liquid nitrogen. A total of 50–100 µg of adipose tissue was separated from fresh frozen samples stored at −160°C. RNA was isolated using the Qiagen RNeasy Lipid Tissue Mini Kit and eluted in 35 µL nuclease-free water. 0.5–1 µg of total RNA was used as the input for cDNA library synthesis using TruSeq RNA Sample Prep Kit v2 (Illumina), and libraries were constructed according to manufacturer’s instructions. Samples were sequenced on a HiSeq 2500 (Illumina) using 101 base paired-end chemistry, aiming for 50 million mapped paired-end reads per sample.

  Dataset EGAD00001004971

• Genome Wide Association for Asthma and Lung Function

  The SNP Typing for Association with Multiple Phenotypes from Existing Epidemiologic (STAMPEED) asthma project includes subjects with asthma and controls from the Chicago Asthma Genetics Study (CAG), NHLBI multicenter Severe Asthma Research Program (SARP) and NHLBI Collaborative Studies on the Genetics of Asthma CSGA (Wake Forest). All studies included European American and African American children and adults with asthma ranging from mild to severe and adult controls. CAG participants were collected at the University of Chicago. SARP participants were recruited at the NHLBI SARP sites with an emphasis on recruiting severe asthmatics (Moore et al, Am J Respir Crit Care Med, 2010, PMID: 19892860). CSGA cases and controls collected by the Wake Forest investigators were also included. Asthma status was based on both a physician&#39;s diagnosis and either bronchodilator reversibility or hyper-responsiveness to methacholine as well as less than 5 pack years of smoking. Genotyping was performed on the Illumina 1Mv1 platform, with individual genotypes called using clustering algorithms as implemented in the BeadStudio software by Illumina. The total number of markers following standard QC was 1,025,129. Imputation was performed using the HapMap phase 2, release 21 SNPs using MACH with the phased HapMap CEU and YRI haplotypes as a reference. Case/control association tests for asthma status were performed using logistic regression in R (http://CRAN.R-project.org/) on genotype dosages, and adjusting for the first principal component from EIGENSTRAT.

  Study phs000355

• Data access agreement for ATRT

  Dac EGAC00001000306

• EGAD00010000498

  Affymetrix SNP6.0 genotype data for prostate cancer patients

  Dataset EGAD00010000498

• EGAD00010000536

  21 unlinked autosomal microsatellite loci for 30 Central Asian populations

  Dataset EGAD00010000536

• Variant_files_100_ID_trios

  High Quality Variant Call files, generated by bioscope, converted to vcf format. Complete dataset for all 300 samples.

  Dataset EGAD00001000277

• Whole Exome Sequencing for Verhaak-GBM

  Dataset EGAD00001001111

• DATA FILES FOR BALL-PAX5-WES

  Dataset EGAD00001001056

• Whole Exome Data for Verhaak-GBM

  Dataset EGAD00001001112

• Whole Exome sequencing for Verhaak-GBM

  Dataset EGAD00001001113

• lnFXI_metaanalysis_summarydata

  Summary data from Meta-analysis of Genome-Wide-Association Studies for plasma levels of Coagulation Factor XI (FXI)

  Dataset EGAD00010001141

• SAFIR02_Agilent

  Genomics to select patients with metastatic breast cancer for targeted therapy (microarray_agilent)

  Dataset EGAD00010002243

• AS_genotyping

  AS genotyping data for lead SNPs using Illuminia Global Array V2.0

  Dataset EGAD00010002476

• DAC for the study molecular biomarkers associated with the diagnosis and severity of genetic and diseases from PAIDI-BIO354 GENYO-UGR)

  Dac EGAC00001003090

• WES for cell lines UWB1.289 and COV362

  exon 11 mutated UWB1.289 and COV362 cell lines

  Dataset EGAD50000000189

• DAC for BCP-LBL Kiel

  Whole exome sequencing and RNA sequencing of B-Cell Precursor Lymphoblastic Lymphoma tissue biopsies.

  Dac EGAC50000000181

• DAC for study involving the spatial transcriptomics analysis of HPV-dependent and HPV-independent vulval squamous cell carcinoma at Imperial College London.

  Dac EGAC00001003515

• Structural and Non-Coding Variants Increase the Diagnostic Yield of Clinical Whole Genome Sequencing for Rare Diseases

  Study EGAS00001007575

• Human embryo ATAC+RNA single cell sequencing samples DAC (Linnarsson)

  DAC for human embryo ATAC+RNA single cell sequencing samples

  Dac EGAC50000000657

• Linnarsson lab general data access committe

  Committee that handles the majority of policies for the Linnarsson Lab at Karolinska Institutet

  Dac EGAC50000000835

• DAC for datasets from study 'Single-nucleus multi-omic sequencing of the human motor cortex in ALS/ALS-FTD'

  Dac EGAC50000000856

• Aggregated count table

  RNA-seq count matrix for 296 bulk pre-treatment tumors from IMblaze370

  Dataset EGAD00001008552

• Complete Genomics dataset for study EGAS00001002275.

  TBD

  Dataset EGAD00001003187

• FGFP_16S

  Firs 1106 16S rDNA data for the Flemish Gut Flora Project

  Dataset EGAD00001001936

• ICGC_Pedbrain_WGBS_Pilocytic_Astrocytoma

  18 WGBS lanes for 9 samples of pilocytic astrocytoma.

  Dataset EGAD00001005504

• Multi-Modal Single-Cell, Spatial, and Genomic Analyses of Human Non-Small Cell Lung Cancer Brain Metastases

  We performed single nuclei RNA-sequencing (snRNA-seq) with matched T cell receptor sequencing (TCR-seq), and pool matched low pass whole genome sequencing (WGS) of 12 treatment-naive non-small cell lung cancer (NSCLC) primary tumors (PTs) and 31 treatment-naive NSCLC brain metastases (BMs). In total, we recovered 277,206 cell transcriptomes in 43 samples. Single-nuclei suspension from frozen NSCLC metastases were generated using methods published in Slyper et al. (Nature Medicine, 2020, PMID:32405060) with modifications. The tissue was first cut in 20 &#181;m sections using a cryostat and stored on dry ice until the next step. Then the tissue was put on wet ice and washed once with 5 ml PBS to remove OCT. After this step nuclei were extracted by vigorous pipetting in salt-tris buffer with Tween-20 (TST) followed by a high-volume wash in salt-tris buffer (ST). Nuclei were counted and 10,000-14,000 and were loaded using a Chromium controller (10X genomics) and Chromium Single Cell 5' Reagents (V1.1 and V2). Complementary DNA libraries were generated according to manufacturer's instructions, with the modification of one additional cycle of amplification. Matched single nuclei T cell receptor (snTCR) sequencing libraries were prepared from amplified cDNA libraries using either Chromium Single Cell V(D)J Enrichment Kit for human T cells Reagent Kit, v1.1, or single cell human TCR amplification kit. Final snTCR sequencing libraries were prepared using Single Index Kit T Set A for V1.1 libraries or Library construction kit and Dual Index Kit TT set A for V2 libraries. Sequencing libraries were quantified using Tapestation D5000 reagents and a 2200 TapeStation and pooled for sequencing. Pool matched low pass whole-genome sequencing (lp-WGS) was performed in addition to snRNA-seq to improve the identification of the malignant and non-malignant cell compartments. Nuclei from snRNA-seq sample preparations were collected by centrifugation (500g, 5 min), snap frozen after removing excess ST buffer, and stored at -200C until further processing. If insufficient nuclei (0C for 9 minutes. Adapters were not diluted, and the optional PCR (5 cycles) and cleanup were performed. After library cleanup with AMPure beads (Beckman Coulter, Brea, CA), libraries were quantified with Tapestation D5000 HS tapes (Agilent) and stored at -200C until sequencing.Using multiplexed immunofluorescence in an independent cohort of treatment-na&#239;ve pairs of primary tumors and brain metastases from the same patients with NSCLC, we validated genomic and tumor-microenvironmental findings and identified a cancer cell population characterized by neural features that strongly enriched in brain metastases. This comprehensive analysis provides insights into human NSCLC brain metastasis biology and serves as an important resource for additional discovery.

  Study phs003865

• Ludwig Center for Cancer Genetics and Therapeutics at Johns Hopkins

  Dac EGAC00001000507

• Data access committee for study - The subclonal architecture of metastatic breast cancer: Results from a prospective community-based rapid autopsy program "CASCADE".

  Dac EGAC00001000574

• Data Access Commitee for Dietrich and Wendisch et al., SARS-CoV-2 infection triggers profibrotic macrophage responses and lung fibrosis (Submitted)

  Dac EGAC00001001884

• Data Access Commitee for Dietrich and Wendisch et al., SARS-CoV-2 infection triggers profibrotic macrophage responses and lung fibrosis (Submitted)

  Dac EGAC00001002335

• EXOME_ARRAY_ANALYSIS

  EXOME ARRAY ANALYSIS OF ADVERSE REACTIONS TO FLUOROPYRIMIDINE-BASED THERAPY FOR GASTROINTESTINAL CANCER

  Dataset EGAD00010001499

• DNA methylation for EGAS00001003603

  Genome-wide DNA methylation profiling of Waldenstrom's macroglobulinemia (WM) patient samples

  Dataset EGAD00010001861

• NativeAmericans_InstitutoNacionaldeSalud_hg38_autosomic_3group

  Genome-wide data for 130 Native American individuals from Peru

  Dataset EGAD00010001992

• NativeAmericans_InstitutoNacionaldeSalud_hg37_autosomic_1group

  Genome-wide data for 71 Native American individuals from Peru

  Dataset EGAD00010001991

• NativeAmericans_InstitutoNacionaldeSalud_hg38_autosomic_2group

  Genome-wide data for 59 Native American individuals from Peru

  Dataset EGAD00010001990

• BRACOVID_genotype

  Cohort: Raw genotype files for BRACOVID cohort. Genotype Chip: Axiom_PMRA.r3 array genomic build: b37

  Dataset EGAD00010002172

• Genotype_HSM1_HSM2

  Genotypes for 2 human skeletal muscle samples

  Dataset EGAD00010002248

• OICR-DAC, Ontario Institute for Cancer Research

  Dac EGAC00001000591

• OICR-DAC, Ontario Institute for Cancer Research

  Dac EGAC00001000710

• CCA NanoString data (60CCA)

  Raw .RCC files for NanoString. nCounter PanCancer IO 360 Panel was used

  Dataset EGAD00010002612

• Sample Sheet

  Sample sheet for aligning samples with patients.

  Dataset EGAD50000000484

• Lifelines NEXT HMO Data

  The dataset contains HMO measurements for 1542 samples from Lifelines NEXT cohort

  Dataset EGAD50000000531

• Genome-wide array data from Eivissa and Menorca

  DAC for the Genome-wide array data from 22 Eivissan and 20 Menorcan individuals.

  Dac EGAC50000000297

• Metadata associated with sequencing

  Associated metadata for sequencing data.

  Dataset EGAD50000000528

• Analysis of circulating miRNAs for the identification of new prognostic and predictive markers in gastro-entero-pancreatic neuroendocrine tumour (GEP-NET)

  Study EGAS00001007227

• DAC anti-MPO BCR sequences

  DAC for the requests of access to data of anti-MPO BCR sequences in the EGA repository,

  Dac EGAC50000000446

• NGS WGS Data - Unic TDP

  WGS data from the Unicorn-PASS cohort for the Tandem Duplicator Phenotype paper

  Dataset EGAD50000001567

• UMCG Immunogenetics DAC

  DAC for the data generated in the Immunogenetics group in the genetics department of the University Medical Center Groningen

  Dac EGAC50000000785

• Soegaard Laboratory Data Access Committee

  Data Access Committee for data generated by the laboratory of Prof. O.S. Soegaard at Aarhus University Hospital.

  Dac EGAC50000000888