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• A Sequential Window of Opportunity Trial of Anti-PD-L1/TGF-β trap (M7824) Alone and in Combination with TriAd Vaccine and N-803 for Resectable Head and Neck Squamous Cell Carcinoma not Associated with Human Papillomavirus Infection

  This submission includes the whole exome and bulk RNA sequencing associated with the correlative study of clinical specimens from a prospective clinical study of neoadjuvant bintrafusp alfa in patients with newly diagnosed, surgically resectable oral cavity or laryngeal squamous cell carcinoma. 

  Study phs002849

• RNA sequecing of primary B cells infected with Epstein-Barr virus (EBV) or stimulated with heat-inactivated EBV

  Naïve (CD27-IgD+) B cells were isolated from buffy coat preparations of healthy donors using CD19 magnetic beads, followed by reals of CD19 beads and incubation with IgD-biotin and anti-biotin magnetic beads. B cells were infected with EBV by spinoculation or stimulated with heat-inactivated EBV and control cells were left uninfected. RNA was extracted immediately after isolation in un-infected B cells. From EBV-infected B cells and B cells stimulated with heat-inactivated virus, RNA was extracted 24 and 96 hours after infection / stimulation.

  Dataset EGAD50000000305

• Single-nuclei ATAC sequencing of pheochromocytoma and paraganglioma arising from germline SDHB mutations

  10x genomics single-nuclei ATAC sequencing of 7 SDHB-deficient non-metastatic and metastatic pheochromocytoma and paraganglioma, and 1 normal adrenal medulla sample. snATAC-seq was conducted using the "Van Helsing" protocol (dx.doi.org/10.17504/protocols.io.bw52pg8e). Once processed, snATAC-seq libraries were sequenced on the Illumina NextSeq 500 (Illumina, USA) using 50bp paired-end sequencing. Raw sequencing data in BCL format was demultiplexed using cellranger-atac mkfastq (V2.0.0). This dataset contains sequencing reads in FASTQ format. R1/R3 files contain the forward and reverse sequencing reads, respectively, R2 contains the 10x Barcode.

  Dataset EGAD50000000503

• Data Access Committee of CiRA Foundation

  The iPS Cell Stock Project promoted by the CiRA Foundation is intended to generate and distribute iPS cells for medical use so they can be effectively utilized for research and development of cell transplantation therapy and contribute to the advancement of regenerative medicine that may become a novel treatment for patients suffering from intractable diseases or trauma who are not expected to improve with conventional therapies. In order to achieve this objective, CiRA Foundation establish the DAC based on the basic policies and rules for handling analysis information including iPS cell stocks for the purpose of proper sharing of samples and analyzed data collected directly or indirectly from the donors of iPS cell stocks.

  Dac EGAC50000000128

• Long-read whole-genome sequencing-based concurrent haplotype phasing and aneuploidy profiling of single cells

  This dataset contains long-read whole-genome sequencing (lrWGS) data from 14 samples. Five lrWGS data are from single-cell (sc, sc_2, sc_3), multi-cell (mc, 10 cells), and bulk samples of HG002. The remaining nine lrWGS data are from two preimplantation genetic testing (PGT) families, including four from blood bulk DNA of the parental pairs and five from trophectoderm biopsies of two embryos from one family and three embryos from another family. The data are provided in raw FASTQ format and were generated using the PromethION device from Oxford Nanopore Technologies.

  Dataset EGAD50000000787

• Single nucleus and bulk transcriptomics in prefrontal cortex of individuals with alpha synucleinopathies

  We explore cell-specific changes in gene expression across different α-synucleinopathies. We perform single nucleus RNA sequencing using 10X Genomics, and bulk RNA sequencing from the prefrontal cortex of individuals with alpha synucleinopathies - Parkinson's Disese (PD), monogenic LRRK2 PD, and multiple system atrophy (MSA), together with neurologically healthy controls.

  Study EGAS50000000301

• PRO-SPeCT: PROstate cancer heterogeneity deconvolution through Single cell Profiling of Chromatin accessibility and Transcriptomic output

  38 prostate cancer specimens derived from five human patients with ISUP ≥ 3 pathology who underwent radical prostatectomy and pelvic lymph node dissection at surgery as part of the International Cancer Genome Consortium (ICGC) late-onset cohort. Using single-cell multiome (expression and chromatin accessibility from RNA and ATAC, respectively) sequencing assay, we characterized 282,956 nuclei/cells, with a median of 6 primary tumor foci from the prostate gland and 3 locoregional lymph node metastases across all patients.

  Dataset EGAD50000000745

• Comprehensive molecular and clinicopathological profiling of salivary duct carcinoma

  Molecular targets and predictive biomarkers for prognosis in salivary duct carcinoma (SDC) have not fully identified. We conducted comprehensive molecular profiling to discover novel biomarkers for SDC. A total of 67 SDC samples were examined with DNA sequencing of 464 genes and transcriptome analysis in combination with the clinicopathological characteristics of the individuals.

  Study JGAS000534

• Integrative understanding of human immune system by functional genomics and development of intervention strategies for the prevention of autoimmune diseases

  To elucidate the feature of age-associated helper T (ThA) cells and its contribution to autoimmune diseases, single-cell RNA-sequencing analysis of peripheral blood CD4+ T cells from healthy control, CD4+ T cells in muscles and bronchoalveolar lavage fluid (BALF) from patients with idiopathic inflammatory myopathy were conducted.

  Study JGAS000648

• Transcriptome analysis of adolescents and young adults with Acute Lymphoblastic Leukemia

  The primary purpose of the research is identification of novel chromosome translocations in adolescents and young adults (AYA) with Acute Lymphoblastic Leukemia (ALL). We searched for novel chromosome translocations in 99 philadelphia-chromosome negative ALL cases (including 76 AYA cases) by RNA-seq using next-generation sequencers, and have discovered some novel chromosome translocations.

  Study JGAS000047

• EM-seq data from plasma cfDNA samples of ALS patients, control and C9-carriers

  This dataset contains targeted EM-seq data from 61 plasma cfDNA samples spanning 20 sporadic ALS, 10 C9orf72-ALS, 10 asymptomatic C9orf72 expansion carriers, and 21 non-disease controls. Libraries were prepared with the NEBNext Enzymatic Methyl-seq (EM-seq) kit, captured using the Twist Human Methylome Panel (3.98 M CpGs; 123 Mb), and sequenced on Illumina NovaSeq 6000 (150 bp paired-end; ~45× on-target depth) with unmethylated lambda DNA spike-in and a 20% PhiX balance library. The dataset includes per-sample gzipped FASTQ files (R1/R2) and minimal metadata.

  Dataset EGAD50000001808

• Identification of cell type differences in FOXN1 mutation carriers by scRNA-seq

  scRNA-seq was performed on the BD Rhapsody platform. CD45+ lymphocytes from two FOXN1het patients and one cord blood sample as control were sorted from frozen cryopreserved samples. The samples were split and each sample was stained with 4 Sampletag antibodies before Abseq staining with the BD Immune Discovery panel and 6 additional antibodies was performed to better classify immune cell subsets. The sorted and stained populations were pooled before loading onto the BD Rhapsody cartridge. The manufacturer's protocol was followed for library construction and samples were sequenced on an Illumina NovaSeq 6000.

  Dataset EGAD50000001708

• 10X single-cell Multiome (RNA+ATAC) and single-cell RNAseq of xenograft-derived HSPC, progenitors and myeloid progeny

  10X genomics chromium single-cell ATAC+RNA (Multiome) was use to prepare single-nucleus RNA- and ATAC-seq libraries for human HSPC sorted from xenografts recovered from inflammatory challenge. 10X genomics 3' kits were used to prepare single-cell RNA-seq libraries for committed progenitors and myeloid cells from the same xenografts. These were sequenced on an Illumina NovaSea 6000 platform; BAM files are provided. Samples from 3 conditions were sequenced for each cell type; 3 chromatin accessibility runs and 9 gene expression runs are provided.

  Dataset EGAD50000002328

• Whole exome sequencing of 49 tumor-blood pairs and transcriptome sequencing of 44 tumors for adrenocortical tumors

  Adrenal Cushing syndrome, which leads to type 2 diabetes, obesity and hypertension, is caused by ACTH-independent production of glucocorticoid by adrenocortical tumors. To investigate the genetic origins of cortisol-producing adrenocortical tumors, we performed whole exome sequencing of 49 tumor-blood pairs and transcriptome sequencing of 44 tumors

  Study EGAS00001000712

• Whole Exome Sequencing data of glioma from the Chinese Glioma Genome Atlas (CGGA) project

  Glioma is the most common and aggressive brain cancer in adults. While primary glioma has been widely studied, molecular characterization of recurrent glioma is still rare. The high-quality sequencing data that we generated provides a useful resource for the community. The CGGA project contains over 2,000 samples from Chinese cohorts. It totally includes the whole-exome sequencing (286), DNA methylation (159), mRNA sequencing (1,018), mRNA microarray (301) and microRNA microarray (198) and matched clinical data. CGGA removes the barriers to researchers, providing rapid and convenient access to high-quality functional genomic data resources for biological research and clinical applications.

  Dataset EGAD00001006445

• BRCA2, ATM, and CDK12 defects differentially shape prostate tumor driver genomics and clinical aggression

  This dataset contains all available targeted exon sequencing bam files from our study, "BRCA2, ATM, and CDK12 defects differentially shape prostate tumor driver genomics and clinical aggression". Patient identifiers are denoted by the first segment of the sample aliases (e.g. "P1"), and additional information is appended to reflect which sample is referenced. These include serial cfDNA samples ("-1", "-2", "-3", etc.), paired white blood cell or benign tissue control samples ("-Control"), or primary archival tissue samples derived from a diagnostic biopsy, prostatectomy, or transurethral resection of the prostate ("-Tissue"). All samples were sequenced using Illumina technology.

  Dataset EGAD00001006733

• Identification of molecule relationship between intravenous leiomyomatosis and uterus myoma

  Up to now, there are two hypothesis about the pathogenesis of the relationship of intravenous leiomyomatosis and uterine myoma. One theory suggests that the IVL comes from the smooth muscle cell in the vessel wall.The other theory indicates that the IVL derives from the uterine myometrium. However, limited to the technology, few studies have been deeply explore the underlying relation. In this study, we employ the RNA sequencing to explore the molecule relationship between IVL and uterus myoma. In order to identify the molecule relationship between IVl and uterine myoma we conducted transcriptome sequencing and bioinformaitc analysis

  Dataset EGAD00001003356

• High-Coverage Whole-Exome Sequencing Identifies Candidate Genes for Suicide in Victims with Major Depressive Disorder

  In this study, we applied an Illumina HighSeq platform-based high-coverage WES technique, which, in addition to the exons, allows the determination of 5′- and 3′-UTRs, promoters to a certain length, along with off-target sequences, such as introns, intergenic regions and infecting viruses. Brains from suicide victims (n = 23; 15 males and eight female) who had suffered from major depressive disorder and from control participants (n = 21; 14 males and seven females) who had died from other causes were used for whole-exome sequencing. Alignment files in bam format were uploaded.

  Dataset EGAD00001004082

• Genomic Evolution of Breast Cancer Metastasis and Relapse

  Recurrent breast cancer is almost universally fatal. We characterize 170 patients locally relapsed or distant metastatic cancers using massively parallel sequencing. We identify that the relapse-seeding clone disseminates late from the primary tumor. TP53 and AKT1 appear to be enriched in ER-positive cancers predisposed to relapse. Mutation acquisition continues at relapse as the same mutation signatures continue to operate and new signatures, such as that caused by radiotherapy appear de novo. In 49% of cases we identify drivers mutations private to the relapse and these are sampled from a wider range of cancer genes, including SWI-SNF complex and JAK-STAT signaling.

  Dataset EGAD00001002697

• SPATC1L variants associated with age-related and hereditary hearing loss

  Next-Generation Sequencing techniques (i.e, targeted re-sequencing and whole exome sequencing) have been employed for the study of two Italian patients affected by age-related hearing loss and of an Italian family affected by hereditary hearing loss. Data analysis led to the identification of three variants in SPATC1L, associated with the clinical phenotype.

  Study EGAS00001003047

• ADAPTeR Study: scRNA and scTCR data from TILs from two ccRCC patients treated with anti-PD1

  TILs were extracted from two ccRCC patients treated with (Nivolumab) anti-PD1, one was responsive to treatment, the other non-responsive. IgG4 staining was used to separate cells into anti-PD1 bound and unbound, the samples then underwent paired scRNA and scTCR sequencing on the 10x Genomics platform.

  Study EGAS00001005640

• Exome sequencing of 142 gastric cancer and matched normal from Japanese cohorts (UT)

  As a contribution to the International Cancer Genome Consortium, exome sequencing of 142 Japanese gastric cancer with various histological subtypes have been conducted. This study aims to identify unique and common driver genes and molecular subtypes in Japanese gastric cancer. Please refer ICGC website for detail: http://icgc.org/icgc/cgp/69/420/1012357

  Study EGAS00001002891

• Mutator phenotype and specific mutational signature explain an increased risk of hematological malignancies in patients with Xeroderma Pigmentosum

  In this study we report for the first time the unique collection of 6 leukemias and two sarcomas from XP-C. Comprehensive WGS-based mutational analysis provides genetic explanation for the increased incidence of leukemia in XP-C and describes an unique mutational process in internal tumors associated with NER deficiency.

  Study EGAS00001004511

• Exome sequencing of 102 gastric cancer and matched normal from Japanese cohorts (YCU)

  As a contribution to the International Cancer Genome Consortium, exome sequencing of 102 Japanese gastric cancer with various histological subtypes have been conducted. This study aims to identify unique and common driver genes and molecular subtypes in Japanese gastric cancer. Please refer ICGC website for detail: http://icgc.org/icgc/cgp/69/420/1012357

  Study EGAS00001002892

• An integrated molecular study of 20 hepatoblastoma pairs using whole genome sequencing and RNA sequencing

  Hepatoblastoma is an uncommon malignant liver cancer occurring in infants and children. The mutant background of hepatoblastoma has not been fully demonstrated. The aim of this study is to genomically depict the mutational landscape of hepatoblastoma through an integrative analysis of whole genome sequencing and RNA sequencing of 20 hepatoblastomas from Chinese individuals.

  Study EGAS00001002772

• Loss of RREB1 in pancreatic beta cells reduces cellular insulin content and affects endocrine cell gene expression

  Genome-wide studies have uncovered multiple independent signals at the RREB1 locus associated with altered type 2 diabetes risk and related glycemic traits. However, little is known about the function of the zinc finger transcription factor RREB1 in glucose homeostasis or how changes in its expression and/or function influences diabetes risk.

  Study EGAS00001006314

• Multi-region RNA-Seq data of 10 neuroblastoma cases

  To investigate intratumour heterogeneity and to better understand tumour evolution in neuroblastoma, we have performed a multi-region RNA sequencing on a total of 51 spatially separated tumor samples from 9 primary neuroblastomas (2 low-risk, 1 intermediate-risk and 6 high-risk) and 1 relapsed neuroblastoma. We also assessed the impact of chemotherapy on the clonal expansion by sequencing tumour regions from one medium risk and one high-risk tumour for which we had matched samples obtained at diagnosis and after chemotherapy.

  Dataset EGAD00001008133

• WGS for fibroblasts colonies

  This dataset contains WGS for fibroblasts colonies obtained from carriers and non-carriers of germline POLD1 L474P. Data for single-cell colonies obtained from immortalized fibroblasts are present for eight out of 16 family members (six carriers and two non-carriers). Sequences obtained for colonies after approximately 40 passages also present for six out of these eight colonies (four carriers and 2 non-carriers). Samples marked with "_F2" and "_F3" represent sequences of single cell-derived colonies and colonies after ~40 passages correspondingly.

  Dataset EGAD00001009283

• Embryonic tumour transmission in monozygotic twins

  We have a case of two siblings (twins) who were born with nodular blue rashes over their body. The first twin had a large periorbital subcutaneous mass which was diagnosed as infantile undifferentiated sarcoma. This baby was too systematically unwell for chemotherapy and died at 12 days of age. The second sibling received two cycles of emergency chemotherapy however died due to disease progression and secondary haemorrhage at 2 months of age. Post-mortem normal and tumour samples have been taken. In addition to placental tissue and parental germline DNA, the goal will be to investigate intra-uterine transfer of sarcoma and the phylogenetic relationship of tumours in both twins.

  Dataset EGAD00001015681

• scRNA-seq and scATAC-seq data of bone marrow

  17 scRNA-seq and 16 scATAC-seq datasets on bone marrows derived from 16 patients. The sequencing dataset consists of 5 samples without bone marrow infiltration, defined as controls (C1, C2, C3, C4, and C5) and 11 neuroblastoma infiltrated bone marrow samples from patients with MYCN amplification (M1, M2, M3, M4), ATRX mutations (A1, A2), and cases lacking either alteration (S1, S2, S3, S4, S5).

  Dataset EGAD00001008635

• Uncovering RNA Signatures of C9orf72-Linked ALS and Related Disorders

  Substantial clinical and pathological variability has been reported in patients carrying an expanded repeat in C9orf72, who are generally diagnosed with amyotrophic lateral sclerosis (ALS) and/or frontotemporal dementia (FTD). Emerging evidence suggests that C9orf72 expression, RNA foci, and dipeptide-repeat proteins contribute to C9orf72-related diseases; however, the majority of the clinicopathological variability remains unexplained. We hypothesize that RNA sequencing (RNA-Seq) might reveal individual genes or groups of highly correlated genes (modules) that could account for this variability, which may help to identify much-needed druggable targets and/or biomarkers. Our preliminary studies performed in the frontal cortex, where we compared C9orf72 expansion carriers to (disease) controls, demonstrated that the top differentially expressed gene was C9orf72 itself. We also noticed that differentially expressed genes were enriched for the endocytosis pathway, which is consistent with the reported function of the C9orf72 protein in vesicle trafficking. Furthermore, we detected a module enriched for vesicular pathways, and additionally, we discovered an association with survival after onset for several promising candidates involved in vesicular transport. To find new therapeutic targets and biomarkers, here we have completed RNA-Seq on an increased number of samples to examine another relevant region: the cerebellum. As such, we performed RNA-Seq on a well-characterized cohort of C9orf72 expansion carriers, patients without this expansion, and control subjects without neurological diseases. We used multivariable linear regression models for gene-level analysis, weighted correlation network analysis for module-level analysis, and leafcutter for splicing analysis. Using the cerebellar RNA-Seq data, we found a large number (>6,000) of differentially expressed genes, with a notable increase in expression of homeobox genes in C9orf72 expansion carriers, as well as many gene modules that were associated with C9orf72 expansion status. Additionally, using leafcutter, we detected over 1,000 differential splicing events and an increase in the number of cryptic splicing events in C9orf72 expansion carriers.

  Study phs003065

• National Institute of Neurological Disorders and Stroke (NINDS), Family Study of Essential Tremor (FASET), Identification of Susceptibility Genes for Essential Tremor

  The Familial Study of Essential Tremor (FASET) was designed to identify susceptibility genes for Essential Tremor. ET is among the most common neurological diseases with a prevalence (age > 40 years) estimated to be 4.0% and prevalence in advanced age (> 90 years) exceeding 20%. ET, often referred to as "familial tremor", is generally regarded as a highly genetic disorder with families, with affected members over multiple generations, and twin studies show high concordance among monozygotic twins. Probands (affected with ET) and relatives were enrolled in a family study of ET at Columbia University, New York between 2011 - 2014. The study was approved by the Institutional Review Board at Columbia University and written informed consent was obtained from all enrollees. The criteria for enrollment were: 1) the proband had early-onset ET with age at onset < 50 years, 2) the proband had a diagnosis of definite or probable ET, 3) in addition to the proband, there were at least two affected relatives in the family, 4) additional affected and unaffected family members were willing to participate in the study, and 5) the families contained more than two affected individuals in different generations. Blood samples were also collected for genetic research. For the genetic analyses, we excluded enrollees that we or others had diagnosed with Parkinson's disease (PD) or dystonia. The final sample includes 52 families (52 probands [affected with ET]) and 155 relatives). The number of affected individuals enrolled per family ranged from 3 - 7 (mean = 4.1). Genetic samples from FASET were analyzed with whole genome SNP genotyping (for linkage analyses) and whole exome sequencing. It is hoped that this resource will better help researchers to understand the genetic causes of ET and underlying disease pathogenesis.

  Study phs000966

• Bulk-RNA Sequencing of high-grade pancreatic and non-pancreatic Neuroendocrine Neoplasms

  Therapeutic decisions in oncology depend on a precise pathological classification of individual neoplasms. Recent years have seen an intensification of research activities aimed at the extraction of clinically relevant information from patient-derived 'omics' data based on Machine-Learning models. However, a comprehensive training of Machine-Learning models requires sufficiently large numbers of training samples, which are usually not available for rare cancer types. The problem is worsened when individual tissues segregate into different cancer subtypes, as their discrimination would require even more training samples. Methods: Here, we report on a new data-augmentation technique to support the training of Machine-Learning models on ‘omics’ data from pancreatic neuroendocrine neoplasms (panNEN). PanNENs display all properties described above: Only about 2-3% of all pancreatic neoplasms are neuroendocrine and they fall into different subtypes with distinctly different prognosis, which makes the precise classification of such samples both difficult and important for therapy decisions. The approach reconstructs a given transcriptome based on healthy pancreatic cell type signatures and creates a Machine-Learning model that integrates the observed reconstruction error and predicted cell type proportions as features. Results: A benchmark of the deconvolution model predictions with the ground-truth found that the model could efficiently predict the sample grading, disease-related patient survival time, and differentiate between different subtypes in four panNEN and one mixed panNEN and non-pancreatic NENs dataset. We compared the predictive performance of the deconvolution-trained model to that of a model trained directly on the transcriptomic data, under inclusion of the Ki-67 classification gold standard biomarker, and found the performances to be comparable. Conclusion: Our approach serves as a data-augmentation technique to facilitate the training of Machine Learning models for rare cancer types via utilization of data from healthy origin. Additionally, the deconvolution results were clinically interpretable and further research can render the deconvolution approach an effective complementary asset for the clinical classification of neoplasms.

  Study EGAS00001004861

• Best Practices for DACs

  Best Practices Data access committees (DACs) are institutional safeguards responsible for ensuring a balance between data protection and accessibility. However, there are no procedural standards that apply across DACs, which can lead to inconsistencies in their reviews and compromise their quality and effectiveness. Standardising DAC processes can foster trust and mutual recognition, paving the way for greater coordination, collaboration, and delegation between DACs and other oversight bodies to improve the efficiency of data access without sacrificing protection. To provide guidance, the following are suggestions for actions a DAC might take upon receiving a data access request: Aim to respond to all initial requests in less than 2 weeks. Failure to do so may result in follow-up emails from the EGA, journals, and ultimately dataset withdrawal. First, check that the data/EGAD number is consistent with your data submission. In other words, ensure that the requester has contacted the correct DAC. Verify that the user will be using the data within the terms of consent by asking them to sign up to the terms within the DAA. Ensure that data users who are granted access to the data comply with the terms of a Data Access Agreement (DAA) and to use the data only in approved ways. Look for an institutional email address for the requester. Search for evidence that the requester is "appropriately qualified/bona fide" for using the data, for example on PubMed, Research Gate, LinkedIn, etc. Confirm that the affiliated organisation is real and that the requester still works there. Inquire with the requester about who should have accounts created at the EGA under the terms of the agreement. If a negative decision is made, promptly communicate it to the requester and support it with the terms of the Data Access Policy that the requester has not met or cannot meet. Keep the information in the DAC up to date. If you leave your institution and are unable to manage data access requests on their behalf, you should add your replacement as a new contact in the DAC. Assist with data access requests for any further questions related to your data. The EGA can only check information that has been deposited in the repository. If the user has a specific question that the EGA cannot answer, we will redirect the user to the DAC. All the EGA studies and datasets referenced in a publication under your DAC must be publicly searchable on the EGA website before the paper is released. If possible, describe the permitted purposes for subsequent research projects, including associated limits and conditions, for all resources hosted in a repository using a common ontology, such as the GA4GH Data Use Ontology (DUO). It is considered best practice to try and release data only to those with an institutional email address. This gives reassurance to the EGA, research participants, and the general public that an appropriate individual is accessing and using the data. To prevent potential data breaches and ensure adherence to GDPR regulations, it is essential that the European Genome-Phenome Archive (EGA) is informed via the Helpdesk team of any changes to the Data Access Committee (DAC). This should be done in addition to any changes being made on the DAC portal. Data Controllers (as per the definition in the DPA) are also responsible for notifying the previous DAC of any modifications. Without proper notification, changes might not be automatically updated in our system, leading to the risk of incorrect permissions being applied and potential data access issues. Therefore, it is imperative that all Data Controllers follow this protocol to maintain data integrity and security.

  Documentation access/data-access-committee/best-practices

• RNA-seq of whole blood and PBMC samples from immunotherapy treated NSCLC patients

  This dataset contains 228 paired fastq files sequenced with Illumina Novaseq 6000, and the file with the sample and clinical data.

  Dataset EGAD50000000389

• H3Africa ACEGID Omni Array Phenotype

  Phenotype data for Lassa Fever cases and population controls from Nigeria and Sierra Leone associated with genotype data generated using Illumina Omni 2.5M and 5M.

  Dataset EGAD00001010922

• H3K27Ac ChIP-seq of 9 cHL cell lines

  The dataset contains 36 ChIP-seq data for H3K27Ac and their corresponging inputs for 9 cHL cell lines. Data are raw paired-end fasq files for each histone and input, and for each cell line.

  Dataset EGAD50000001272

• Whole-exome sequencing data from a head and neck cancer patient

  This dataset contains paired-end whole-exome sequencing data (2x50 bp) from the normal sample, three synchronous primary tumors and the recurrence of a head and neck cancer patient.

  Dataset EGAD00001006653

• Hi-C and promoter capture Hi-C data

  Hi-C and promoter capture Hi-C data for HT29 and LoVo. 2 replicates per cell line for the Hi-C. 3 replicates per cell line for the CHi-C.

  Dataset EGAD00001003257

• Whole exome-sequencing of pediatric and adult H3-K27M diffuse midline glioma

  H3-K27M mutant difffuse midline gliomas across different age groups and anatomical locations were profiled by WES.

  Study EGAS00001006431

• The temporal mutational and immune tumour microenvironment remodelling of HER2-negative primary breast cancers

  WES and clonality characterization of different timepoints in HER2-negative primary breast cancers receiving neoadjuvant eribulin therapy.

  Study EGAS00001004953

• Single cell whole genome sequencing of primary and metastatic samples with Direct Library Preparation (DLP+)

  Single cell whole genome sequencing of primary and metastatic samples with Direct Library Preparation (DLP+)

  Study EGAS00001007912

• The University of Hong Kong Gastric Cancer XClone Study Single Cell CNV Data

  Single cell encapsulation and DNA libraries were prepared by Chromium™ Single Cell DNA Reagent Kits and Chromium™ Single Cell C and D Chip Kits.

  Dataset EGAD00001015383

• Genome-wide array data Tunisia and Morocco

  This dataset contains genome-wide array data from Tunisian and Moroccan individuals. Tunisian individuals were sampled in the city of Tunis (n = 64), and Moroccan individuals in different urban areas in the country (n = 45).

  Dataset EGAD00001009071

• Germline BAMs from patients with both uveal and cutaneous melanoma

  Germline BAMs from blood/saliva samples from patients diagnosed with both uveal and cutaneous patients. Reads have been aligned, deduplicated and recalibrated.

  Dataset EGAD00001011676

• WES raw data for study "Molecular and functional profiling of plasmablastic lymphoma"

  1 cell line and 123 patient samples including 38 normal (22 paired normal and 16 unpaired), 85 tumor-initial, FASTQ file types, Agilent SureSelect Human All Exon V6 Kit

  Dataset EGAD00001006400

• National Cancer Institute (NCI) Genome Wide Association Study (GWAS) of Lung Cancer in Never Smokers

  A genomewide study of lung cancer in never smokers Abstract and specific aims In the United States, lung cancer incidence and mortality rates have been steadily declining over the past decade, following decline in the prevalence of tobacco smoking. However, lung cancer remains the leading cause of cancer death, killing more patients than breast, colon, and prostate cancers combined. Although tobacco smoke is the predominant risk factor for development of lung cancer, some patients develop the disease without a history of tobacco smoking. About 10 - 15% of all lung cancers occur in lilfetime never smokers. This figure will increase as the proportion of never smokers increases in the population. Even at present rates, lung cancer in never smokers, if considered a separate disease, is 6th to 8th top cause of cancer death. The growing number of never smokers in the USA and other countries emphasizes the importance of understanding the epidemiology and biology underlying lung cancer in this group. Genetic polymorphisms associated with the risk of lung cancer in never smokers are expected to overlap with those associated with the risk of lung cancer in ever smokers only partially. Epidemiological, molecular and clinical data suggest that molecular mechanisms of LC may differ in smokers and non-smokers, implying that lung cancer in never smokers is a different disease compared to the lung cancer in smokers. One can expect that there should be stronger genetic component in the control lung cancer in never smokers because effects of the genetic factors in never smokers are unmasked by the lack of tobacco smoke exposure. The genetic epidemiology of lung cancer in never smokers has not been well explored, largely because of difficulties in accruing the needed sample size for association studies. We propose a multicenter (total 14 sites from the US and Europe) genomewide association study of lung cancer in never smokers with the following specific aims: Aim 1: To identify candidate SNPs influencing risk for lung cancer in never smokers using Discovery sample. In the Discovery phase we will genotype 1256 Caucasian cases and 1365 age- and gender-matched never smoker controls using the Illumina Human660W-Quad platform. In addition, we will include in the analysis 284 cases and 175 matched controls already genotyped on the 610Quad platform. In this phase we will only include the study sites that have collected blood specimens (MDACC, Mayo Clinic, Karmanos Cancer Institute, The University of Liverpool Cancer research Centre, Institute of Cancer Research in Sutton, and Lunenfeld Research Institute in Toronto, Canada). All the samples will be sent to the independent lab for genotyping, to reduce site-specific technical artifacts. The final sample will consist of 1540 cases and 1540 controls matched by study site. Aim 2: To perform the second phase (validation) analysis of significant SNPs identified in aim 1 using an independent set of cases and controls. SNPs associated with risk at the significance level of 0.01 or below in the discovery set will be included in the replication phase. The proposed threshold guarantees an adequate power to retain SNPs with the typical effect size of 1.3. We plan to carry 6000-7000 SNPs for validation. The independent replication set will include 800 cases and 800 controls, mostly from sites that collected tissue (Mayo Clinic, Karmanos Cancer Institute, UT Southwestern) or buccal specimens (UCLA), but also blood samples (Imperial College London, University of Pennsylvana, German Cancer Research Center, Heidelberg, National Research Center for Environment and Health, Neuherberg, Carmel Medical Center, Haifa). We will then perform a joint analysis to test the significance of the SNPs identified in the first stage using a stringent critical p-value of 10-7. There will be 2340 cases and 2340 controls in the joint set. Based on our experience with GWAS in smokers and assuming that genetic component in lung cancer risk in never smokers can be higher than genetic component in smokers, we expect to identify about 5-10 candidate regions associated with lung cancer risk in never smokers. Aim 3: To identify and explore pathways associated with the risk of lung cancer in never smokers. Results of the number of studies on the molecular mechanisms and drug response suggest that lung cancer in never smokers is a different disease and different pathways will be associated with lung cancer risk in non-smokers and smokers. To identify pathways and molecular functions associated with lung cancer risk in never smokers we will apply Ingenuity and DAVID bioinformatics tools. We will use at least 300 top candidate genes identified in joint and discovery analysis. The reason why we select rather large number of candidate genes for functional annotation is two-fold: 1. Both algorithms are looking for enrichment of pathways and function by most significant genes and they produce statistically robust results only when number of genes is relatively high. 2. Despite the fact that this study will be largest possible for never smokers we still are underpowered to detect SNPs with relatively small effect size. But though those SNPs will not reach genome wide level of significance they will tend to be on the top of the list. In other words genes from the gray zone (significant on individual level and non-significant for genome wide level) are expected to be enriched by true discoveries. True discoveries are likely to be associated with limited number of pathways / functions while false positives are expected to be uniformly distributed across functions and pathways. Therefore significant clustering of the gene to a given function will suggest that that those genes are true discoveries. This is the first GWAS aiming at identifying the genetic control of susceptibility to lung cancer in Caucasian never smokers. We will combine the available resources from the multiple sites to achieve the sample size sufficient for this study. The study will identify genetic architecture of the predisposition to the lung cancer in never smokers.

  Study phs000634

• Resuscitation Outcomes Consortium (ROC) Prehospital Resuscitation Using an Impedance Valve and Early Versus Delayed Analysis (PRIMED) (ROC-PRIMED-BioLINCC)

  Accessing Data: Please refer to “Authorized Access” below regarding accessing data through the BioData Catalyst ecosystem. The data from this accession is not available for download through dbGaP.Objective: The purpose of this study was to examine two different treatments during a cardiac arrest that occurs outside of the hospital and whether either or both treatments would increase the number of people who lived to hospital discharge with satisfactory functional status. The first treatment involved using a device called the Impedance Threshold Device (ITD). The other treatment involved the amount of CPR given before the emergency medical services (EMS) providers first looked at the heart rhythm to determine if a shock is needed.Background: Out-of-hospital cardiac arrest is a common and lethal problem with a low survival rate, leading to an estimated 330,000 deaths each year in the United States and Canada. The traditional approach to out-of-hospital cardiac arrest has been to emphasize early analysis of cardiac rhythm, with delivery of defibrillatory shocks, if indicated, as quickly as possible. It has been suggested, however, that many participants may benefit from a period of CPR before the first analysis of rhythm.The impedance threshold device (ITD) is designed to enhance venous return and cardiac output during CPR by increasing the degree of negative intrathoracic pressure. Previous studies have suggested that the use of an ITD during CPR may improve survival rates after cardiac arrest. This effect is achieved by preventing the passive inflow of air into the chest during chest recoil between chest compressions without impeding active ventilation. The ITD has been found to improve hemodynamics, the perfusion of vital organs, and neurologically intact survival in studies in animals. The results of small, short-term clinical trials have suggested that the ITD can increase systolic blood pressure during resuscitation and improve short-term survival rates. Participants: In the ITD study, 4,345 participants were assigned to sham ITD and 4,373 to active ITD, while in the early versus later rhythm analysis, 5,290 participants were assigned to early cardiac rhythm analysis, and 4,643 were assigned to later cardiac rhythm analysis. This study qualified for exception from informed consent required for emergency research.Design: Most participants were enrolled simultaneously in both the early analysis versus later analysis component and the active ITD versus sham ITD component of the trial.The use of an active ITD was compared with that of a sham ITD in participants at 10 ROC sites in the United States and Canada. Participants, investigators, study coordinators, and all care providers were unaware of the treatment assignments. EMS personnel were trained in ITD function, proper use of the ITD, and all aspects of protocol implementation, with an emphasis on the optimal performance of CPR according to local guidelines. The first EMS responders to arrive at the scene of the arrest who were equipped with a randomly assigned ITD (active or sham) attached the device between the ventilation bag and face mask or between the bag and an advanced airway. Responders were encouraged to implement use of the device within 5 minutes after their arrival or as soon as clinically possible. Each of the 10 participating ROC centers was also divided into approximately 20 clusters. All episodes of cardiac arrest in a cluster were randomly assigned to one CPR strategy; after a set period of time, ranging from 3 to 12 months, all episodes in that cluster were then assigned to the other strategy. Participants in the early-analysis group were assigned to receive 30 to 60 seconds of chest compressions and ventilations (sufficient time to place defibrillator electrodes) before electrocardiographic (ECG) analysis, and those in the late-analysis group were assigned to receive 3 minutes of chest compressions and ventilations before ECG analysis. The start and stop times for CPR were recorded by the responders, and the information was supplemented by the recording of defibrillator time. Conclusions: All 10 sites halted enrollment in November 2009 when the data and safety monitoring board recommended termination because interim analysis showed that the findings were not likely to change with continuation of the study. Neither use of the ITD nor the amount of CPR given before cardiac rhythm analysis significantly improved survival with satisfactory function (i.e., a score of ≤3 on the modified Rankin scale) among participants with out-of-hospital cardiac arrest receiving standard CPR. There were also no significant differences in the secondary outcomes, including rates of return of spontaneous circulation on arrival at the emergency department, survival to hospital admission, and survival to hospital discharge.

  Study phs003825

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

  Study EGAS00001004218

• Obesity and hyperinsulinemia drive adipocytes to activate a cell cycle program and senesce

  Study EGAS00001005770