13306 results for ""pdc"+"heritage+language"+census+study"

in 34.70 milliseconds.

• Single Patient BRAF Mutant Brain Tumor, Pre- and Post-dabrafenib WES.

  A single adolescent patient with a BRAF V600E mutated brain tumor was treated with dabrafenib and had a complete response, followed by progression. The pre-treatment and post-progression tumors were both sequenced in order to identify potential drivers of resistance.

  Study phs001629

• Baylor Hopkins Center for Mendelian Genomics (BH CMG)

  The Centers for Mendelian Genomics project uses next-generation sequencing and computational approaches to discover the genes and variants that underlie Mendelian conditions. By discovering genes that cause Mendelian conditions, we will expand our understanding of their biology to facilitate diagnosis and new treatments.

  Study phs000711

• Broad Institute Center for Mendelian Genomics

  The Centers for Mendelian Genomics project uses next-generation sequencing and computational approaches to discover the genes and variants that underlie Mendelian conditions. By discovering genes that cause Mendelian conditions, we will expand our understanding of their biology to facilitate diagnosis and new treatments.

  Study phs001272

• University of Washington Center for Mendelian Genomics (UW-CMG)

  The Centers for Mendelian Genomics project uses next-generation sequencing and computational approaches to discover the genes and variants that underlie Mendelian conditions. By discovering genes that cause Mendelian conditions, we will expand our understanding of their biology to facilitate diagnosis and new treatments.

  Study phs000693

• COVID_Methyl_scRNA

  DAC for the study of whole-genome enzymatic DNA methylation sequencing and single-cell RNA sequencing of nasal cells from COVID-19 patients. Nasal swabs were collected from COVID-19 patients during the acute phase of infection as well as 3 and 12-months post-infection. Cells isolated from nasal swabs were subjected to whole-genome enzymatic DNA methylation sequencing (n=33) and scRNA-seq (n=24). For n=12 former COVID-19 pateints, follow-up samples were collected at 3 and 12 months post-infection and subjected to scRNA-seq.

  Dac EGAC50000000197

• Developing therapeutics for ovarian cancer using ovarian cancer organoids

  To identify effective drugs for clear cell ovarian cancer (CCC) and high-grade serous ovarian cancer (HGSC) through high-throughput drug screening using ovarian cancer organoids and to identify novel therapeutic targets based on the biological characteristics of CCC and HGSC through omics analysis.

  Study JGAS000764

• Application of organoid culture system of human gastrointestinal and thoracic cancer in genome medicine

  In order to establish preclinical models, we have established a kind of lung cancer tumoroids derived from a mucus-producing solid pulmonary adenocarcinoma patient. We performed whole exome sequencing and RNA sequencing to analyze genetic background of the tumoroids.

  Study JGAS000664

• Application of organoid culture system of human gastrointestinal and thoracic cancer in genome medicine

  In order to establish preclinical models, we have established three kinds of lung cancer tumoroids derived from three different pulmonary large cell neuroendocrine carcinoma patients. We performed whole exome sequencing to analyze genetic background of these kinds of tumoroids.

  Study JGAS000641

• Application of organoid culture system of human gastrointestinal and thoracic cancer in genome medicine

  In order to establish preclinical models, we have established a kind of lung cancer tumoroids derived from a mucus-producing solid pulmonary adenocarcinoma patient. We performed whole exome sequencing and RNA sequencing to analyze genetic background of the tumoroids.

  Study JGAS000653

• Elevated circulating tumor cells reflect high proliferation and genomic complexity in multiple myeloma - RNA validation cohort

  This reposiroty contains bulk RNA data generated by Blood Cancer Research Group (Ostrava, Czech Republic) as a part of publication named "Elevated circulating tumor cells reflect high proliferation and genomic complexity in multiple myeloma" published in Hemapshere.

  Study EGAS50000001212

• Elevated circulating tumor cells reflect high proliferation and genomic complexity in multiple myeloma - WGS validation cohort

  This reposiroty contains bulk WGS data generated by Blood Cancer Research Group (Ostrava, Czech Republic) as a part of publication named "Elevated circulating tumor cells reflect high proliferation and genomic complexity in multiple myeloma" published in Hemapshere.

  Study EGAS50000001211

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

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

  Study JGAS000853

• Targeted sequencing data of regulatory regions in 200 Spanish ASD trios

  This dataset consists of genomic sequencing data obtained through targeted sequencing of regulatory regions ( 85,394 human cCREs from ENCODE v2, version 2, https://screenv2.wenglab.org/) in 200 ASD (Autism Spectrum Disorder) trios (father and mother unaffected and proband affected)(600 samples total). Sequencing was carried out at the Centre for Genomic Regulation (CRG), Barcelona, Spain. Uploaded files are .vcf (600 samples). The goals of our study were to detect de novo and inherited variants in ASD probands. Sequencing data were obtained in an Illumina NovaSeq6000 instrument.

  Dac EGAC50000000695

• Hi-C analysis of patient-derived pancreas neoplasm organoids

  Pancreatic cancers arise from two different precursors; intraductal papillary mucinous neoplasms (IPMN) and pancreatic intraepithelial neoplasm (PanIN), while biological differences in cancers originated from thme remain obscure. Here, we analyzed their three-dimensional genome structure by Hi-C using patient-derived organoids.

  Study JGAS000262

• Biobank Japan genotype and phenotype data

  The Biobank Japan (BBJ) Project started at the Institute of Medical Science, the University of Tokyo in 2003. To date, the BBJ Project has collected around 200,000 individuals with disease cases consisting of 47 diseases. The purpose of the BBJ is to realize personalized medicine.

  Study JGAS000114

• Transcriptome sequencing, DNA methylation analysis, and SNP array analysis of acute lymphoblastic leukemia in Down syndrome

  Pathogenesis of acute lymphoblastic leukemia in Down syndrome (DS-ALL) is poorly understood. To investigate molecular basis of DS-ALL, we performed whole transcriptome sequencing, DNA methylation array, and SNP array analysis in 43 cases of DS-ALL.

  Study JGAS000147

• Single cell RNA sequencing of human umbilical cord blood lymphoid progenitors

  We performed single cell RNA sequencing of human umbilical cord blood. To explore the differentiation pathway for human lymphoid lineage deeply, our target cells contain CD34+CD38+CD45RA+CD19-CD7-CD10+ cells (CD10SP). All these populations are evaluated by single cell RNA sequencing.

  Study JGAS000551

• Comprehensive analysis of the abnormality of the genes in juvenile myelomonocytic leukemia

  To develop a simple and robust methylation test for risk stratification of patients with juvenile myelomonocytic leukemia. We used the DREAM method, a method for whole genome methylation analysis using NGS, to analyze methylation profiling of patients with juvenile myelomonocytic leukemia.

  Study JGAS000292

• Multi-omics analysis of pediatric high-risk neuroblastoma

  Neuroblastoma is the most common extracranial solid malignancy among children originating from undifferentiated neural crest cells. Despite recent intensified treatment, high-risk patients still show a high mortality rate. To explore a new therapeutic strategy, we performed integrated analysis in 30 neuroblastoma cases.

  Study JGAS000246

• intratumor heterogeneity in colorectal adenoma and carcinoma

  To investigate intratumor heterogeneity in precancerous lesions of colorectal cancers (PCRCs), we performed whole-exome sequencing of 53 tumor and 10 matched-normal samples from 10 laterally spreading tumors in the colon and rectum, which were histologically diagnosed as adenoma with/without adenocarcinoma.

  Study JGAS000092

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

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

  Study JGAS000852

• Indonesian Single Cell Data Access Committee

  This Data Access Committee manage and oversee the Data Access Policy sets forth the terms, conditions, and limitations governing access to and use of the raw sequencing data of samples in the Indonesian Single Cell dataset by individuals who are not part of the Data Producer. The IndoSC dataset comprises 203 human whole blood and PBMC samples collected in 4 communities in both Bali and Papua Provinces in Indonesia, that was collected to study the immune cell atlas of ancestrally- and environmentally diversed populations in Indonesia.

  Dac EGAC50000000870

• Genome-wide association scan in Parkinson's disease

  Genome-wide association scan was performed in 1,705 cases of parkinson's genotyped on the Illumina Human 660W SNP array, and 5,175 controls genotyped on the Illumina1.2M-Duo. Analysis was carried out on the overlaps set of SNPs.

  Study EGAS00000000034

• Treatment of CAR T cells with immunomodulatory metabolites

  Anti-Her2-CAR T cells produced from T cells derived from healthy human donors were treated with DMSO (control) or either of the immunomodulatory metabolites indole‐3‐carboxaldehyde (ICA), valeric acid (VA) and isovaleric acid (IVA) to assess effects on CAR T cell function.

  Study EGAS50000001386

• Extrachromosomal DNA-driven oncogene dosage heterogeneity determines therapy response in neuroblastoma

  Characterization of ecDNA copy number-dependent plasticity of neuroblastoma patient-derived xenograft models. Data corresponds to single-cell G&T sequencing from an untreated neuroblastoma PDX and single-cell multiome ATAC + gene expression sequencing of a SHH medulloblastoma tumor.

  Study EGAS50000001040

• Clonal expansion and epigenetic reprogramming following deletion or amplification of mutant IDH

  Initially IDH1 mutant gliomas are shown to have IDH1 is deletions or amplifications at recurrence yielding a higher-grade tumor with a reprogrammed epigenome. We also report systematic selection for cells with IDH1 CNA in vitro and in vivo.

  Study EGAS00001002618

• 54 metastatic colorectal cancer patients from Schleswig-Holstein in North Germany

  Personalized treatment vs standard of care is much debated, especially in clinical practice. Here we investigated whether overall survival differences in metastatic colorectal cancer patients are explained by their tumor mutation profiles or by their treatment differences in real clinical practice.

  Study EGAS00001004108

• ATAC-seq data in normal colon mucosa

  This dataset includes ATAC-seq data generated in normal colon mucosa obtained in four healthy volunteers during colonoscopy indicated for colorectal cancer screening. Subjects had no lesions in the colon. Also includes one frozen sw480 colon adenocarcinoma cell line sample for piloting the protocol

  Study EGAS00001005281

• metastatic uveal melanoma tumour biopsies

  Tumour biopsies were obtained from uveal melanoma patients pre and 16 days post treatment with tebentafusp. Biopsies, which were either snap frozen or put in RNA later, were analysed by bulk RNA sequencing (50 million reads per sample) using the Illumina NovaSeq system.

  Study EGAS50000000864

• metastatic uveal melanoma tumour biopsies (n=35)

  Tumour biopsies were obtained from uveal melanoma patients (n = 35) pre and 16 days post treatment with tebentafusp. Biopsies, which were either snap frozen or put in RNA later, were analysed by bulk RNA sequencing (50 million reads per sample) using the Illumina NovaSeq system.

  Study EGAS50000000836

• A Novel APP p.V742L variant in a patient with ischemic small vessel disease enhances FE65 signalling

  We identified a novel variant in the APP gene associated with cerebral ischemic strokes, which is not seen before with APP variants. This results in increased affinity of APP for FE65, APP’s most important intracellular interactor that regulates gene transcription.

  Study EGAS50000001283

• Yemen_and_Chad_Genotyping

  HumanOmni2.5-8 data from Chad and Yemen.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 EGAS00001001231

• Comprehensive genomic characterization of early stage bladder cancer - nanopore sequencing

  For this project about non-muscle invasive bladder cancer (NMIBC), we analysed long read sequencing data from 4 patients using the Nanopore platform. The dataset is composed of 8 BAM files: 4 tumor samples and 4 paired blood samples.

  Study EGAS50000000510

• Single cell RNA-seq profiling of CD8 T cells from elder adults

  Single cell RNA-seq profiling of ~62k purified CD8+ T cell transcriptomes, from six healthy older adult donors using 10X genomics. Cells from each donor were separated based on their IL-7R protein expression (i.e. CD8+ IL7R+ and CD8+ IL7R- T cells).

  Study EGAS00001004255

• Screening of 2.5 million SNPs in 142 samples from the western Mediterranean area

  The analysis of 2.5 million SNPs in 142 samples from the western Mediterranean area, including southern Spain, Andalusia (Huelva: 35 samples, Granada: 35), southern Portugal (36 samples) and Moroccan Berbers (Asni: 15, Bouhria: 12 and Figuig: 9).

  Study EGAS00001003901

• Using RNA-sequencing to characterize the resistance to lirafugratinib

  In addition to Exome-sequencing, we used RNA-sequencing to also characterize resistance to lirafugratinib with whole exome sequencing in patients with FGFR2-driven cancers, treated in the phase 1/2 ReFocus trial (NCT04526106) and enrolled in the UNLOCK program at Gustave Roussy

  Study EGAS50000001370

• RNA004 Nanopore DRS of peripheral blood

  Direct RNA Sequencing offers the capability of standard transcriptomic analyses + RNA modification analysis, which holds promising applications for future clinical workflows. To this end, we tested the newly available RNA004 kit on human peripheral blood and provide orthogonal GLORI measurement for benchmarking of m6A-detection.

  Study EGAS50000001201

• Resistance_to_MAPK_inhibitor_induces_internal_duplication_in_BRAF

  2 BRAFV600E cell lines that have been made resistance to 1. the BRAF inhibitor PLX4720 and 2. the combination therapy of dabrafenib and trametinib seem to have a internal duplication in the kinase domain. We would like to know if this is caused by a translocation.

  Study EGAS00001001304

• Single cell RNA sequencing of co-culture of human organoids with polarized pro-inflammatory (M1) or anti-inflammatory (M2) macrophages

  Human intestinal organoids co-cultured with pro-inflammatory (M1) or anti-inflammatory (M2) human macrophages for 48 hours. 3 days after the co-culture alive cells were sorted and processed for single cell RNA sequencing

  Study EGAS50000000467

• Comprehensive genomic characterization of early stage bladder cancer - shallow whole genome sequencing data

  For this project about non-muscle invasive bladder cancer (NMIBC), we analysed shallow WGS data from 362 patients. The dataset is composed of 392 BAM files: 362 tumor samples, 15 female normal samples and 15 male normal samples.

  Study EGAS50000000513

• Human_Evolution_3B

  The mtDNA and Y chromosome of up to 15 Australian Aborigines, concentrating on individuals with indigenous lineages will be sequenced using the standard whole-genome sequencing followed by filtering out autosomal and X sequences, so that only mtDNA and the Y chromosome would be analysed and released.

  Study EGAS00001000718

• Genetic landscape of pediatric Low Grade Gliomas & Glioneuronal tumors

  We performed whole-genome sequencing of 42 paired tumor/normal LGG genomes and analyzed somatically acquired single nucleotide variations (SNVs), insertion/deletions, structural variations and copy number variations in the cancer genomes

  Study EGAS00001000255

• 3D chromatin contacts of iPSC (controls) and mDAN (differentiated neurons) cells

  Sequencing of 3 replicates per condition to gather insights on the 3D chromatin conformation of iPCS-derived neuronal progenitors (smNPCs) and mDANs using LowC. The downstream analysis studies changes in A and B compartment interactions and in topologically associated domains (TADs).

  Study EGAS50000001578

• Single-nucleus transcriptome sequencing of the ALS-FTD motor cortex after sorting by TDP-43

  Single-nucleus RNA-sequencing of NeuN+ nuclei of the post-mortem human primary motor cortex from patients with ALS-FTD confirmed for TDP-43 pathology, after sorting for TDP-43 signal, TDP-43 Low vs. TDP-43 High

  Study EGAS50000001566

• RE_NanoSeq___TwinsUK_Buccal

  Utilising restriction enzyme NanoSeq, we hope to explore the somatic mutation burden and mutational signatures in buccal cells from TwinsUK donors. Some donors have paired blood samples and data from this will help contextualise that work. All donors have paired Targeted NanoSeq data from buccal swabs.

  Study EGAS00001007740

• Pediatric HGG WES and RNA-Seq

  Paediatric high-grade glioma (pHGG) is the leading cause of paediatric brain tumour death. Here we performed RNA and whole exome sequencing on pHGG samples to analyse transcriptomic and genetic alterations associated with this devastating disease, and to understand the relationship between them.

  Study EGAS00001005687

• Taste Receptor Gene Variants: Body Mass Index (BMI) and Longevity

  We evaluated differences in genotype and allele frequencies at the TAS1R2, TAS1R3, TAS2R38, and CD36 single-nucleotide polymorphisms (SNPs) and their associations with BMI and sex in two genetically and environmentally distinct populations: a cohort of near centenarian participants and a control cohort.

  Study EGAS00001008403

• RNAseq_of_patients_with_Ewings_sarcoma

  Cancer is driven my mutations in the genome. We will uncover the mutations that give rise to Ewing’s sarcoma, a bone tumour that largely affects children. We will use second generation Illumina massively parallel sequencing, and bespoke software, to characterise the genomes and transcriptomes of Ewings’ sarcoma tumours.

  Study EGAS00001000267

• Ewings_Sarcoma_Rearrangement_Screen

  Cancer is driven by mutations in the genome. We will uncover the mutations that give rise to Ewing’s sarcoma, a bone tumour that largely affects children. We will use second generation Illumina massively parallel sequencing, and bespoke software, to characterise the genomes and transcriptomes of Ewings’ sarcoma tumours.

  Study EGAS00001000362

• Clonal_architecture_of_pre_malignant_and_malignant_tumours

  Single cells have been isolated from normal and pre-invasive lung cancer lesions from one patient. These have been grown into colonies that will then be whole genome sequenced. This will reveal the mutational burden in normal and premalignant tissues, and the heterogeneity between different cells.

  Study EGAS00001001676

• Mutant_clone_mapping_in_normal_oesophagus

  We will use targeted exome sequencing to examine normal appearing epithelium and whole exome and whole genome sequencing of microdissected clones identified by immunostaining Some of the samples will be of low DNA concentration and therefore may require extra rounds of amplification during library prep.

  Study EGAS00001001874

• Landscape of gene mutations in Down syndrome-related myeloid disorders

  To identify the spectrum of gene mutations in Down syndrome-related myeloid disorders, whole genome sequencing of 4 trio samples from TAM/AMKL/complete remission (CR) phases and whole exome sequencing of 15 TAM and 14 DS-AMKL samples were performed.

  Study EGAS00001000546

• Targeted proteomics for endotyping of chronic rhinosinusitis

  To identify biomarkers allowing for the distinction between different chronic rhinosinusitis patient groups and disease controls (n=20 of each DC, CRSsNP, CRSwNP and N-ERD), we use high-throughput targeted proteomics (Olink Multiplex platform) in nasal secretions and serum samples.

  Study EGAS50000000907

• Whole genome sequencing of metastatic melanomas from a patient with primary resistance to BRAF inhibition

  Here, we investigated the underlying cause of treatment failure in a patient with BRAF mutant melanoma who presented primary resistance. We used whole-genome sequencing (WGS) to characterise five metastatic tumours from a BRAF mutant melanoma patient who presented intrinsic resistance.

  Study EGAS00001000580

• Whole genome sequencing of preneoplasia lung adenocarcinoma

  Whole genome sequencing of 42 pulmonary samples including lung preneoplasia atypical adenomatous hyperplasia (AAH, N=5), adenocarcinoma in situ (AIS, N=7), minimally invasive adenocarcinoma (MIA, N=6) and invasive lung adenocarcinoma (ADC, N=8) and adjacent lung tissues (Normal, N=16).

  Study EGAS50000000272

• 3D chromatin analysis of clear cell renal cell carcinoma using micro-C

  To investigate the 3D structure of chromatin in ccRCC, we performed micro-C on 3 ccRCC cell lines (786-O, A498, UMRC-2), and 1 normal kidney epithelium cell line (HK-2), cultured under normoxic (20% O2) and hypoxic (0.05% O2) conditions

  Study EGAS50000001323

• Identification of genetic etiology of CAMRQ2

  We aimed to identify genetic etiology of cerebellar ataxia, mental retardation, and disequilibrium syndrome (CAMRQ). Targeted sequencing of the entire CAMRQ2 locus, 7.1 Mb interval on chromosome 17p13, in three affected individuals and two obligate carriers uncovered the mutation associated with CAMRQ2.

  Study EGAS00000000099

• Mutations in PNPLA6 are linked to photoreceptor degeneration and various forms of childhood blindness

  In this work, using exome sequencing, we identified biallelic PNLPA6 mutations in patients with childhood blindness due to severe photoreceptor death and clinical features of Leber congenital amaurosis (LCA) and, interestingly, also of the rare Oliver McFarlane Syndrome

  Study EGAS00001001013

• Genomic profiling of Rare Tumors Release 2

  Utilizing the rare and unique patient samples provided by Pattern Medicine, LLC, MD Anderson will molecularly characterize rare cancer samples, and potentially generate a collection of preclinical models to enable identification of novel therapeutic targets and concepts, as well as evaluation of innovative treatment strategies.

  Study EGAS50000000615

• Pre_clinical_evolution_of_haematological_malignancies

  Deep targeted sequencing of 291 peripheral blood samples taken 1-20 years prior diagnosis of a haematological malignancy alongside age- and sex-matched controls. Key objective is to distinguish indolent age-related clonal haematopoiesis from pre-cancer and to derive predictive models for early risk-stratification.

  Study EGAS00001002964

• Determinants of DNA methylation patterning in human placental development and trophoblast stem cell models.

  To assess whether the DNA methylation landscape of human trophoblast stem cells resembles an in vivo cell type, we used post-bisulfite adaptor-tag sequencing to measure genome-wide DNA methylation of preimplantation human trophectoderm and sorted first trimester cytotrophoblast.

  Study EGAS50000000661

• Exome_sequencing_of_patients_with_Ewings_sarcoma_

  Cancer is driven by mutations in the genome. We will uncover the mutations that give rise to Ewing’s sarcoma, a bone tumour that largely affects children. We will use second generation Illumina massively parallel sequencing, and bespoke software, to characterise the genomes and transcriptomes of Ewings’ sarcoma tumours.

  Study EGAS00001000266

• Frequent mutation of the FOXA1 untranslated region in prostate cancer

  We sequenced the coding and untranslated regions of 72 prostate cancer driver genes in 712 plasma cell free DNA samples from 428 men with metastatic prostate cancer, in an effort to understand the role of untranslated region mutations in late stage prostate cancer.

  Study EGAS00001003113

• Integrative and comparative genomic analyses identify clinically relevant groups of pulmonary carcinoids and unveil the supra-carcinoids

  Multi-omic data for lung neuroendocrine neoplasms, including the first multi-omic sequencing data for the understudied lung atypical carcinoids. The data includes Whole-exomes, whole-genomes, RNA-seq, and EPIC 850K methylation array data.

  Study EGAS00001003699

• A fast, affordable and minimally-invasive diagnostic test for Cancer of Unknown Primary (CUP) using DNA methylation profiling

  CUP diagnosis on FFPE tissue and liquid biopsies (blood, pleural and peritoneal effusions) using cfRRBS (cell-free reduced representation bisulfite sequencing), a technique that allows for identification of the methylation profile starting from minimal amounts of highly fragmented DNA.

  Study EGAS50000000257

• ST dataset of subcortical MS

  Spatial transcriptomics from subcortical white matter controls and MS lesions, specifically chronic active (CA) and chronic inactive (CI), that paired with single-nuclei RNA-sequencing from the same samples , was used to identify spatial niches and key cell interactions driving inflammation and disease progression

  Study EGAS50000000353

• Myeloproliferative_Neoplasms__MPN__Targeted_Gene_Screen

  Pulldown experiments will be performed on a number of patients with Myeloproliferative Neoplasms (MPN). The pulldown will be a bespoke design targeting known mutations, this pulldown will be sequenced and analysed to inform prevalence of mutations and to inform to the possibility of use as a diagnostic tool.

  Study EGAS00001000406

• Scywalker: scalable end-to-end data analysis workflow for nanopore single-cell transcriptome sequencing

  Existing nanopore single-cell data analysis tools showed severe limitations in handling current data sizes. We developed novel scalable methods for cell barcode demultiplexing and single-cell isoform calling and quantification and incorporated these in an easily deployable package called scywalker.

  Study EGAS50000000537

• Mutational context and diverse clonal development in early and late bladder cancer

  Bladder cancer shows multiple recurrences probably originating from a malignant field disease in the mucosa. Deep sequencing was used on a series of tumors to look into the clonal composition, mutational spectrum in non-aggressive tumors, and mutational context.

  Study EGAS00001000641

• ICARUS-LUNG01-RNAseq

  Bulk RNA-seq was carried out on 20 pairs of frozen tumor biopsies. Differential gene expression (DGE) analyses was conducted, looking at the fold change of gene expression of matched on-T/BL samples in the overall population and, then, separately in responders and non-responders.

  Study EGAS50000000732

• CD4+ T cell subsets stratified by complement receptor type 2 (CR2) expression

  FACS-sorted CR2+ and CR2- naive and memory CD4+ T cells from healthy donors, plus CR2+ naive CD4+ T cells activated using CD3/CD28 beads, were analyzed ex-vivo. Exome-enriched RNA sequencing was carried out for all subsets.

  Study EGAS00001001870

• BLUEPRINT RNA-seq data for rare cells in the haematopoietic lineages, from adult and cord blood samples.

  RNA-seq data for rare cells in the haematopoietic lineages, from adult and cord blood samples.

  Study EGAS00001000284

• Human melanoma samples with and without resistance to BRAF inhibitor therapy

  Human melanoma samples were collected pre, on, and progression on BRAF inhibitor therapy. RNA was extracted and run on RNA-seq. This has provided insights into different categories of BRAF inhibitor resistance mechanisms.

  Study EGAS00001000992

• FRCC_Exome_sequencing

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from FRCC patients. one lane of Illumina Hiseq sequencing will be performed on the resulting exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes.

  Study EGAS00001000176

• Whole exome sequencing of trio with primary immunodeficiency (IL2RB)

  A novel homozygous mutation in human IL2RB results in decreased IL-2RB protein expression and dysregulated IL-2/15 signaling. This hypomorphic mutation leads to decreased regulatory T cell frequency and abnormal NK cell compartment, with clinical manifestations of autoimmunity and susceptibility to CMV.

  Study EGAS00001003599

• Whole exome sequencing of Finnish hereditary breast cancer families

  A remarkable proportion of factors causing genetic predisposition to breast cancer (BC) are unknown in non-BRCA1/2 families. Exome sequencing was performed for 13 high-risk Finnish hereditary breast and/or ovarian cancer (HBOC) families to detect variants contributing to BC susceptibility

  Study EGAS00001001835

• Targeted_sequencing_of_cylindroma_patients

  Patients with cylindroma show multiple large tumours on the scalp and forehead. These large tumours will allow us to look at clonality within a tumour. We wish to asses the mutational load and diversity within and across tumours as well as compare with perilesional skin.

  Study EGAS00001002708

• The_contribution_of_POT1_variants_to_sporadic_melanoma_development

  A case-control series of melanoma cases from Leeds, UK have been sequenced in the Fluidigm platform to identify genetic variants associated with sporadic melanoma development. Samples in which potentially contributing variants have been detected are being sequenced in an orthogonal platform for variant confirmation.

  Study EGAS00001001964

• The genomic landscape of germinal center derived B-cell lymphomas other than follicular, diffuse-large B-cell and Burkitt lymphom

  As part of the ICGC, the ICGC MMML-Seq project performed whole genome sequencing and RNA sequencing of germinal center derived B-cell lymphoma. Analyses were performed in concordance with the guidelines of the ICGC.

  Study EGAS00001002422

• Isotype_resolved_sequencing_of_B_cell_receptor__in_health_and_disease

  Sequencing of B-cell receptor repertoires in healthy individuals and patients with chronic lymphocytic leukemia. 1) 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 please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001002634

• Tumor intrinsic and extrinsic mechanisms of response and resistance to blinatumomab in relapsed/refractory acute lymphoblastic leukemia

  Key Points• Multiple mechanisms of acquired CD19 mutations and splicing contribute to CD19 loss and relapse to blinatumomab.• Identification of CD19 ex2part levels represents a new biomarker predictive of resistance or likely failure of blinatumomab

  Study EGAS00001004027

• Breast implant-associated anaplastic large cell lymphoma shallow whole genome sequencing for copy number analysis and Whole exome sequencing data.

  Breast implant-associated anaplastic large cell lymphoma (BIA-ALCL) shallow whole genome sequencing of 29 BIA-ALCL patients for copy number analysis and 24 Alk-negative ALCL samples as control cohort. 7 Whole exome sequencing BIA-ALCL samples.

  Study EGAS00001003962

• Targeted sequencing about core genes involved in telomere biology in colorectal cancer patients

  We sequenced the coding exons of core genes involved in telomere maintenance using peripheral blood DNA of 192 CRC patients. The primary sequencing data were generated by using Ion Torrent Personal Genome Machine® (PGM™) platform (Life Technologies, Carlsbad, CA, USA).

  Study EGAS00001002977

• Cell type-specific transcriptomics of esophageal adenocarcinoma as a scalable alternative for single cell transcriptomics

  We developed a protocol for the separation of esophageal carcinoma tissue into leukocytes (using CD45 as a marker), epithelial cells (EpCAM), and fibroblasts (two out of PDGFRA, CD90, anti-fibroblast) by fluorescence-activated cell sorting followed by RNA-sequencing

  Study EGAS00001004053

• Efficacy of CDK4/6i in preclinical models of malignant pleural mesothelioma

  Assessment of antitumor activity of CDK4/6 inhibitors using in vitro and in vivo preclinical models of MPM using RNA-sequencing. We also include the genomic characterization (whole exome sequencing) of patient-derived cell lines used in the in vitro experiments.

  Study EGAS00001005352

• Nucleosome footprinting in plasma cell-free DNA for diagnosis of ovarian cancer

  Fragmentation patterns of plasma cell-free DNA (cfDNA) are known to reflect nucleosome positions of cell types contributing to cfDNA. Based on cfDNA fragmentation patterns, the deviation in nucleosome footprints was quantified between diagnosed ovarian cancer patients and healthy individuals.

  Study EGAS00001005361

• RNA sequencing of multiple myeloma identifies genes dysregulated by structural variants.

  Multiple myeloma is a disease of structural changes brought about by copy number abnormalities and translocations. Many of these changes result in super-enhancers being placed next to key oncogenes. Here, we have investigated which genes are commonly dysregulated by these changes.

  Study EGAS00001003411

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

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

  Study EGAS00001006143

• Placental multi-omics data-mining in Intra-Uterine Growth Restriction

  Methylomics and transcriptomics array-based analysis of 36 placentas: 28 with IUGR (Intra-Uterine Growth Restriction) vs. 8 control pregnancies. Methylomics data were obtained using Illumina HumanMethylation-450k microarrays. Transcriptomics data were obtained using Illumina HumanHT-12 v4 Expression BeadChips.

  Study EGAS00001003467

• Single cell RNA sequencing of colorectal cancer patients (KUL3/KUL5)

  Libraries for scRNA-seq were generated using the Chromium Single Cell 3′ or 5′ library and Gel Bead & Multiplex Kit from 10x Genomics. Aimed to profile 5000 cells per library (if sufficient cells were retained during dissociation).

  Study EGAS00001006049

• Single cell analyses of transcriptome and epigenome in neuroblastoma infiltrated bone marrow

  We report transcriptional and genome-wide ATAC-seq analyses at single cell resolution of 16 bone marrow samples with and without neuroblastoma infiltration. Our samples span across several neuroblastoma models, including MYCN amplified, ATRX mutated, and sporadic (lacking either alteration).

  Study EGAS00001006106

• Whole-Transcriptomic Profiling of Sorted Human Renal Cell Carcinoma Immune Populations

  It is poorly understood how the tumor immune micro-environment influences disease progression in renal cell carcinoma (RCC). Here we performed whole-transcriptomic profiling of immune cell populations which were derived from RCC patients representing distinct flow-sorted immune lineages.

  Study EGAS00001006593

• A living biobank of patient-derived ductal carcinoma in situ Mouse-INtraDuctal xenografts identifies factors associated with risk of invasive progression

  Create a living biobank of patient-derived ductal carcinoma in situ (DCIS) Mouse-INtraDuctal (MIND) xenografts to find factors explaining invasive growth. Samples exist of both primary and pdx samples. Invasive growth was scored in the pdx.

  Study EGAS00001006554

• Transcriptomic analysis of TFEB knockdown in LT-HSC.

  Long-term hematopoietic stem cells (LT-HSC) were sorted from human cord blood and cultured overnight before transduction with lentiviral vectors overexpressing an shRNA against Renilla (shCTRL) or TFEB (shTFEB). Six days later, mCherry+ transduced cells were sorted for RNA extraction and sequencing.

  Study EGAS00001004967

• Advanced molecular neuropathology to increase diagnostic accuracy in pediatric neurooncology

  To assess their utility in routine neuropathology, we prospectively integrated DNA methylation-based CNS tumor classification and targeted gene panel sequencing of tumor and constitutional DNA with blinded neuropathological reference diagnostics for a population-based cohort of > 1,200 newly-diagnosed pediatric patients.

  Study EGAS00001006680

• Molecular evolution of classic Hodgkin lymphoma revealed through whole genome sequencing of Hodgkin and Reed Sternberg cells

  Here we leveraged whole genome structural variant copy number analysis to report the first whole genome sequencing landscape of HRS cells and reconstruct the chronology and likely etiology of pathogenic events prior to the clinical diagnosis of cHL.

  Study EGAS00001006884

• Gtag&T single-cell genome and transcriptome data

  This submission contains single-cell genome and transcriptome data that is used for the following manuscript: https://doi.org/10.1101/2023.01.13.521174. All Illumina data deposited here is retrieved from HCC38(BL) cell lines and a melanoma PDX model as described in the paper.

  Study EGAS00001007043

• WES on tumor DNA and germline DNA in pediatric cancer

  This dataset contains whole exome sequencing (WES) data from tumor DNA samples of various pediatric cancer entities. Files are provided in fastq format. Samples were sequenced on a Novaseq6000 or Hiseq2500 (Illumina). Data analysis is available at https://github.com/rmvpaeme/sWGS_pediatric_cancer.

  Study EGAS00001005429

• A novel Patient-Derived 3D Model Recapitulates Mantle Cell Lymphoma Lymph Node Signaling, Immune Profile and in vivo Ibrutinib Responses

  RNA-seq data from CD20+ sorted cells obtained from peripheral blood Mantle Cell Lymphoma patients. These samples were unstimulated after thawing or stimulated during 7 days in culture as described in Araujo-Ayala F et. al.

  Study EGAS00001006964

• Genomic profiling of Rare Tumors

  Utilizing the rare and unique patient samples provided by Pattern Medicine, LLC, MD Anderson will molecularly characterize rare cancer samples, and potentially generate a collection of preclinical models to enable identification of novel therapeutic targets and concepts, as well as evaluation of innovative treatment strategies.

  Study EGAS00001007103