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• Identification_of_genes_involved_in_congenital_disorders_of_glycosylation_and_3_methylglutaconic_aciduria

  Identification of genes involved in congenital disorders of glycosylation and 3-methylglutaconic aciduria. There are more than 100 genes known for congenital disorders of glycosylation and new disorders are discovered each year. WE included patients with a so far unsolved glycosylation disease. The diagnostic group 3-methyglutaconic aciduria is a heterogenous group of disorders mostly caused by abnormal phospholipid synthesis or in association with mitochondrial dysfunction. We included patients with a so far unsolved disease and 3-methylglutaconic aciduria. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001002064

• Lebanon_HighCov_seq

  We propose to investigate the genomics of a Lebanese sample. we plan (1) genotyping (2.5M) of 120 Lebanese individuals, choosing this platform to allow comparison with the 1000 Genomes and African Genome Variation project populations, (2) 8x sequencing of 100 individuals to provide unbiased population-level sequence information including allele frequencies, and (3) 30x sequencing of four individuals to allow inferences such as from PSMC/MSMC to be obtained. The current form is for the high-coverage sequencing. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001002085

• South Asia Rheumatic Heart Disease Genetics Network

  Rheumatic heart disease (RHD) is a major cause of cardiovascular death and disability amongst young adults. Building on a sample collection established for and genotyped in several earlier successful candidate gene studies, this case-control study investigated host genetic susceptibility to RHD using a genome-wide approach. The current dataset comprises over 850 individuals recruited in Uttar Pradesh, India, including cases of RHD based on echocardiographic diagnosis and controls recruited on the basis of normal echocardiograms. For this analysis all available samples were genotyped using the Illumina HumanCore-24 BeadChip platform. Efforts are now underway to establish new sample collections in other areas of India as well as Pakistan and later other neighbouring countries.

  Study EGAS00001003565

• Multi-layered molecular characterization defines prognostic subtypes of lung adenocarcinoma in Asian never-smokers

  Multi-layered genomic studies such as the TCGA project have greatly advanced our understanding on molecular pathogenesis of lung cancer. For Asian nonsmoker patients, however, majority of studies have been limited to mutational analyses, emphasizing ethnic differences in driver mutations (e.g. more frequent EGFR mutations and ALK fusions). In essence, a comprehensive multi-layered characterization that could lead to molecular etiology and patient stratification scheme to be translated into clinical applications for this patient group is still missing. Here we report molecular profiling of tumor and matched normal tissues from 114 non-small-cell lung adenocarcinoma patients using whole exome sequencing, transcriptome sequencing, and array comparative genomic hybridization (CGH).

  Study EGAS00001003705

• Splicing signature analysis of RNU2-2 samples

  Dominant pathogenic variants in the snRNA RNU2-2 were recently reported as a cause of neurodevelopmental disorders. In our study we identified additional individuals with dominant variants (n.4G>A and n.35A>G) and we also identified biallelic variants as a novel frequent cause of neurodevelopmental disorder. We obtained blood samples and performed short-term lymhocytes cultures for 19 cases (5 n.4; 5 n.35; 9 biallelic). We generated exome-capture RNA-Seq for these cases that we compared to 49 controls (probands affected from a neurodevelopmental disorder but without RNU2-2 variants). We observed that RNU2-2 variants mainly disturb alternative exon skipping, although affecting different exons.

  Study EGAS50000001410

• Genetic landscape of pediatric Medulloblastoma

  Medulloblastoma is a heterogenous disease made up of at least four distinct subtypes of disease which appear to exploit and disrupt naturally occurring developmental pathways of cellular growth and hindbrain development. To better understand the driver mutations of this disease, we performed whole genome sequencing of 37 medulloblastomas and the corresponding normal DNA of the 37 affected children treated at St. Jude Children's Research Hospital. We have found several novel mutations which appear subtype specific. These mutations were checked for frequency in a separate tumor cohort of 56 children with medulloblastoma, also treated on the St. Jude Medulloblastoma 2003 trial, and were tested in several animal models of medulloblastoma for proof of oncogenic potential.

  Study EGAS00001000347

• Identification_of_drug_resistance_genes_in_melanoma

  Our aim is to analyze the genome of human melanoma cell lines and short term culture from human melanoma samples in order to identify genes that confer drug resistance to clinically relevant targeted therapies. We will perform whole-exome sequencing, copy number variation analysis and methylome analysis in a collection of human melanoma cell lines and short term culture that will be then screened for drug sensitivity/resistance through a library of clinically relevant drugs and drug combinations. By the combined analysis of the genomic lesion and the drug sensitivity/resistance profile of different cell lines, we will look for genes whose mutation is associated to the sensitivity or resistance to a specific drug in different samples.

  Study EGAS00001000617

• Genomic Analysis of Primary Plasma Cell Leukemia reveals Complex Structural Alterations and High Risk Mutational Patterns

  Primary plasma cell leukemia (pPCL) is a rare and aggressive form of multiple myeloma (MM) that is characterized by circulating plasma cells. Overall survival remains poor despite advances of anti-MM therapy. In an attempt to identify key biological mechanisms that result in the aggressive pPCL phenotype we performed whole exome sequencing of 23 patients with pPCL. For matched non-tumor control for each patient to exclude germline variants we used CD34+ cells from stem cell harvest (n=20) or cells obtained from buccal swabs (n=3). Tumor samples were from bone marrow derived CD138+ cells. Tumor samples were compared to the germline control to identify somatic abnormalities.

  Study EGAS00001003834

• Comprehensive analysis of the (epi)genome of pediatric atypical teratoid/rhabdoid tumours (AT/RTs)

  Whole exome sequencing of atypical teratoid /rhabdoid tumors (AT/RTs) revealed recurrent mutations only in SMARCB1, a gene involved in chromatin remodeling. However, preliminary data from our lab using gene expression and DNA methylation arrays shows that there are three distinct molecular subgroups of AT/RTs, suggesting that other molecular alterations underlying the development of these aggressive pediatric brain tumors must be found outside the coding genome or at the epigenomic level. Identification of these (epi)genomic alterations, which we intend to address in this project, may lead to novel treatment strategies for these tumors and reveal options for meaningful patient stratification.

  Study EGAS00001001297

• Genomic profiling of IBC

  We collected matched pretreatment blood and tumor samples from 19 patients with primary TN-IBC enrolled in a phase II clinical trial (NCT02876107). Patients were treated with neoadjuvant chemotherapy (NAC) or the anti-EGFR antibody panitumumab (PmAb) plus NAC (PmAb/NAC). We conducted whole-exome sequencing, RNA sequencing, and CIBERSORT analyses for these TN-IBC samples and compare the genetic and molecular profiles with similarly analyzed stage III TN-non-IBC patient samples. We also compared the genetic and molecular characteristics of TN-IBC in patients who had a pathologic complete response (pCR) to NAC or PmAb/NAC treatment, a suitable surrogate endpoint for IBC, with those who did not have pCR (non-pCR).

  Study EGAS00001007520

• RNA-Sequencing of cervical cancers

  Question: Can we identify cervical cancer patients who are at risk for distant metastatic (DM) recurrence following treatment with radiotherapy, concurrent weekly cisplatin and brachytherapy (RTCT). Findings: An immune-based 55 gene risk score was developed using a cohort of 81 patients treated with RTCT that was strongly predictive of DM and cause-specific survival (CSS). The risk score was validated in two independent patient cohorts. A high immune metastatic risk score was associated with a high tumor mutational burden and a ‘cold’, immune-excluded tumor microenvironment at diagnosis. Meaning: The immune gene expression risk score may help to identify patients at risk of DM and potential targets for mitigating this risk.

  Study EGAS50000000087

• WES analysis in identifying additive genetic factors that may contribute to the occurrence of moyamoya in neurofibromatosis type 1

  Moyamoya is a progressive cerebral vasculopathy, for which genetic susceptibility factors were mainly identified in Asian populations. When associated with other medical conditions, such as neurofibromatosis type 1 (NF1), this vasculopathy is frequently reported as Moyamoya syndrome (MMS). Intriguingly, most cases of MMS-complicated NF1 have been described in Caucasians, inverting the population ratio for moyamoya vasculopathy observed in Asians, despite NF1 prevalence being constant worldwide. This study aims to investigate whether, among Caucasians, additive genetic factors may contribute to the occurrence of MMS in NF1. WES analysis has been carried out on an Italian family with co-occurrence of NF1 and MMS, as well as other cerebral vasculopathies.

  Study EGAS00001003053

• ROBUST (NCT02285062)

  The ROBUST clinical trial is a Phase III, randomized, double-blind, placebo-controlled study designed to compare the efficacy and safety of lenalidomide plus R-CHOP chemotherapy (R2-CHOP) versus placebo plus R-CHOP in newly diagnosed Diffuse Large B-cell Lymphoma (DLBCL). Molecular data was collected for all patients at screening, but the only patients of the Activated B-cell (ABC) cell-of-origin subtype were eligible for study inclusion and clinical follow-up. We have performed unsupervised clustering on this cohort and identified 7 novel transcriptional subtypes of DLBCL, one of which represents a high-risk subset of patients with high MYC expression, ABC-associated biology, and low immune infiltration.

  Study EGAS50000000333

• CpG methylation changes associated with hyperglycemia in type 1 diabetes occur at angiogenic glomerular and retinal gene loci.

  Retinal and glomerular microangiopathy, and cardiovascular disease, contribute to the morbidity and mortality observed in adults with type 1 diabetes (T1D). While the level and duration of hyperglycemia are primary factors influencing these complications, the underlying molecular mechanisms behind glucose-induced organ damage remain poorly understood. In this study, blood samples from young T1D patients at diagnosis and three years later in average were analyzed for DNA methylation using whole-genome bisulfite sequencing. Significant DNA methylation changes in critical angiogenic gene loci were associated with HbA1c, a direct hallmark of chronic hyperglycemia. This finding may offer novel epigenetic insights for a better understanding of T1D complications.

  Study EGAS50000000370

• Single-cell RNA sequencing of pediatric Hodgkin Lymphoma to study the inhibition of T cell subtypes

  Here, we applied single-cell RNA-sequencing (scRNA-seq) on isolated HRS cells and the immune cells from the same cHL tumors. This allowed us to identify genes of cell surface proteins that are consistently overexpressed in HRS cells and can potentially be used as targets for antibody-drug conjugates or CAR T cells. Finally, we identify potential interactions by which HRS cells inhibit T cells, among which the Galectin-1/CD69 and HLA-DRA/LAG3 interactions. However, high levels of inter-patient heterogeneity of the interaction strength were observed. In conclusion, this study identifies new potential therapeutic targets for cHL and highlights the importance of studying heterogeneity when identifying therapy targets.

  Study EGAS50000000432

• Alveolar Rhabdomyosarcoma case report

  Rhabdomyosarcoma (RMS) is a mesenchymal malignancy phenocopying muscle and is among the leading causes of death from childhood cancer. Metastatic alveolar rhabdomyosarcoma is the most aggressive subtype with an 8% five-year disease-free survival rate when a chromosomal fusion is present, and 40% five-year disease-free survival rate when negative for a fusion event. The underlying biology of PAX-fusion negative alveolar rhabdomyosarcoma remains largely unexplored and is exceedingly rare in Li-Fraumeni syndrome patients. Here, we present the case of an 11-year old male with fusion-negative alveolar rhabdomyosarcoma studied at end of life with a comprehensive functional genomics characterization, resulting in identification of potential therapeutic targets for broader investigation.

  Study EGAS00001004828

• ABIS_1_MeDIP-seq

  We investigated changes in whole genome DNA-methylation in a group of 48 healthy five-year-old children differentiated by their hair cortisol levels. By combining this novel biomarker for chronic stress with methylated DNA immunoprecipitation sequencing (MeDIP-seq), we found that high cortisol were associated with a genome-wide decrease in DNA-methylation targeted to specific zinc finger transcription factor binding sites, repetitive elements and genes important for neurodevelopment and calcium transport. Large scale hypomethylation of repetitive regions, as well as a deficient calcium transport, have been reported in many stress related diseases, as well as in many cancers and biological aging. Thus our findings may aid in our understanding of how susceptibility to these diseases develops.

  Study EGAS00001001099

• Lebanon_LowCov_seq

  we propose to investigate the genomics of a Lebanese sample. we plan (1) genotyping (2.5M) of 120 Lebanese individuals, choosing this platform to allow comparison with the 1000 Genomes and African Genome Variation project populations, (2) 8x sequencing of 100 individuals to provide unbiased population-level sequence information including allele frequencies, and (3) 30x sequencing of four individuals to allow inferences such as from PSMC/MSMC to be obtained. The current form is for the low-coverage sequencing. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001002084

• Transcriptomic analysis of cell-of-origin CNS neuroblastoma, FOXR2 activated

  The transcription factor FOXR2 is the universal driver of childhood central nervous system neuroblastoma, FOXR2 activated (NB-FOXR2). NB-FOXR2 tumors arise exclusively in the brain hemispheres, and despite morphological similarities to other pediatric brain tumors, they are a molecularly distinct entity based on DNA methylation profiling. The cell-of-origin is unknown. Here, we profiled a cohort of rare NB-FOXR2 tumors by bulk and single-cell transcriptomics. Through systematic comparative analyses, we delineate tumor transcriptional states and candidate cell-of-origin. More broadly, we demonstrate systematic molecular profiling of childhood cancers to orient oncogenic targeting for in vivo modeling, a critical resource for the study of rare tumors and development of therapeutics.

  Study EGAS00001007247

• RNA-sequencing from duodenal bipsies of Celiac disease patients

  Samples, in a form of PAXgene fixed and paraffin-embedded biopsies, were collected from the multi-site, double-blind, randomized, placebo-controlled trial, aimed at dose-finding and assessing the efficacy and tolerability of a 6-week treatment with ZED1227 capsules vs. placebo in subjects with well-controlled celiac disease undergoing gluten challenge. Total RNA was extracted from the PaxFPE biopsy specimens (n = 116) using additional cuttings from the samples on which histomorphometry was previously assessed. For the extraction, an RNeasy Kit (Qiagen, Hilden, Germany) was used according to the manufacturer’s instructions. Library preparation and next-generation sequencing (NGS) were performed by the Qiagen NGS Service. A total of 10 ng of purified RNA was converted into cDNA NGS libraries. Library preparation was quality controlled using capillary electrophoresis. Based on the quality of the inserts and the concentration measurements, the libraries were pooled in equimolar ratios and then sequenced on a NextSeq (Illumina Inc., San Diego, USA) sequencing instrument according to the manufacturer’s instructions, with 100 bp read length for read 1 and 27bp for read 2. The raw data were de-multiplexed, and FASTQ files for each sample were generated using bcl2fastq2 software (Illumina Inc., San Diego, USA).

  Dataset EGAD50000000491

• scRNA-seq of HSPC treated with gemcitabine and carboplatin

  4 samples of 2000000 HSPCs in 2 ml media each were then prepared and treated for 24 hours: carboplatin-high: 150 µg/ml carboplatin carboplatin-low: 18.75 µg/ml carboplatin gemcitabine: 25 ng/ml gemcitabine control: no drug Single-cells were subsequently extracted using the ddSEQ™ Single-Cell Isolator (Bio-Rad) and later sequenced using the SureCell™ Whole Transcriptome Analysis 3' Library Prep Kit (Illumina) on the NextSeq 500 System (Illumina) using the NextSeq 500/550 High Output Kit v2.5 150 Cycles (Illumina) all following the manufacturer's instructions. The raw FASTQ-files are available as read 1 and read 2 files from 4 lanes for each sample giving a total of 16 FASTQ-files. The FASTQ-files were also processed following the ddSeeker (Romagnoli, D., et al., BMC Genomics 2018, doi:10.1186/s12864-018-5249-x) and Drop-seq (Macosko, E.Z., et al., Cell 2015, doi:10.1016/j.cell.2015.05.002) protocols for processing scRNA-seq data to yield the final digital gene expression (dge) for each cell of each sample. This has resulted in one dge text file and one dge summary text file per sample. These 8 text-files with dge data are found in the zip-compressed analysis data-file.

  Dataset EGAD00001006080

• RNA-seq study of human long-term and short-term hematopoietic stem cells from umblical cord blood with lentiviral overexpression of S1PR3

  To investigate the molecular and biological pathways altered by S1PR3OE in human hematopoietic stem cells (HSC), we performed RNA-sequencing (RNA-seq) of LT- and ST-HSC 3 days after transduction with control or S1PR3 overexpression (OE) lentiviral vectors. LT-HSC and ST-HSC from 3 pool of CB lin- were FACS-purified, cells were prestimulated for 4 hours and transduced with lentiviral vectors. At day 3, 2000-5300 BFP+ cells were FACS-purified for RNA isolation with a PicoPure kit. We were able to isolate only 1600-1800 BFP+ cells from LT-HSC control samples as opposed to 4000-5400 BFP+ cells from S1PR3OE samples. Thus, we pooled all control BFP+ LT-HSC cells into one sample for RNA-seq analysis. BFP- LT-HSC from control vector transduction were purified from CB1 as an additional LT-HSC control. Nextera libraries generated from 10 ng RNA from 5 LT-HSC samples (2 controls, 3 S1PR3OE) and 6 ST-HSC samples (3 controls, 3 S1PR3OE) were subjected to 125 bp, paired-end RNA-sequencing on the Illumina HiSeq 2500 with an average of 50 million reads/sample at the Center for Applied Genomics, Sick Kids Hospital.

  Dataset EGAD00001006582

• CINECA synthetic data.Please note: This study contains synthetic data (with cohort “participants” / ”subjects” marked with FAKE) has no identifiable data and cannot be used to make any inference about cohort data or results.

  Please note: This study contains synthetic data (with cohort “participants” / ”subjects” marked with FAKE) has no identifiable data and cannot be used to make any inference about cohort data or results. The purpose of this dataset is to aid development of technical implementations for cohort data discovery, harmonization, access, and federated analysis. In support of FAIRness in data sharing, this dataset is made freely available under the Creative Commons Licence (CC-BY). Please ensure this preamble is included with this dataset and that the CINECA project (funding: EC H2020 grant 825775) is acknowledged. For any questions please contact isuru@ebi.ac.uk or cthomas@ebi.ac.uk

  Study EGAS00001002472

• Genomic Sequencing of Pediatric Rhaboid Cancers

  In this study, we sequenced the exomes of 35 rhabdoid tumors, highly aggressive cancers of early childhood. This study is part of a larger effort to characterize pediatric cancers as part of the Slim Initiative for Genomic Medicine (SIGMA) project.

  Study phs000508

• Blood Handling and Leukocyte Isolation Methods Impact the Global Transcriptome of Immune Cells

  In order to characterize the effects of upstream sample handling on the transcriptome of isolated leukocyte populations, we simulated various sample handling methods on whole blood prior to leukocyte isolation for low-input RNA-sequencing.

  Study phs001563

• Ultrasensitive Profiling of UV Mutations in Facial Tumors in TSC

  In this study we searched for mutations in the TSC2 and TP53 genes in sample sets from individuals with Tuberous Sclerosis Complex (TSC) and from subjects without TSC. The study was focused on the analysis of TSC facial angiofibroma.

  Study phs002914

• Whole Exome Sequencing of Parathyroid Cancer Identifies Candidate Driver Mutations and Core Pathways

  Here we performed genomic characterization of twenty-nine sporadic parathyroid cancers using next generation whole exome sequencing. Thirty-three novel candidate driver genes for sporadic parathyroid cancer were proposed, in addition to previously known driver genes CDC73 and MEN1.

  Study phs001765

• The Normal Human Tissue Sequencing Project: Non-Diseased, Non-Malignant Tissues

  The Normal Human Tissue Sequencing Project provides RNA expression and DNA methylation data from normal (non-diseased) human tissues. This data set from a variety of source tissue is a valuable resource for human disease studies.

  Study phs000819

• Systematic Analysis of Coding and Non-coding Elements in Developmental Pathways Implicated in Holoprosencephaly Pathogenesis

  We applied targeted capture to examine 153 genes representative of all the major vertebrate developmental pathways among 340 probands and 285 of their unaffected parents to rank their relative significance as causes for holoprosencephaly (HPE).

  Study phs001653

• Germline Genetic Variants in Cancer-Susceptibility Genes in Patients with Osteosarcoma

  We conducted whole-exome sequencing of germline DNA from patients with osteosarcoma to estimate the frequency of pathogenic/likely pathogenic germline genetic variants in known cancer-susceptibility genes in a large population of osteosarcoma patients unselected for family history.

  Study phs002444

• An Omics View of Asthma through Monozygotic Twins

  The etiology of asthma involves both genetic and non-genetic factors. We performed whole transcriptome sequencing on monozygotic twins discordant or concordant for asthma (with concordant healthy twins as controls), and identified multiple potential transcriptomic profiles associated with the asthma phenotype.

  Study phs000886

• Single Cell ATAC-Seq of MELAS

  This dataset includes combined single Assay for Transposase-Accessible Chromatin, using sequencing (ATAC-seq), and mitochondrial DNA sequencing of peripheral blood mononuclear cells from three individuals with m.3243A>G associated MELAS (Mitochondrial Encephalopathy, Lactic Acidosis, and Stroke-like episodes).

  Study phs002217

• Kids First: Genetics of Kidney and Urinary Tract Malformations

  Congenital defects of the kidney and urinary tract are a common cause of kidney failure in children and adults and elucidation of the genetics of these disorders will provide new opportunities for diagnosis, risk stratification and prevention of complications.

  Study phs002162

• Comprehensive sequencing analyses of uterine and ovarian carcinosarcoma

  We collected 109 primary tumor and mached normal samples of uterine and ovarian carcinosarcoma. The purpose of this study is to find novel therapeutic options for carcinosarcoma as well as a clue to understand the molecular histogenic mechanism.

  Study JGAS000172

• Comprehensive molecular and clinicopathological profiling of desmoid tumors

  Previous studies have not clearly identified a prognostic factor for desmoid tumors (DT). Whole-exome sequencing and/or RNA sequencing were performed in 64 cases of DT to investigate the molecular profiles in combination with the clinicopathological characteristics.

  Study JGAS000270

• Arkansas Children’s Research Institute (ACRI) Data Access Committee – Kelly Research Group

  The Arkansas Children’s Research Institute (ACRI) Data Access Committee – Kelly Research Group oversees requests for access to controlled human genomic and transcriptomic data generated by the Kelly Research Group. The committee ensures that all data access requests are consistent with participants’ informed consent, institutional review board (IRB) approvals, and applicable regulatory requirements. All approved users must agree to use the data solely for biomedical research purposes, maintain data confidentiality, and acknowledge the data source in resulting publications.

  Dac EGAC50000000819

• Whole exome sequencing of virus-associated HCC

  To understand comprehensive combinations of molecular alterations and seek for potential therapeutic targets/pathways in virus-associated HCC, we have conducted a whole exome sequencing (in-solution capturing all human coding exons) of 150 pairs of HCC cases.

  Study EGAS00001000389

• Liquid biopsy to identify taxane resistance in castration-resistant prostate cancer patients

  Taxanes are life-prolonging treatments for patients with advanced prostate cancer. However, treatment resistance and lethal disease invariably develops. We here used liquid biopsies to identify and characterize resistance to cabazitaxel using a targeted sequencing panel (PCF-SELECT).

  Study EGAS50000001292

• smallRNA-seq of isolated pancreatic islets

  In this study we performed smallRNA-sequencing, a sequencing method designed for small noncoding RNAs, to investigate the miRNA expression profile of human islets isolated from pancreata of donors without diabetes mellitus (n=3) and donors with type 2 diabetes (n=3).

  Study EGAS50000000865

• Mutational_burden_in_skin_following_UV_treatment_Nanoseq

  We wish to assess the changes in mutational burden in patients under going UV treatment for psoriasis. Using duplex sequencing we will assess mutational burden in traditionally sun exposed (arm) and non-sun exposed (buttock) skin epidermis both pre and post UV treatment.

  Study EGAS00001007681

• BGISEQ-500 Cancer Dataset - WGS tumour/normal pairs

  This study contains whole genome sequencing data for 3 matched tumour / normal pairs from Mesothelioma patients. The sequencing is 50bp paired-end generated using the BGISEQ-500 and is provided as 6 aligned and duplicate-marked BAM files.

  Study EGAS00001002298

• Mutational_burden_in_skin_following_UV_treatment_WGS

  We wish to assess the changes in mutational burden in patients under going UV treatment for psoriasis. Using duplex sequencing we will assess mutational burden in traditionally sun exposed (arm) and non-sun exposed (buttock) skin epidermis both pre and post UV treatment.

  Study EGAS00001007682

• Evaluation_of_size_selection_on_cancer_specific_sequencing_libraries

  A couple of previously characterized and sequenced libraries will be repeated using a couple of differing size selection criteria and skim sequenced using an Illumina HiSeq. The resulting sequence will be analyzed to determine the optimal DNA library size for our specific downstream analysis.

  Study EGAS00001000293

• scD&D Multiome of GATA1 regulatory network dynamics during erythropoiesis

  Ex vivo differentiation experiments of human CD34+ hematopoietic stem and progenitor cells and profiled cells along the erythropoietic trajectory at multiple timepoints (differentiation days 0, 5, 8, 18, and 24), for simultaneous assessment of transcriptome, chromatin accessibility and GATA1 binding

  Study EGAS50000001606

• Cohort B tumor exome sequencing

  Cohort B includes IDH-wild type, EGFR amplified, surgically derived glioblastoma tissue samples from male and female individuals. Tumor DNA was isolated from FFPE tissue. Both tumor and germline DNA are present for each sample in the overall dataset.

  Study EGAS50000000955

• WNT7B-reporter organoids sorted

  Transcriptomic data from pancreatic ductal adenocarcinoma (PDAC) organoids to investigate the role of WNT7B. This dataset includes: - Bulk mRNA sequencing of WNT7B-reporter pancreatic ductal adenocarcinoma (PDAC) organoids sorted for cells displaying low, medium and high expression of the reporter

  Study EGAS50000001543

• GWAS data (Illumina 2.5 M SNPs) in Cuban cohorts of dengue disease

  We will have 274 individuals typed for the Illumina Human Omni 2.5 chip. The individuals are from two locations in Cuba (Havana and Guantanamo) and from four phenotype classes (asymptomatic, control dengue fever and dengue hemorrhagic fever).

  Study EGAS00001002276

• Integrated genetic and epigenetic analysis of myxofibrosarcoma

  Myxofibrosarcoma (MFS) is a common histological subtype of adult soft tissue sarcoma characterized by an infiltrative growth pattern and a high propensity for local recurrence. We underwent whole exome sequencing, RNA sequencing, and methylation analysis of MFS.

  Study EGAS00001002889

• Mutational_burden_in_oesophagus__nanoseq_

  We wish to accurately assess mutational burden and signature from patients of different ages using clonal oesophageal epithelium and duplex-seq. We will also attempt to look for differences between smokers and non-smokers and individuals with different levels of alcohol consumption.

  Study EGAS00001007695

• Parallel Detections of Somatic Gene Mutations in Surgically Resected Tumor tissues and Matched Plasma Specimens in Early-Stages of Primary Breast Cancer

  We developed two panel successively, contain 68 and 136 genes respectively. Combination with ultrasound or mammography, it could be used for breast cancer early detection and avoided unnecessary surgery or other invasive detection.

  Study EGAS00001003075