14971 results for "cancer studies using rna-seq"

in 19.88 milliseconds.

• A Genome-Wide Association Study of Lung Cancer Risk

  Three genetic loci for lung cancer risk have been identified by genome-wide association studies (GWAS), but inherited susceptibility to specific histologic types of lung cancer is not well established. We conducted a GWAS of lung cancer and its major histologic types genotyping 515,922 single nucleotide polymorphisms (SNPs) in 5,739 incident lung cancer cases and 5,848 controls from one population-based case-control study and three cohort studies. Results were combined with summary data from 10 additional studies for a total of 13,300 cases and 19,666 controls of European descent. Four studies also provided histology data for replication resulting in 3,333 adenocarcinomas (AD), 2,589 squamous cell carcinomas (SQ), and 1,418 small cell carcinomas (SC). In analyses by histology, rs2736100 (TERT) on chromosome 5p15.33, was associated with risk of adenocarcinoma (OR=1.23, 95%CI=1.13-1.33, P=3.02x10-7), but not other histologic types (OR=1.01, P=0.84, and OR=1.00, P=0.93, for SQ and SC, respectively). This finding was confirmed in each replication study and overall meta-analysis (OR=1.24, 95%CI=1.17-1.31, P=3.74x10-14 for AD and OR=0.99, P=0.69 and OR=0.97, P=0.48, for SQ and SC, respectively). Other previously reported association signals on 15q25 and 6p21 were also refined, but no additional loci reached genome-wide significance. In conclusion, a lung cancer GWAS identified a distinct hereditary contribution to adenocarcinoma. Note: The lung study dataset to be released to dbGaP and caBIG excludes 47 individuals from the PLCO cohort who consented to participate only in cancer research projects and 22 individuals because of updated QC. Thus, the released dataset is derived from 11517 subjects, 5699 cases and 5818 controls. After the updated QC, the dataset to be released to dbGaP and caBIG includes 506062 SNPs.

  Study phs000336

• The Genetics of Lung Cancer Susceptibility in Smokers

  Over 85% of all patients diagnosed with lung cancer report a history of tobacco use, though only 10% of tobacco smokers eventually develop lung cancer. Epidemiologic studies have shown that family members of patients with lung cancer have a higher risk of developing lung cancer than controls. In an effort to identify variants associated with tobacco induced lung cancer, we have sequenced germline DNA from affected and unaffected members of families with strong histories of tobacco related lung cancer.

  Study phs000728

• Transcriptomic Characterization of Human Innate T Cells

  We performed low input RNA-seq and single-cell RNA-seq on 7 lymphocyte populations with the objective of finding the common transcriptional programs shared among innate T cells. In brief, we drew blood from healthy donors and isolated CD4+ T cells, CD8+ T cells, Natural Killer cells, invariant natural killer T (iNKT) cells, mucosal-associated invariant T (MAIT) cells, and two γδ T cell populations: Vδ1 and Vδ2. We performed low input RNA-seq on samples with 1000 cells each, for 6 healthy individuals, in duplicate. We performed single-cell RNA-seq with DNA-barcoded hashing antibodies to identify the cell type of origin for each cell. We found a common transcriptional program across lymphocytes that is gradually turned on as lymphocytes have a more "innateness" state, promoting effector functions and sacrificing proliferative capacity. Additionally, we performed low input RNA-seq for Vδ3-expressing γδ T cells and δ/αβ T cells for one healthy individual in duplicate (1000 cells per sample). This revealed δ/αβ T cells are transcriptionally more adaptive-like and Vδ3 more innate-like.

  Study phs002007

• This dataset includes FASTQ for single-nucleus RNA-seq of normal controls, and multiple system atrophy (MSA) or Parkinson's disease (PD) patients.

  The dataset includes more than 130k nuclei isolated using 10x Genomics Chromium Next GEM Single Cell 3' Reagent Kits v3.1. In total, 30 samples are included from 10 controls, 8 MSA (including one sample that was omitted during QC), or 12 PD patients. Samples were sequenced on Illumina Novaseq 6000 or NextSeq 550 instruments.

  Dataset EGAD50000002041

• RNA-seq FASTQ files studied in Generation of hypoimmunogenic induced pluripotent stem cells by CRISPR-Cas9 system and detailed evaluation for clinical application

  This data set contains 12 paired fastq files (RNA-seq) from one wild-type iPS cell, two HLA-KO iPS clones and three CD14+ monocytes differentiated from them. The RNA-seq libraries were generated with Illumina TruSeq Stranded Total RNA library prep kit. The libraries were sequenced with Illumina NovaSeq 6000 in paired-end mode.

  Dataset EGAD50000001700

• mapped Bam files from whole transcriptome RNA-seq

  In this study we characterized genomic alterations in two to five metachronous bladder tumors from 29 patients initially diagnosed with early stage disease. Fourteen patients (32 tumors) had non progressive disease (NPD) and 15 patients (34 tumors) had progressive disease (PD). Whole exome sequencing (WES, ~50x mean read depth and whole transcriptome RNA-seq was performed (RNA was not advalible for 4 tumors). Data provided here consist of 71 mapped Bam files form whole transcriptome RNA-seq.

  Dataset EGAD00001002718

• unmapped Bam files from whole transcriptome RNA-seq

  In this study we characterized genomic alterations in two to five metachronous bladder tumors from 29 patients initially diagnosed with early stage disease. Fourteen patients (32 tumors) had non progressive disease (NPD) and 15 patients (34 tumors) had progressive disease (PD). Whole exome sequencing (WES, ~50x mean read depth and whole transcriptome RNA-seq was performed (RNA was not advalible for 4 tumors). Data provided here consist of 71 unmapped Bam files form whole transcriptome RNA-seq.

  Dataset EGAD00001002717

• Human Epidermis scRNA

  Single cell RNA-seq analysis of human skin.

  Dataset EGAD00010001620

• Exome reads and RNA-seq

  Exome sequencing for 26 patients with matched blood RNA-seq for 41 patients

  Dataset EGAD00001002722

• GCLJ RNA-Seq data

  RNA-Seq data from 6 Giant Cell Lesions of the Jaw (GCLJ) samples.

  Dataset EGAD00001004320

• nccRCC RNA-Seq data of consented samples

  nccRCC RNA-Seq data of consented samples

  Dataset EGAD00001001022

• PCF SELECT data on liquid biopsy samples from 3 clinical studies on prostate cancer patients

  Dac EGAC50000000758

• Combinatorial CRISPR screen identifies fitness effects of paralogues FAM50A and FAM50B

  Genetic redundancy has evolved as a way for human cells to survive the loss of genes that are single copy and essential in other organisms, but also allows tumours to survive despite having highly rearranged genomes. In this study we CRISPR screen 1,191 gene pairs, including paralogues and known and predicted synthetic lethal interactions to identify 105 gene combinations whose co-disruption results in a loss of cellular fitness. 27 pairs influence fitness across multiple cell lines including the paralogues FAM50A/FAM50B, two genes of unknown function. Silencing of FAM50B occurs across a range of tumour types and in this context disruption of FAM50A reduces cellular fitness whilst promoting micronucleus formation and extensive perturbation of transcriptional programmes. This dataset includes CRISPR screening of cancer cell lines, RNA sequencing studies of cancer cell lines and also data from the sequencing of tumour xenografts collected from mice.

  Dataset EGAD00001006648

• All available datasets of DEEP

  All available datasets of DEEP. There are several Reference Epigenomes available. For metadata check out www.deep.dkfz.de One reference epigenome represents a set of 6 ChIP-Seqs, WGBS, RNA-Seq, smallRNA-Seq and sometimes DNase1 and/or NOME-Seq.

  Study EGAS00001001608

• StemNet - in vitro differentiation of human hepatocytes

  Integrative epigenomic and transcriptomic characterization of hepatocyte-like cells differentiated in vitro from human induced pluripotent stem cells in comparison with primary human hepatocytes. This study comprises single cell RNA-seq, bulk mRNA-seq, ATAC-seq and RRBS.

  Study EGAS00001004201

• Characterization of a Metastatic Cervical Cancer Patient and HPV18 Integration Using Next Generation Sequencing

  In this study, we used shallow whole genome, exome, and RNA sequencing to genomically and transcriptomically characterize a cervical squamous carcinoma lesion metastatic to the lung and to detect and analyze HPV infection in the same sample.

  Study phs000628

• Extracellular RNA Profiling of Serum, Plasma, and Urine of Healthy Subjects

  This study was conducted to generate a reference dataset of extracellular RNA (exRNA) from standard human biofluids. Small RNA-seq data was obtained from plasma, serum, and urine of healthy subjects.

  Study phs003054

• Genomic Profiling Reveals Spatial Intra-tumour Heterogeneity in Follicular Lymphoma

  Follicular lymphoma (FL) is an incurable indolent non-Hodgkin’s lymphoma (NHL) that behaves heterogeneously and is synonymous with the reciprocal translocation t(14;18)(q32;q21), leading to aberrant constitutive over-expression of BCL2 [ref]. High risk groups with poor overall survival include patients that transform to a high grade lymphoma, most commonly diffuse large B cell lymphoma (DLBCL) or progress early (within 2 years) of receiving treatment. Recently several studies have shed light on the diverse genomic landscape of FL, with frequently mutated genes including those involved in chromatin remodelling, (CREBBP, KMT2D, EZH2, EP300), immune modulation (TNFRSF14), JAK-STAT (STAT6, SOCS1), NF-ĸB (CARD11, MYD88, TNFAIP3) and mTORC1 signalling (RRAGC) [ref]. To date, the majority of these studies have either focussed on inter-patient genetic heterogeneity or established the extent of clonal heterogeneity as a patient’s tumour evolves over time. Furthermore, these temporal studies have alluded to the existence of a tumour-repopulating population (referred to as the common progenitor cell (CPC)) that evades treatment and acts as a reservoir, seeding each subsequent relapse and transformation event. Although these previous studies have illuminated the longitudinal clonal dynamics that occur in FL, our understanding of the degree of spatial or intra-tumour heterogeneity (ITH) that exists within an individual patient thus far remains limited. Earlier studies have predominantly focused on differences in cytological grade and immunophenotype between spatially separated lymph nodes and bone marrow, the most common site of extra-nodal involvement in FL, with genomic profiling restricted to examining somatic hypermutation patterns in IgVH genes [ref]. In contrast next generation sequencing has been increasingly utilised in solid organ malignancies to derive comprehensive genomic profiles from spatially separated sites. The seminal study by Gerlinger et al revealed profound differences in the genetic make-up between individual primary and metastatic sites of renal cell carcinoma [ref]. Significant heterogeneity has since been demonstrated both between and within lesions in the same patient in lung, pancreas and breast cancer with presumed driver mutations distributed within the “branches” of the evolutionary phylogenetic tree, suggesting that a single biopsy is incapable of capturing the full genomic heterogeneity of an individual’s malignancy [ref]. This geographical heterogeneity not only adds to the diverse pool of tumour subclones that may contribute to drug resistance mechanisms but importantly, presents a major obstacle for precision-based approaches focussed on targeting specific lesions within a single biopsy. In FL, the exponential increase in clinical trials using novel agents such as EZH2, PI3K and BTK inhibitors reflects this shift in cancer care and along with the development of molecular prognostic scores such as the m7-FLIPI highlights the clinical need to accurately define genomic alterations with clinical relevance. As the majority of FL patients manifest disseminated tumour involvement, we sought to uncover the extent and clinical importance of spatial heterogeneity in FL by comprehensively genetically profiling 22 synchronously removed spatially separated biopsies from 9 patients. Using a combination of whole exome and targeted deep sequencing, our results inferred the complex subclonal architecture within these tumours and the mutational differences between anatomical sites, demonstrating cases with significant intrinsic genetic diversity.

  Study EGAS00001002492

• Human adipocyte bulk RNA-seq dataset

  The dataset contains raw RNA-seq data of human adipocytes from 13 individuals.

  Dataset EGAD00001008335

• RNA-Seq for academic use only

  RNA-Seq transcriptome data is only for academic use.

  Dataset EGAD00001009675

• RNA-seq for IgA BMPC project

  7 RNA-seq samples in total: CD19n_IgAn (x2) , CD19n_IgAp (x2) , CD19p_IgAn (x1), CD19p_IgAp (x2)

  Dataset EGAD00001006862

• A Whole Genome Association Scan for Myopia and Glaucoma Endophenotypes using Twin Studies

  Myopia and glaucoma are highly prevalent ophthalmic disorders worldwide and contribute significantly to ocular morbidity. There is substantial evidence that genetic factors play a significant role in the development of non-syndromic myopia and glaucoma. We propose to perform mapping studies for well-characterized twin populations in the United Kingdom and Australia in order to ultimately identify implicated genes for these disorders and related ocular parameters. This will provide a fundamental molecular understanding of how these disorders develop, and may lead to directed physiologic (i.e. pharmacologic, gene therapy) interventions. Our aim is to dissect the genetic basis of the eye disorders myopia and glaucoma. Instead of limited analyses of the trait/disease in a dichotomous manner, we are using continuous phenotypes of measures of refraction and intermediate phenotypes of glaucoma to analyze quantitative traits in unselected population samples of volunteer twins. Achievement of this goal requires cooperative efforts and large sample sizes. Thus, we have created an international collaboration of large complementary studies.

  Study phs000142

• Whole genome sequencing data of pediatric B-other subtype acute lymphoblastic leukemia

  For a long time, approximately 70% of childhood B-ALL cases could be classified routinely, and the remaining 30% were classified into the “B-other” group lacking the known genetic features. However, more recently, new genomic tools have uncovered new subtypes among the B-other groups. Approximately 10% of B-ALL cases lack the recurrent genetic abnormalities, and are referred as "B-other". They are typically more heterogeneous than other subtypes of B-ALL, and their prognoses are more variable. In a more recent update of the B-ALL classification, 27 subtypes were identified (Arber et al., 2022). The identification of some of these subtypes is dependent on NGS methods, such as RNA sequencing, which are not routinely used in all clinical laboratories. For example, ETV6::RUNX1-like and DUX4-rearranged subtypes have been identified using RNA sequencing. For this study, subtype predictions for some of the cases is acquired from ALLIUM (Krali et al., NPJ Precis Oncol., 2023) and ALLCatchR (Beder et al., Blood, 2022) based on the RNA-seq profiles.

  Study EGAS50000001497

• RNA Seq OMELib

  The transcriptional landscape of haematopoietic cells will be characterized by RNA Seq following amplification of RNA/cDNA and preparation of libraries by PTA(primary template-directed amplification). Samples have been sourced from the Cambridge Biobank.

  Dataset EGAD00001015252

• Single-cell RNA-seq of PBMC from 2 patients iGRAN-Low and 2 patients iGRAN-High

  Single-cell RNA-seq of PBMC from 2 patients iGRAN-Low and 2 patients iGRAN-High [Publication title] CXCL8 secreted by immature granulocytes inhibits wildtype hematopoiesis in chronic myelomonocytic leukemia

  Study EGAS50000000556

• Longitudinal RNA-seq (whole blood) in a twin cohort

  The dataset consists of 232 RNA-seq samples (whole blood) obtained from healthy female from the TwinsUK adult registry cohort. The samples were obtained at two time points separated on average by 22 months.

  Study EGAS00001001763

• RNA-seq data: Histone mutations in human Pre-Leukemic HSC and AML

  RNA-seq data from TEX cells transduced with HIST1H3H WT, HIST1H3H K27M, HIST1H3F WT, HIST1H3F K27I and Luc2 control in triplicate. In addition, RNA-Seq was performed on untransduced TEX cells. Libraries [rRNA-depleted stranded (HMR)] were sequenced on an Illumina Hiseq 4000 platform to generate 100 bp paired-end reads.

  Dataset EGAD00001004437

• Resilience and Susceptibility Patterns in the Viral Immune Response Using RNA-Seq (ReSP VIRUS Study)

  This is a cross sectional study to investigate the relationship between nasal mucosa gene expression and clinical outcomes in infants with critical Respiratory Syncytial Virus (RSV) infection. We collected nasal mucosa samples from infants admitted to the pediatric intensive care unit with polymerase chain reaction confirmed RSV bronchiolitis. Samples were obtained by mucosal scrape biopsy of the inferior turbinate using a sterile plastic curette and bulk RNA-sequencing of mRNA was performed. Clinical data was extracted from the electronic health record including: demographics, medical history, duration of symptoms, time from admission to sample collection, hospital and intensive care unit length of stay, and type and duration of respiratory support.

  Study phs003053

• Transcriptomics for LUNG-NSCLC2 cohort

  The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes patients with non-small cell lung cancer who had surgical resection. This is a subcohort of the EORTC SPECTAlung study. This dataset contains transcriptomics data processed with the STAR pipeline. Two sequencing kits were employed: Roche KAPA for high-quality RNA samples and Takara SMART-Seq Stranded for samples with limited RNA quantities.

  Dataset EGAD50000002236

• Translation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma - RNA-Seq

  This study aims to investigate the dysregulation of RNA translation and identify functional non-canonical open reading frames (ORFs) as potential targets for medulloblastoma treatment. The study involves ribosome profiling and RNAseq of medulloblastoma tissues and cell lines to observe the translation of non-canonical ORFs. Multiple CRISPR-Cas9 screens will be used to identify functional non-canonical ORFs implicated in medulloblastoma cell survival.

  Dataset EGAD00001011192

• University of Hull

  Tumour Regulatory Molecules in Early Pancreatic Cancer Detection (TEM-PAC) and EARLY DIAgnosis of PAncreatic Cancer by combined proteomics and genomics testing of pancreatic cyst fluid (DIA-PAC) studies.

  Dac EGAC50000000402

• A phase II trial of the aurora kinase A inhibitor alisertib for patients with castration resistant and neuroendocrine prostate cancer: efficacy and biomarker evaluation

  Neuroendocrine prostate cancer (NEPC) is an aggressive variant of prostate cancer that may develop de novo or as a mechanism of treatment resistance. N-myc is capable of driving NEPC progression. Alisertib inhibits the interaction between N-myc and its stabilizing factor Aurora-A, inhibiting N-myc signaling, and suppressing tumor growth. In this single arm, multi-institutional open label phase 2 clinical trial of alisertib, sixty men were treated with alisertib 50mg twice daily for 7 days every 21-days. Eligibility included metastatic prostate cancer and at least one: small cell neuroendocrine morphology; ≥50% neuroendocrine marker expression; new liver metastases without PSA progression; elevated serum neuroendocrine markers. The primary endpoint was six-month radiographic progression free survival. Pre-treatment biopsies were evaluated by whole exome and RNA-seq.

  Study phs001666

• International Standards for Cytogenomic Arrays

  The International Standards for Cytogenomic Arrays (ISCA) Consortium is a rapidly growing group of clinical cytogenetics and molecular genetics laboratories committed to improving quality of patient care related to clinical genetic testing using new molecular cytogenetic technologies including array comparative genomic hybridization (aCGH) and quantitative SNP analysis by microarrays or bead chip technology. The ISCA Consortium is now working with the sequencing community to extend the goals of standardization, collaboration, and data sharing. To reflect this combined effort, we are becoming ICCG, or the International Collaboration for Clinical Genomics. Efforts of the Consortium include: Clinical Utility: The ISCA Consortium has made recommendations regarding the appropriate clinical indications for cytogenetic array testing (Miller et al. AJHG 2010, PMID: 20466091). Currently, discussions are focused on pediatric applications for children with unexplained developmental delay, intellectual disability, autism and other developmental disabilities. A separate committee has been developed to address appropriate cancer genetic applications (http://www.urmc.rochester.edu/ccmc/). Evidence-based standards for cytogenomic array design: The Consortium will develop recommendations for standards for the design, resolution and content of cytogenomic arrays using an evidence-based process and an international panel of experts in clinical genetics, clinical laboratory genetics (cytogenetics and molecular genetics), genomics and bioinformatics. This design is intended to be platform and vendor-neutral (common denominator is genome sequence coordinates), and is a dynamic process with input from the broader genetics community and evidence-based review by the expert panel (a Steering Committee with international representation). Public Database for clinical and research community: It is essential that a publicly available database be created and maintained for cytogenetic array data generated in clinical testing laboratories. This will be integrated into the current dbGaP database at NCBI/NIH and released through dbVar, and curated by a committee of clinical genetics laboratory experts. The very high quality of copy number data (i.e., deletions and duplications) coming from clinical laboratories combined with expert curation will produce an invaluable resource to the clinical and research communities. Standards for interpretation of cytogenetic array results: Using the ISCA Database, along with other genomic and genetics databases, the Consortium will develop recommendations for the interpretation and reporting of pathogenic vs. benign copy number changes as well as imbalances of uncertain clinical significance. Membership in the ISCA Consortium is open to all individuals and laboratories involved in cytogenetic array testing who are committed to free data sharing and to participation in a process to develop evidence-based standards and guidelines to improve patient care. ISCA is available through dbVar: http://www.ncbi.nlm.nih.gov/dbvar/studies/nstd37/ http://www.ncbi.nlm.nih.gov/dbvar/studies/nstd75/ http://www.ncbi.nlm.nih.gov/dbvar/studies/nstd45/ http://www.ncbi.nlm.nih.gov/dbvar/studies/nstd101/

  Study phs000205

• scRNA-seq of monochorionic dizygotic twin chimera PBMC

  Single cell RNA-seq of PBMC of monochorionic dizygotic twin chimeras. 10x chromium v3.1 was used to generate barcoded scRNA library.

  Study EGAS50000000097

• SF11612 scRNA-Seq Recurrent oligodendroglioma

  Single Cell RNA seq from Recurrent oligodendroglioma sample. Gender Male Age 67. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference through Cellranger count (10xGenomics.)

  Dataset EGAD00001005411

• RNAseq following LDC67 or JQ1 treatment

  For RNA-Seq total RNA was isolated following LDC67 or JQ1 treatment. 3’RNAseq libraries were prepared with QUANT SEQ FWD 3´mRNA-Seq Kit (Lexogen, Austria), sequenced on an Illumina HiSeq 4000

  Dataset EGAD00001003464

• SF9259S snRNA-Seq Primary GBM

  Single Nuceli Primary GBM 73 Male. Single Nuclei RNA seq from high grade primary glioma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference.

  Dataset EGAD00001005428

• Single-cell RNA-seq cases

  Single-cell RNA-seq cases (Tumor and adjacent tissue)

  Dataset EGAD00001008835

• Asan Medical Center Data Access Committee

  This DAC is responsible for reviewing and approving data access requests to protect the sensitive information of patients. The dataset includes RNA-seq data from CRLM patients treated with FOLFOX, bevacizumab, and atezolizumab, and supports research in gene expression analysis and therapeutic response. Data access requests require an approved ethical research plan, limited to projects related to cancer biology and therapy development.

  Dac EGAC50000000439

• RNA-Seq data for paper titled 'Genomic Landscape of Pediatric Myelodysplastic Syndromes'

  When available (25 primary MDS, 12 MDS/MPN, and 6 AML-MRC cases), high quality RNA (stranded-total) was submitted for RNA-seq. RNA was extracted from bulk myeloid cells which was used as the tumor population. Files uploaded are mapped BAM files.

  Dataset EGAD00001003782

• Diffuse Intrinsic Pontine Glioma

  This study contains DNA and RNA sequencing data for 5 DIPG patients. All patients have tumor DNA data, 4 have matched normal DNA data and 3 have tumor RNA seq data

  Study EGAS00001006353

• HipSci HumanHT_12v4 Expression BeadChip analysis-Healthy volunteers

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Expression analysis using the Illumina HumanHT -12 Expression BeadChip on iPS cells generated from skin biopsies from healthy volunteers.

  Study EGAS00001000867

• Low_depth_whole_genome_sequencing_across_multiple_isolated_populations

  Isolated populations have unique population genetics characteristics that can help boost power in genetic association studies for complex traits. Leveraging these advantageous characteristics requires an in-depth understanding of parameters that have shaped sequence variation in isolates. This study performs a comprehensive investigation of these parameters using low-depth whole genome sequencing (WGS) across multiple isolates.

  Study EGAS00001001597

• HipSci-Whole Exome sequencing-healthy volunteers

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sup-study we perform whole exome sequencing using Agilent whole exome pulldown method on iPS cells generated from skin biopsies from healthy volunteers.

  Study EGAS00001000592

• Three-dimensional patient-derived models of glioblastoma retain intra-tumoral heterogeneity

  The intra- and inter- tumoral heterogeneity of glioblastoma represents a significant therapeutic challenge, as well as difficulty in generating reliable models for in vitro studies. Here, we quantify the tumor cell composition from matched patient-derived neurospheres (PDN) and organoids (PDO) established from the same primary tumor using a series of multi-omic interrogations, relative to primary tissue

  Study EGAS00001008023

• RNA-seq derived from metastatic Castration-Resistant Prostate Cancer

  Patients with progressive, metastatic castration-resistant prostate cancer (mCRPC) underwent metastatic tumor biopsy. 118 total samples including 14 paired samples (baseline and later progression). Various organ sites including soft tissue & bone were present. Published in DOI: 10.1200/JCO.2017.77.6880 Journal of Clinical Oncology 36, no. 24 (August 20, 2018) 2492-2503.

  Dataset EGAD00001008991

• Exome sequencing of paired primary tumor and metastatic breast cancer

  Prognosis evaluation of advanced breast cancer and therapeutic strategy are mostly based on clinical features of advanced disease and molecular profiling of the primary tumor. Very few studies have evaluated the impact of a prospective documentation of metastatic subtyping. The genomic landscape of metastatic breast cancer has mostly been described in very advanced, pretreated disease, limiting its transferability to clinical use.

  Study EGAS00001004578

• Mutational landscapes of primary triple negative breast cancers - RNA seq

  Mutational landscapes of primary triple negative breast cancers - RNA seq

  Dataset EGAD00001000132

• Mapped RNA-Seq data

  Mapped whole transcriptome RNA-Seq data from 476 human samples of early stage urothelial carcinoma.

  Dataset EGAD00001001939

• NKI-AvL OpACIN RNA-seq of stage III melanoma patients

  The dataset “NKI-AvL OpACIN RNA-seq of stage III melanoma patients" includes 18 FASTQ files from single-end total RNA sequencing on Illumina HiSeq2500 for 18 stage III melanoma patients.

  Dataset EGAD00001004216