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• Human Microbiome Project Demonstration Study of Cutaneous Microbiome in Psoriasis

  Psoriasis, a highly prevalent disease of humans of unknown cause, is a chronic inflammatory disorder primarily involving skin, with distinctive clinical characteristics. With the newly developed tools that facilitate microbiome research, it now is possible to assess whether the cutaneous microbiome plays a role in the pathogenesis of this disorder. Preliminary data from our studies suggest that the cutaneous microbiome in psoriasis is complex and possibly different from normal. To deal with this complexity, we propose to examine the cutaneous microbiome in relation to psoriasis with explorations at several taxonomic and informatic levels. Our overall objective is to examine how changes in the normal cutaneous microbiome contribute to the pathogenesis of psoriasis. Since causality is complex and often difficult to prove, and beyond the scope of this RFP, our overall hypothesis is that there are alterations in the cutaneous microbiome in areas of skin affected by psoriasis in comparison with the range observed in clinically unaffected areas, or in healthy persons. We also hypothesize that the characteristics of the microbiome may affect clinical responses to the immunomodulatory agents used to treat psoriasis. An alternative hypothesis is that effective treatment of psoriasis with systemic immunomodulatory agents will not substantially affect the disordered microbial ecosystem. Such observations would provide evidence for the roles of the microbiota in this disorder. Since an important consideration in microbiome research is the optimal level (e.g. phylum, genus, species, strain, gene) at which to examine a scientific question, and we are not yet certain what are the optimal levels for psoriasis, this also will be examined. Our studies of psoriasis should allow development of both approaches and tools that will have general utility for Microbiome research. To test our hypothesis, we propose the following specific aims: 1) To understand the cutaneous microbiome species composition overlaying psoriatic lesions; 2)To investigate differences in metagenome content for psoriatic lesions compared to normal skin; 3) To identify differences in the transcriptional profiles of the microbiome and the host between normal skin and psoriatic lesions using high-throughput sequencing; and 4) To estimate the effects of systemic immunomodulatory therapy for psoriasis on microbiome composition. In total, these studies should help us understand the role of the microbiome in psoriasis pathogenesis. We sought to characterize and compare the cutaneous microbiota of psoriatic lesions (lesion), unaffected contralateral skin from psoriatic patients (normal), and similar skin loci in matched healthy controls (control) in order to discern patterns that govern skin colonization and their relationship to clinical diagnosis. Using high-throughput 16S rRNA sequencing, we assayed the cutaneous bacterial communities of 51 matched triplets and characterized these samples using community data analysis techniques.

  Study phs000251

• National Epidemiologic Survey on Alcohol and Related Conditions-III (NESARC-III)

  The National Epidemiologic Survey on Alcohol and Related Conditions-III (NESARC-III) is a nationally representative cross-sectional survey of the U.S. general population, which was sponsored by the National Institute on Alcohol Abuse and Alcoholism (NIAAA) and conducted in 2012-2013. The NESARC-III's target population was the U.S. noninstitutionalized civilian population, 18 years and older, including residents of selected group quarters (e.g., group homes, workers' dormitories). Multistage probability sampling was used to randomly select respondents. Primary sampling units (PSUs) were individual counties or groups of contiguous counties, secondary sampling units (SSU) comprised groups of Census-defined blocks, and tertiary sampling units were households within SSUs. Finally, eligible adults within sampled households were randomly selected. Hispanics, Blacks, and Asians were oversampled and resulted in a total of 36,309 respondents. All respondents provided informed consent for survey participation. Data were adjusted for oversampling and screener - and person-level nonresponse, then weighted through post-stratification to represent the US civilian population based on the 2012 American Community Survey. These weighting adjustments were found to compensate adequately for nonresponse. Interviewer field methods involved initial structured home study, in-person training, ongoing supervision, and random respondent callbacks to verify data. The NESARC-III collected information on alcohol and drug consumption, alcohol use disorder, other substance use disorders (e.g., nicotine, cannabis and opioid), and associated physical and psychiatric adverse consequences. In addition to a full array of sociodemographic characteristics such as race/ethnicity, gender, age, risk and environmental factors including adverse childhood experiences (e.g., sexual, physical abuse and neglect) and family history for alcohol, drug use disorders and other psychiatric disorders (e.g., mood, anxiety, personality disorders and PTSD) were included (phenotypic variables=4,320). As part of the NESARC-III, 22,848 informative samples were genotyped on Affymetrix Axiom Exome Array consisting of 319,283 SNPs and 103,404 custom-selected SNPs Array (refer to the SNP annotation file). The latter array was selected based on the addiction associated genes, the results of 5 GWAS of alcohol and other psychiatric disorders, and animal models with addiction phenotypes. After filtering out poor quality SNPs using the standard Affymetrix pipeline there are 295,218 SNPs in the NESARC-III genetic data. The 22,848 subjects in this study were all deeply and consistently phenotyped via structured diagnostic interview. Controls group can be selected for specific disorders from a pool of all samples. Here are numbers of cases for major DSM-5 mental disorders in NESARC-III genetic data: Alcohol use disorder (7,075); Nicotine use disorder (6,641); Drug use disorder (2,570); Major depressive disorder (5,214); Persistent depression(1,429); Bipolar I (543); Anxiety disorders (4,226); PTSD (1,674); Personality disorders (4,014); Eating Disorders (457).

  Study phs001590

• A Randomized, Double-Blind, Crossover Study of Sodium Phenylbutyrate (Buphenyl) and Low-Dose Arginine (100 mg/kg/day) Compared to High-Dose Arginine (500 mg/kg/day) Alone on Liver Function, Ureagenesis and Subsequent Nitric Oxide Production in Patients with Argininosuccinic Aciduria (ASA)

  Individuals with Urea Cycle Disorders (UCD) cannot remove ammonia, a waste product, from the blood. At present there is little information on the use of sodium phenylbutyrate (Buphenyl™) in children with argininosuccinic aciduria (ASA). It is hoped that this drug may help lower ammonia and argininosuccinic acid levels in patients with ASA. Through this study we hope to learn whether the use of sodium phenylbutyrate (Buphenyl™) in patients with ASA, in addition to diet and arginine therapy, will decrease liver damage and the number of periods during which ammonia levels are high. The primary study objective is to determine if the treatment of ASA patients with sodium phenylbutyrate (Buphenyl™) in conjunction with lowered doses of arginine improves liver function as measured by short-term assessment of synthetic activity and the use of stable isotope tracers to assess ureagenesis and nitric oxide production. Twelve patients with ASA will be studied using a randomized, cross-over design. Medical records will be reviewed to confirm the diagnosis prior to enrollment. Patients will be on the each arm of the study for one week each preceded by a three day washout period. Patients will come to the Baylor College of Medicine General Clinical Research Center in Texas Children's Hospital for an inpatient hospitalization. This hospitalization is for diet control, clinical evaluation, and stable isotope infusions for measurement of in vivo rates of ureagenesis and nitric oxide production. During the washout periods Buphenyl™ or other alternative route medications, e.g., benzoate, will be discontinued and arginine will be administered at the standard therapeutic dose of 500 mg/kg/day or 10 grams/m2. Following randomization, subjects will be maintained on either high-dose arginine (500 mg/kg/day or 10 grams/m2) alone, or the alternative of low-dose arginine (100 mg/kg/d or 2 grams/m2) along with sodium phenylbutyrate (500 mg/kg/day or 10 grams/m2). For the second week they will be crossed over to the other arm of the study preceded by another three day washout. Previous medications and dietary protein intake (0.6 g/kg/day or current metabolic diet) will be continued during both arms of the study. The two arms may be performed as separate ten-day admissions. The decision to design the study with two arms, high-dose arginine and low-dose arginine/Buphenyl™, was reached after weighing several considerations. First, the current accepted practice for treatment of ASA is high-dose arginine. Based on metabolic flux studies, we have quantified the effects of this dose of arginine as compared to standard doses of Buphenyl™/phenylacetate on ureagenesis. Since the study is not designed or intended to address the independent effects of Buphenyl™ as compared to arginine alone, Buphenyl™ was added for safety reasons to accommodate loss of clearance of nitrogen by decreasing the arginine dose. Moreover, based on our experience with recruiting for previous versions of this study, most ASA patients with liver dysfunction are on an alternative route ammonia scavenger medication in addition to arginine. We found that this has in fact become an accepted practice. Hence, when considering study design from both a safety and recruitment perspective, it was most reasonable to design the study to investigate specifically the hypothesis that the production and presence of argininosuccinic acid leads to liver dysfunction. Since both low-dose arginine with Buphenyl™ and high-dose arginine alone lead to a decreased production of argininosuccinic acid, and both are currently accepted therapies in ASA and UCDs in general, the need to address their effects distinctly is not being investigated at this time. Sodium phenylbutyrate dosage will be 500 mg/kg/day in patients weighing less than 20kg and 10 g/m2/day in larger patients. Daily dosage will be given in equally divided doses 4 times per day. In order to ensure that the study remains double-blind to investigators, study staff and subjects, the Investigational Pharmacy Service at Texas Children's Hospital will dispense both the Buphenyl™ and arginine in powder form which is compounded into capsules or will be mixed with syrpalta (up to 5 grams will dissolve in 10cc liquid) and administered orally or through nasogastric or gastrostomy tube. No nasogastric tube should be placed or gastrostomy performed solely for the purpose of inclusion in this study. Because the reported adverse effects of sodium phenylbutyrate include gastritis, participants will be started on a standard dose of ranitidine (Zantac™), or comparable drug, during both arms of the study.

  Study phs001305

• Cancer Discovery Hub (CDH), National Cancer Center Singapore

  This is a DAC for data deposited into EGA generated by Cancer Discover Hub, NCCS. The use of datasets in this portal is solely for research and academic use only, uses other than the have to be approved by the relevant DAC members.

  Dac EGAC50000000039

• DAC for study CMMRD–associated high-grade glioma

  This Data Access Committee (DAC) is responsible for de-identified, summarized somatic variant call data derived from paired tumor–blood Whole-exome sequencing of human samples in a glioma research study. Access requests are approved without additional restrictions and are granted solely for health-related research purposes.

  Dac EGAC50000000855

• Long-read whole genome sequencing as a tool for variant detection in inherited retinal dystrophies

  WGS sequencing using nanopore long reads sequencing. These data is used for the diagnosis of patients with inherited retinal dystrophies.

  Study EGAS50000000846

• WES Analysis of CRC and UC samples from a cohort of Lynch Syndrome carriers

  Whole-exome sequencing (WES) was performed on 73 tumors, including 58 colorectal cancers (CRC) and 15 urothelial cancers (UC), derived from 58 individuals with Lynch syndrome (LS). The cohort comprised both primary and metachronous tumors.

  Dataset EGAD50000001915

• Bulk RNAseq of FFPE and FF tissues at baseline and on-treatment

  Bulk transcriptomics for investigating transcriptomic biomarkers related to response at baseline and exploring treatment dynamics in transcriptomic signatures to gain a better understanding of the effects of ICB on the urothelial cancer tumor microenvironment (TME).

  Dataset EGAD50000002253

• Single-cell multidimensional profiling of tumor cell heterogeneity in supratentorial ependymomas

  55 Supratentorial Ependymomas patient samples were sequenced scRNA-sequencing using Smart-Seq2 and 10x protocol (51 samples) and 10x Genomics protocol (4 samples) on a NextSeq 550 sequencer (Illumina).

  Dataset EGAD50000002186

• mFAST-SeqS

  mFAST‑SeqS, or modified Fast Aneuploidy Screening Test‑Sequencing System, is a streamlined and cost-effective approach to estimate the fraction of ctDNA in blood samples by detecting genome-wide aneuploidy in cfDNA

  Dataset EGAD50000001670

• Single-cell sequencing of PBMC & CSF in neuroinflammatory disorders

  Single-cell sequencing and genotyping for Cambridge samples analyzed as part of a project evaluating single-cell gene expression & lymphocyte receptor sequences in CSF and PBMC of MS and other neuroinflammatory disorders.

  Dataset EGAD50000001023

• DupiAERD

  Dataset contains bulk RNA sequencing reads from 44 NERD patients under dupilumab therapy before and after aspirin provocation at baseline and after 24 weeks of treatment. Dataset is a multiplexed .bam file containing all sequencing reads with tagged identifiers.

  Dataset EGAD50000000565

• Raw ONT R9 data: Rapid brain tumor classification from sparse epigenomic data

  This dataset contains 75 Nanopore sequencing experiments using a MinION sequencer and R9 flow cells from 51 patient biopsies. Gzipped tar files containing all fast5 files per sample are provided.

  Dataset EGAD50000000832

• Bulk transcriptomic analyses of monocyte-derived dendritic cells treated with CES1i

  The data published here contains bulk RNA-sequencing (RNAseq) data as obtainedfrom monocyte-derived dendritic cells in treated with/without LPS and with/without CESi (WWL113). Sequencing was performed in a paired-ended fashion on the NovaSeq6000.

  Dataset EGAD50000000344

• A neoadjuvant, phase II trial demonstrates efficacy and tolerability of Talimogene laherparepvec in cutaneous basal cell carcinoma (NeoBCC trial)

  This dataset is related to the NeoBCC trial and includes 12 human tissue samples

  Dataset EGAD50000000371

• APCIM_Nanostring_FAP

  Expression of immune related genes in 12 familial adenomatous polyposis patients. Expression assessed by analyzing whole blood-derived RNA samples using a Nanostring nCounter Immunology V2 panel (579 genes)

  Dataset EGAD00010002553

• APCIM_Nanostring_HD

  Expression of immune related genes in 12 healthy donors. Expression assessed by analyzing whole blood-derived RNA samples using a Nanostring nCounter Immunology V2 panel (579 genes)

  Dataset EGAD00010002554

• Genotyping_data_total

  Genotyping data for ACE2 (rs2285666), MX1 (rs469390) and TMPRSS2 (rs2070788) variants. Patients are classified as mild (n=34) and severe (n=32). DNA genotyping was performed using the TaqMan® Genotyping Master Mix (Applied Biosystems). Allelic discrimination assays were performed on a 7900HT Fast Real-Time PCR System (Applied Biosystems).

  Dataset EGAD00010002445

• TB-DAR Genotyping Study

  Active TB patients (sputum smear-positive and GeneXpert-positive) recruited at the Temeke District Hospital in Dar es Salaam, Tanzania, as part of a prospective study that ran between November 2013 and June 2022.

  Dataset EGAD00010002507

• Whole Exome Sequencing of healthy Spanish individuals - VCF file

  The need for a detailed catalogue of local variability for the study of rare diseases within the context of the Medical Genome Project motivated the whole exome sequencing of 267 unrelated individuals, representative of the healthy Spanish population.

  Dataset EGAD00001003101

• CLL targeted exome sequencing (2018-03-14)

  Aim to characterise cancer gene landscape in CLL, particularly in cases with mutated POT1 gene. Treatment-naive CLL cases will be interrogated by targeted exome sequencing using a cancer gene panel. . This dataset contains all the data available for this study on 2018-03-14.

  Dataset EGAD00001004037

• Primary plasma cell leukemia genomic abnormalities

  Primary plasma cell leukemia (pPCL) samples were sequenced using the Nimblegen MedExome Plus hybridization capture to detect translocations, copy number changes, and mutations in 20 pPCL samples and patient matched controls. Sequencing was performed on a NextSeq500 using 75 bp paired end reads.

  Dataset EGAD00001004323

• Kidney tumour_DNA (2018-09-19)

  This is a bulk DNA and RNA sequencing study of human renal tumours . This dataset contains all the data available for this study on 2018-09-19.

  Dataset EGAD00001004346

• Breast cancer sequential sampling study

  This study aims to whole genome sequence DNA derived from breast cancer patients who received neo-adjuvany chemotherapy. All patients had multiple biopsies performed before chemotherapy. Patients who had residual disease after the course of treatment underwent a further biopsy. We aim to characterise the mutations involved.

  Dataset EGAD00001000387

• Neoadjuvant Breast Cancer Validations

  This study aims to re-sequence findings from whole genome studies using a bespoke pulldown method to validate mutations in those genomes sequenced.

  Dataset EGAD00001000663

• Deep-Seq: Resistance to anti-EGFR therapy in colorectal cancer

  In this study we performed ultra deep sequencing of genes associated with anti-EGFR resistance, such as KRAS, BRAF, PIK3CA, and EGFR in 17 plasma-DNA samples from a total of 10 patients treated with anti-EGFR therapy.

  Dataset EGAD00001000688

• CGP CORE CELL LINES - RNA-seq

  Genomic characterisation of a large series of cancer cell lines.

  Dataset EGAD00001001357

• IBDCA_Edinburgh

  In this experiment we have sequenced tumour normal pairs from patients presenting with CRC who have a prior history of inflammatory bowel disease. The idea is to identify driver mutations, new genes and novel pathways associated with the development of these malignancies.

  Dataset EGAD00001001330

• Genetic factors underlying premature MI in Greek families without vessel disease

  The study will analyse by exome sequencing 8 Greek family members with an excess of potentially damaging mutations relating to premature MI and no vessel disease, to identify genetic factors underlying this condition. This is a follow on from project GPMI-NVD

  Dataset EGAD00001002178

• Bulk mRNA sequencing of GBM cell lines

  We expressed PDGFRAmut, wild-type PDGFRA and a GFP control from lentivirus, in two primary GBM patient-derived cell lines that we had cultured as monolayers.

  Dataset EGAD00001002269

• Whole-exome sequencing of breast cancer metastasis and corresponding blood samples

  Whole-exome sequencing (WES) of 216 breast cancer metastasis-normal pairs from patients who underwent a biopsy in the context of the SAFIR01, SAFIR02, SHIVA or MOSCATO prospective trials (France).

  Dataset EGAD00001002747

• Targeted deep sequencing

  T200 caner panel sequencing on primary and metastatic sites from highly clinically annotated HGSC samples. Samples were obtained pre-treatment based on a laparoscopic triage algorithm from patients who underwent R0 tumor debulking, or received neoadjuvant chemotherapy (NACT) with excellent (ER) or poor response (PR).

  Dataset EGAD00001005239

• Sporadic and endemic Burkitt lymphoma have frequent FOXO1 mutations but distinct hotspots in the AKT recognition motif

  Sample set of 74 whole-exome sequencing samples from sporadic Burkitt lymphoma patients from the UK. 33 of these samples have matched constitutional data, giving a total number of 107 samples

  Dataset EGAD00001005105

• Whole exome sequencing of 3 primary Plasma Cell Leukemia samples

  Primary plasma cell leukemia (pPCL) samples were sequenced using the Nimblegen MedExome Plus hybridization capture to detect translocations, copy number changes, and mutations in 3 pPCL samples and patient matched controls. Sequencing was performed on a NextSeq500 using 75 bp paired end reads.

  Dataset EGAD00001005306

• ctDNA mutation analysis using the SiMSen-seq approach

  Mutation analysis in plasma samples with low ctDNA levels using a molecular barcoding technology, i.e. the single target approach SiMSen-seq (Simple, multiplexed, PCR-based barcoding of DNA for sensitive mutation detection using sequencing).

  Dataset EGAD00001006104

• TCR sequencing of head and neck cancers

  This data contains the TCR-beta sequences of 10 head and neck squamous carcinomas and 19 nasopharyngeal carcinomas. The library preparation method is a customised targeted amplification of the VDJ regions and is sequenced on the Illumina Miseq.

  Dataset EGAD00001007917

• Single-cell paired sequences from intraepithalial CD8+ αβ T-cells from celiac disease patients and controls

  Paired T-cell receptor sequences sequenced from single cells, from intraepithalial CD8+ αβ T-cells. Sequences are from from untreated and treated (on a gluten-free diet) celiac disease patients and controls.

  Dataset EGAD00001006900

• RNASeq files for Mullighan TXVI dataset

  RNASeq files for paper titled "Prognostic and therapeutic significance of leukemia subtypes and minimal residual disease measurements in pediatric acute lymphoblastic leukemia treated with contemporary risk-directed trial: a cohort study"

  Dataset EGAD00001006609

• WGBS data for EGAS00001004660

  WGBS data for EGAS00001004660, "Aggressive PDACs show hypomethylation of repetitive elements and the execution of an intrinsic IFN program linked to a ductal cell-of-origin"

  Dataset EGAD00001006538

• RNA data for EGAS00001004660

  RNA data for EGAS00001004660, "Aggressive PDACs show hypomethylation of repetitive elements and the execution of an intrinsic IFN program linked to a ductal cell-of-origin"

  Dataset EGAD00001006539

• COVID-19 Postmortem Lung snRNA-seq

  A deeper understanding of the pathological mechanisms of SARS-CoV-2 infection is required to combat COVID-19. Through this dataset, we analyze postmortem lung cells from patients that are infected/uninfected with SARS-CoV-2 with snRNA-seq.

  Dataset EGAD00001006584

• TransNEO neoadjuvant breast cancer study

  Whole exome, shallow whole genome, and RNA-sequencing data from a cohort of 168 women with breast cancer receiving neoadjuvant chemotherapy.

  Dataset EGAD00001008269

• In Utero MPN Twin WGS Data

  The dataset contains sequencing data generated for the publication 'In utero origin of myelofibrosis presenting in adult monozygotic twins after a prolonged disease latency.

  Dataset EGAD00001008319

• Gene expression profile of mesothelial cells from peritoneal adhesion biopsies

  RNA-sequencing analysis was carried out on mesothelial cells isolated from peritoneal adhesion biopsies and compared to control human peritoneal mesothelial cells to identify a mesothelial-to-mesenchymal transition (MMT)-related gene signature in patients.

  Dataset EGAD00001008324

• Clinical data

  Clinical data from GO30140 group A and group F and IMBrave150 biomarker populations including gender, confirmed RECIST response by independent review forum (IRF), overall survival (OS), progression survival by IRF, treatment group and treatment

  Dataset EGAD00001008130

• PacBio HiFi sequencing of telobait-captured DNA from 48 patients

  PacBio HiFi sequencing was performed on 48 barcoded patients' genomic DNA after a telobait-capture protocol to enrich for telomeric regions. The sequencing reads of each patient were de-multiplexed and presented as patient-specific PacBio CCS BAM files.

  Dataset EGAD00001008626

• 17 skin and oral epithelial bulk samples from 2 donors

  Aligned BAM files with removed duplicate reads of targeted sequencing data (exomes of a panel of 153 genes) from 12 skin and 5 oral epithelial bulk samples from 2 donors. Sequences generated by the BGI DNB-SEQ platform.

  Dataset EGAD00001008956

• scATAC-seq of first and second trimester human gonads - HUGODECA dataset

  Comprehensive map of first- and second-trimester gonadal development in humans using a combination of single-cell and spatial transcriptomics, chromatin accessibility assays, and imaging. ArrayExpress Accession: E-MTAB-10570

  Dataset EGAD00001009387

• Variants from germline WES data of pediatric cancer patients

  This dataset contains germline variants (in .vcf format) from six pediatric cancer patients (sample IDs D1 - D6). WES data of the children and their parents was mapped to hg38. A consensus of four variant callers was used to obtain germline variants of the children.

  Dataset EGAD00001009678

• Neuroblastoma deep-sequencing dataset part2

  Dataset including paired tumor-normal whole-genome deep-sequenced samples from 18 neuroblastoma patients (part 2 of a total of 36 patients).

  Dataset EGAD00001010063