10158 results for "cancer rna-seq"

in 60.28 milliseconds.

• Genome and transcriptome sequence data from a metastatic breast cancer patient

  Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003741

• Genome and transcriptome sequence data from a metastatic breast cancer patient

  Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003743

• Genome and transcriptome sequence data from a bilateral breast lobular cancer patient

  Genome and transcriptome sequence data from a bilateral breast lobular cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003711

• Genome and transcriptome sequence data from a metastatic breast cancer patient

  Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004597

• Genome and transcriptome sequence data from a metastatic breast cancer patient

  Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004613

• Genome and transcriptome sequence data from a metastatic pancreatic cancer patient

  Genome and transcriptome sequence data from a metastatic pancreatic cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004604

• Genome and transcriptome sequence data from a metastatic colorectal cancer patient

  Genome and transcriptome sequence data from a metastatic colorectal cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004665

• Genome and transcriptome sequence data from a metastatic breast cancer patient

  Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004707

• Genome and transcriptome sequence data from a metastatic breast cancer patient

  Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004704

• Genome and transcriptome sequence data from a metastatic breast cancer patient

  Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004703

• Genome and transcriptome sequence data from a metastatic breast cancer patient

  Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004701

• Genome and transcriptome sequence data from a metastatic breast cancer patient

  Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004698

• Genome and transcriptome sequence data from a metastatic colorectal cancer patient

  Genome and transcriptome sequence data from a metastatic colorectal cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004694

• Genome and transcriptome sequence data from a metastatic transverse colon cancer patient

  Genome and transcriptome sequence data from a metastatic transverse colon cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004691

• Genome and transcriptome sequence data from a metastatic breast cancer patient

  Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004687

• Genome and transcriptome sequence data from a metastatic breast cancer patient

  Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004686

• Genome and transcriptome sequence data from a metastatic pancreatic cancer patient

  Genome and transcriptome sequence data from a metastatic pancreatic cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004683

• Genome and transcriptome sequence data from a metastatic colorectal cancer patient

  Genome and transcriptome sequence data from a metastatic colorectal cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004646

• Genome and transcriptome sequence data from a metastatic breast cancer patient

  Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004713

• Genome and transcriptome sequence data from a metastatic breast cancer patient

  Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004710

• Genome and transcriptome sequence data from a metastatic pancreatic cancer patient

  Genome and transcriptome sequence data from a metastatic pancreatic cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004717

• Low coverage WGS from plasma DNA

  Low coverage whole genome sequencing plasma DNA from 50 male, 54 female non-cancer donors. For the analysis of nucleosomal positioning all data from the non-cancer controls were merged. Furthermore, two patients with metastasized breast cancer were sequenced on a NextSeq with higher depth.

  Dataset EGAD00001002215

• Genome and transcriptome sequence data from a primary unknown cancer patient

  Genome and transcriptome sequence data from a primary unknown cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001002550

• Genome and transcriptome sequence data from a metastatic colorectal cancer patient

  Genome and transcriptome sequence data from a metastatic colorectal cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001002588

• Genome and transcriptome sequence data from a metastatic colorectal cancer patient

  Genome and transcriptome sequence data from a metastatic colorectal cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001002575

• Genome and transcriptome sequence data from a metastatic colorectal cancer patient

  Genome and transcriptome sequence data from a metastatic colorectal cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001002573

• Genome and transcriptome sequence data from a metastatic colorectal cancer patient

  Genome and transcriptome sequence data from a metastatic colorectal cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001002571

• Genome and transcriptome sequence data from a metastatic endometrial cancer patient

  Genome and transcriptome sequence data from a metastatic endometrial cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001002568

• Genome and transcriptome sequence data from a metastatic colorectal cancer patient

  Genome and transcriptome sequence data from a metastatic colorectal cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001002598

• Genome and transcriptome sequence data from a metastatic breast cancer patient

  Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001002603

• Genome and transcriptome sequence data from a pancreatic cancer (likely PNET) patient

  Genome and transcriptome sequence data from a pancreatic cancer (likely PNET) patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001002607

• Genome and transcriptome sequence data from a metastatic breast cancer patient

  Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001002609

• Genome and transcriptome sequence data from a metastatic pancreatic cancer patient

  Genome and transcriptome sequence data from a metastatic pancreatic cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001002636

• Genome and transcriptome sequence data from a metastatic rectal cancer patient

  Genome and transcriptome sequence data from a metastatic rectal cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001002634

• Genome and transcriptome sequence data from a metastatic colon cancer patient

  Genome and transcriptome sequence data from a metastatic colon cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001002629

• Genome and transcriptome sequence data from a metastatic colorectal cancer patient

  Genome and transcriptome sequence data from a metastatic colorectal cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001002619

• Genome and transcriptome sequence data from a metastatic colorectal cancer patient

  Genome and transcriptome sequence data from a metastatic colorectal cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001002615

• Genome and transcriptome sequence data from a metastatic breast cancer patient

  Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004902

• Genome and transcriptome sequence data from a metastatic breast cancer patient

  Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004910

• Genome and transcriptome sequence data from a metastatic breast cancer patient

  Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004923

• Genome and transcriptome sequence data from a locally advanced breast cancer patient

  Genome and transcriptome sequence data from a locally advanced breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004897

• Genome and transcriptome sequence data from a metastatic pancreatic cancer patient

  Genome and transcriptome sequence data from a metastatic pancreatic cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004900

• Genome and transcriptome sequence data from a metastatic rectal cancer patient

  Genome and transcriptome sequence data from a metastatic rectal cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004918

• Genome and transcriptome sequence data from a metastatic breast cancer patient

  Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004915

• Genome and transcriptome sequence data from a metastatic breast cancer patient

  Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004914

• Genome and transcriptome sequence data from a metastatic pancreatic cancer patient

  Genome and transcriptome sequence data from a metastatic pancreatic cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004913

• Genome and transcriptome sequence data from a metastatic pancreatic cancer patient

  Genome and transcriptome sequence data from a metastatic pancreatic cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004912

• Genome and transcriptome sequence data from a metastatic colon cancer patient

  Genome and transcriptome sequence data from a metastatic colon cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004911

• Genome and transcriptome sequence data from a metastatic serous ovarian cancer patient

  Genome and transcriptome sequence data from a metastatic serous ovarian cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004909

• Genome and transcriptome sequence data from a metastatic breast cancer patient

  Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004908

• Genome and transcriptome sequence data from a metastatic pancreatic cancer patient

  Genome and transcriptome sequence data from a metastatic pancreatic cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004926

• Genome and transcriptome sequence data from a metastatic breast cancer patient

  Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004927

• Genome and transcriptome sequence data from a metastatic breast cancer patient

  Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004928

• Genome and transcriptome sequence data from a metastatic breast cancer patient

  Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004929

• Genome and transcriptome sequence data from a metastatic ovarian cancer patient

  Genome and transcriptome sequence data from a metastatic ovarian cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004930

• Genome and transcriptome sequence data from a oligometastatic colorectal cancer patient

  Genome and transcriptome sequence data from a oligometastatic colorectal cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004935

• The dataset for Genome-wide cell-free DNA fragmentation in patients with cancer

  The dataset for Genome-wide cell-free DNA fragmentation in patients with cancer includes 538 bam files from whole genome next-generation sequencing on the Illumina HiSeq2500. The samples analyzed include plasma samples from healthy individuals and patients with cancer.

  Dataset EGAD00001005339

• Genome and transcriptome sequence data from a metastatic breast cancer patient

  Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001005830

• Genome and transcriptome sequence data from a metastatic breast cancer patient

  Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001005832

• Genome and transcriptome sequence data from a metastatic unknown primary cancer patient

  Genome and transcriptome sequence data from a metastatic unknown primary cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001005845

• Genome and transcriptome sequence data from a metastatic breast cancer patient

  Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001005847

• Genome and transcriptome sequence data from a metastatic breast cancer patient

  Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001005860

• Genome and transcriptome sequence data from a large intestine-colon cancer patient

  Genome and transcriptome sequence data from a large intestine-colon cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001005885

• Genome and transcriptome sequence data from a metastatic adrenocortical cancer patient

  Genome and transcriptome sequence data from a metastatic adrenocortical cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001005897

• WES_localized non-small cell lung cancer (540 samples)_MDACC

  Whole exome sequencing of tumors and paired adjacent uninvolved tissues from 222 early stage NSCLC patients, in order to identify genomic drivers present in early-stage non-small cell lung cancer and determine the overall tumor mutational burden in early-stage non-small cell lung cancer.

  Dataset EGAD00001005956

• Matched_breast_cancer_fusion_gene_study

  Genomic libraries (500 bps) will be generated from total genomic DNA derived from 40 breast cancer samples and subjected to total of eight lanes of 37 bp, paired end sequencing on the llumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions.

  Study EGAS00001000031

• RRBS data from TRACERx non-small cell lung cancer (NSCLC) tumours and matched normal adjacent tissue.

  TRACERx (TRAcking Cancer Evolution through therapy (Rx)) is a prospective cohort study designed to investigate intratumor heterogeneity (ITH) in relation to clinical outcome, and to determine the clonal nature of driver events and evolutionary processes in early stage non-small cell lung cancer (NSCLC). This study looks at multi-region RRBS data from the TRACERx cohort selected for quantity of material available and high tumour purity

  Study EGAS00001006523

• Dual-mTOR inhibitor Rapalink-1 reduces prostate cancer patient-derived xenograft growth and alters tumor heterogeneity

  Bone metastasis is the leading cause of prostate cancer (PCa) mortality, frequently marking the progression to castration-resistant PCa. In this study, we compared the molecular pathways enriched in a set of bone metastasis from breast and prostate cancer from snap-frozen tissue. To further model PCa drug resistance mechanisms, we used two patient-derived xenografts (PDX) models of bone-metastatic PCa, BM18 and LAPC9.

  Study EGAS00001004431

• Targeted sequencing of paired tumour/blood of 34 T1 stage bladder cancer patients

  Stage T1 bladder cancer presents a high risk of progression and requires improved understanding. In continuation of our whole-exome sequencing study on this subtype of the disease, we carried out this targeted paired tumour/blood sequencing study including 34 T1 stage bladder cancer patients. Agilent’s SureDesign tool was used to design a 1.133 Mb SureSelect custom capture for all coding exons of the 140 selected candidate genes.

  Study EGAS00001005767

• Development of blood-based biomarkers for precision medicine in castration-resistant prostate cancer

  Cell-free DNA (cfDNA) testing is emerging as a tool for cancer precision medicine. However, little is known about the clinical significance of low-frequency variants detected in circulating cell-free tumor DNA (ctDNA) from castration-resistant prostate cancer (CRPC) patients. We conducted targeted sequencing of cfDNA and paired leukocyte DNA from CRPC patients using molecular barcodes, and ctDNA variants with a variant allele frequency ??? 0.1% were detected using an in-house pipeline.

  Study JGAS000330

• Anonymized germline variants of prospectively characterized clinical cancer specimens

  These clinical specimens represent solid tumors and matched blood controls that were collected as part of patients' routine care at Memorial Sloan Kettering Cancer Center. They were sequenced on the targeted platform MSK-IMPACT. Here, we performed germline variant calling on the normal blood specimens and assessed their zygosity in the concomitant tumor specimens for comprehensive exploration of the landscape of pathogenic germline variants in patients with advanced cancer.

  Study phs001858

• Improved T Cell Immunity Following Neoadjuvant Chemotherapy in Ovarian Cancer

  This study characterized the evolution of the peripheral immune cell function and composition across the course of standard of care platinum and taxane chemotherapy in ovarian cancer using bulk and single cell transcriptomic approaches. Serial blood samples were collected from ten patients with advanced high-grade serous ovarian cancer treated with chemotherapy. Single cell sequencing was performed on five patients' samples collected before the initiation of chemotherapy and after the third cycle of chemotherapy.

  Study phs002862

• Discovery, Biology, and Risk of Inherited Variants in Breast Cancer (DRIVE) - germline whole genome sequencing

  This study consists of whole genome sequencing (target: average 30x coverage) of 110 European-ancestry (EA), early-onset, family-history-positive breast cancer cases, 21 Asian cases, 25 African-American cases, and 24 controls from six studies participating in the Discovery, Biology, and Risk of Inherited Variants in Breast Cancer (DRIVE) consortium, part of the NCI's Genetic Associations and Mechanisms in Oncology (GAME-ON) initiative ( http://epi.grants.cancer.gov/gameon/ )

  Study phs001483

• Meta-Analysis of Genome-Wide Association Studies of Bladder Cancer Risk

  This meta-analysis consists of genome-wide genotype for 13,447 cases and 342,580 controls of European ancestry to identify novel susceptibility loci for bladder cancer. Cases were defined as histologically confirmed primary carcinoma of the urinary bladder of all stages, including carcinoma in situ (International Classification of Diseases for Oncology, C670-C679, 188). All histologic subtypes were included. Summary-level results for the association between genotyped/imputed variants and risk of bladder cancer are included.

  Study phs003342

• Whole Genome Sequencing Data of High Grade Serous Ovarian Cancer

  Longitudinal whole genome sequencing data to study chemoresponse in ovarian cancer. These samples belong to an ongoing sample collection and the data already includes hundreds of samples from over 200 patients. Samples are from primary and metastatic tissues and ascites. All patients have been treated with platinum-taxane based chemotherapy and majority of them are diagnosed with high-grade serous ovarian cancer.

  Study EGAS00001006775

• MOSAIC - Multi-Omics Spatial Atlas In Cancer

  MOSAIC is a collaborative initiative founded by Owkin, Lausanne University Hospital (CHUV), Charité Universitätsmedizin Berlin, University Hospital Erlangen (UKER), Gustave Roussy Institute in Paris, and University of Pittsburgh. The goal of MOSAIC is to build the largest collection of spatial omics data in cancer. By integrating comprehensive high quality clinical annotations with advanced deep profiling techniques, MOSAIC aims to uncover novel cancer subtypes and identify key drug targets and biomarkers within them.

  Study EGAS50000000689

• Circulating tumour DNA (ctDNA) data of High Grade Serous Ovarian Cancer Patients

  This study contains circulating tumour DNA (ctDNA) data derived from longitudinal plasma samples of High Grade Serous Ovarian Cancer (HGSC) patients belonging to the DECIDER study (NCT04846933). Ovarian cancer kills more than 40 000 women in Europe each year, and HGSC is the most common and most difficult to treat subtype of this disease. This study contains different sequencing datasets with samples from different stages during the treatment of the patients.

  Study EGAS50000000674

• The Landscape of N-6 Methyladenosine in Primary Localized Prostate Cancer

  Using meRIP-sequencing, we profiled N-6 methyladenosine (m6A) in a cohort of 148 primary prostate cancer samples as part of the Canadian Prostate Cancer Genome Network project (CPC-GENE). Paired-end sequencing of 150 bp reads were mapped to GRCh38.p13 using annotations from gencode.v34.chr_patch_hapl_scaff.annotation.gtf. Peaks were called using MeTPeak, joint peaks were identified and IP reads were quantitated, normalized and adjusted using Input reads to obtain estimates of m6A abundance.

  Study EGAS00001006925

• genome-wide cfDNA methylation analysis

  To characterise cfDNA methylome in metastatic prostate cancer

  Study EGAS00001003958

• Breast Cancer Whole Genome Sequencing

  Breast Cancer Whole Genome Sequencing

  Dataset EGAD00001000121

• Breast cancer SNP6 arrays_more

  Affymetrix SNP6.0 array breast cancer data

  Dataset EGAD00010001079

• Genome-wide association study of esophageal squamous cell cancer identifies shared and distinct risk variants in African and Chinese populations

  Study EGAS00001007477

• ImmunoAgeing_Longitudinal

  The objective is to establish whether immunosenescence is associated with the development of clonal haematopoiesis in a healthy ageing population. This will be addressed in collaboration with the European consortium running the ImmunoAgeing project (www.immunoageing.eu). Genomic DNA derived from the peripheral blood of 394 individuals at 3-5 time-points over a 20-year period will be analysed. RNA bait pulldown (Agilent) will be used to perform targeted sequencing of genes known to be recurrently mutated in myeloid malignancies The presence, size and nature of clonal haematopoiesis will be correlated with quantitative measures of immunosenescence.

  Study EGAS00001003183

• Genomic Landscape of Pediatric Myelodysplastic Syndromes

  Pediatric myelodysplastic syndromes (MDS) are a rare disease and unlike their adult counterpart, very little is known about their genomic landscape. We characterized a cohort of patients from a single institution by whole exome sequencing, as well as a subset of patients by whole genome sequencing, RNA-sequencing and targeted deep sequencing. We found a spectrum of mutations, both somatic and germline, that are distinct from those observed in adult MDS. In turn, we observed mutations commonly observed in other pediatric myeloid tumors.

  Study EGAS00001002202

• Diagnosis of multisystem inflammatory syndrome in children by a whole-blood transcriptional signature

  To identify a diagnostic blood transcriptomic signature that distinguishes multisystem inflammatory syndrome in children (MIS-C) from Kawasaki Disease (KD), bacterial infections and viral infections. Children presenting with MIS-C to participating hospitals in the United Kingdom and the European Union between April 2020-April 2021 were prospectively recruited. Whole blood RNA Sequencing was performed, contrasting the transcriptomes of children with MIS-C to those from children with KD, definite bacterial and viral infections. Data deposited here comprises samples from patients recruited into the DIAMONDS study.

  Study EGAS00001007409

• Alternative splicing isoforms in patient-derived hepatocellular carcinoma cells

  The aim of this study was to obtain a landscape of alternative splicing (AS) in human hepatocellular carcinoma (HCC). We applied hybrid sequencing by integrating Pacbio long-read and Illumina short-read RNA sequencing data from 8 patient-derived HCC cell lines, and used an immortalized hepatocyte cell line as reference. This study revealed features of annotated and novel splice variants in HCC cells, including transcript length, AS type and protein changes. We also identified novel isoforms and tumor specific isoforms, which may represent potential biomarkers and targets for therapeutic development.

  Study EGAS00001002697

• RNAseq data from human colon organoid infected by KP

  The aim of this study is to identify the specific bacteria that are responsible for pathological bacterial translocation and subsequent Th17 priming in the liver in primary sclerosing cholangitis (PSC). To clarify the mechanism of how microbiota interacts with the intestinal epithelial barrier, monolayered human intestinal organoids were cultured with the specific bacteria. Gene expression analysis using RNA sequencing in epithelial cells cultured with Klebsiella pneumoniae derived from a PSC patient (KP-P1) or commercially obtained Klebsiella pneumoniae strain (KP JCM1662) was performed in this study.

  Study EGAS00001003332

• An epigenetic single-cell atlas of IDH-mutant glioma reveals the role of ATRX in shaping tumor composition

  Recent single-cell RNA-sequencing studies have identified a hierarchy of cell types that is common to all isocitrate dehydrogenase (IDH) -mutant gliomas. This finding is somewhat paradoxical since the genetic differences between IDH-mutant astrocytomas and IDH-mutant oligodendrogliomas are prognostic, predictive of therapeutic response, and correlated with differences in immune infiltrates. To integrate these disparate findings, we constructed a single-cell atlas of 22 human IDH-mutant primary untreated grade-II/III gliomas.

  Study EGAS00001004523

• Discovery of new fusion transcripts in a cohort of pediatric solid cancers at relapse

  This study aims to dissect further the complexity of fusion landscape in recurrent pediatric cancers. A retrospective study on RNA-sequencing data of 48 pediatric patients at relapse with different malignancies was conducted in order to detect and validate several fusions and predict their probable oncogenic potential and targetability. We obtained a high validation rate of 90% of selected candidates which will serve both clinical and research needs to detect and prioritize experimental validation studies leading to the development of new therapeutic options.

  Study EGAS00001003236

• Gene expression profiling of nasopharyngeal carcinoma

  We retrospectively collected 150 non-metastatic, pretreatment, formalin-fixed, paraffin-embedded (FFPE) nasopharyngeal carcinoma (NPC) samples as validation cohort 1. Also, we prospectively collected 32 FFPE samples from NPC patients enrolled in a trial evaluating anti-PD-1 antibody as validation cohort 2. Total RNA was extracted and hybridised to an Affymetrix HTA 2.0 microarray. In this study, we investigated the immune status of the tumour microenvironment (TME) based on gene expression profiles to classify NPC into biologically distinct immune subtypes, and clarify their associations with prognosis and immunotherapy response.

  Study EGAS00001004542

• NABEC: North American Brain Expression Consortium

  This study utilized neurologically normal control samples deposited in North American Brain Expression Consortium (NABEC). This top-level study, phs001300, makes available all phenotype data of the NABEC study participants. In addition, molecular data from six sub-studies are available through dbGaP: NABEC Genome-Wide Genotyping - phs000249 NABEC Exome Sequencing - phs001301 NABEC CAGE Sequencing of Human Cerebral Frontal Cortex - phs001302 NABEC mRNA Sequencing of human Cerebral Frontal Cortex - phs001353 NABEC Total RNA Sequencing of human Cerebral Frontal Cortex - phs001354 NABEC Neurochip Genotyping - phs001462NABEC Whole-Genome Sequencing - phs002636

  Study phs001300

• Expression Quantitative Trait Locus Mapping Studies in Mid-Secretory Phase Endometrial Cells Identifies HLA-F and TAP2 as Fecundability-Associated Genes

  We performed an unbiased genome-wide expression quantitative trait locus (eQTL) mapping study to identify common regulatory (expression) single nucleotide polymorphisms (eSNPs) in mid-secretory endometrium, corresponding to the luteal phase of the ovarian cycle. Biopsies were collected from 58 women with two or more early pregnancy losses and 53 of these samples passed all quality control. RNA was extracted from endometrial biopsies and DNA was extracted for sequencing from blood. Gene expression data can be found at NCBI GEO Series GSE77688.

  Study phs001146

• Characterization of CNS Metastases

  Metastatic disease to the central nervous system (CNS) is devastating, with a poor prognosis. There are limited treatment options for patients with CNS metastases, and in particular with leptomeningeal carcinomatosis (LMD). In this study, we evaluated the molecular and cellular features of parenchymal brain metastases and LMD. We used single-cell RNA and cell-free DNA profiling of CSF from patients with LMD receiving immunotherapy to demonstrate shifts in the liquid LMD tumor microenvironment. We also characterize the tumor microenvironment of parenchymal brain metastases using single cell sequencing, before and after treatment with immunotherapy.

  Study phs002416

• Transcriptome and TCR Sequencing of T Cells from Metastectomies

  T cells were sorted from metastatic tumors (colon, rectal, breast, anal, melanoma primary histologies) following tumor dissociation and single-cell sequencing was performed (RNAseq and TCRseq). For samples from tumors that had been previously studied, cells were analyzed comparing known neoantigen-reactive TCR-expressing cells to other T cells. For samples without previously identified neoantigen reactivity, TCRs were predicted on the basis of T cell transcriptomic states. To determine candidate neoantigen screening, exome and RNA sequencing were performed on fragments of matched tumors from which T cells were sequenced   

  Study phs002748

• Identification of Putative Neoantigens in Stage III Melanoma

  This study of three metastatic melanoma patients utilized exome sequencing and RNA sequencing to help identify putative neoantigen peptides that could be further validated by standard immunological assays before design of a personalized vaccine. For each set of neoantigens identified and verified by standard assays, we designed GMP peptides that correspond to the top neoantigens, then used these to condition dendritic cell isolates from each patient. The conditioned dendritic cells were used as the vaccine in three rounds of vaccination, followed by monitoring for T cell memory response to each of the neoantigens.

  Study phs001005

• Genomic Translation for ALS Care (GTAC) - WGS

  To look for genetic correlates of disease progression, the GTAC study recruited patients with motor neuron disease from 13 academic medical center clinics and followed them longitudinally for up to 5 years. Participants were regularly assessed for changes in respiratory function, the ALS Functional Rating Scale, and the ALS Cognitive Behavioral Scale. Participants underwent PCR-free whole genome sequencing on the Illumina NovaSeq, as well as repeat-prime PCR assessment of the C9ORF72 repeat expansion. Participants had PBMCs and whole blood RNA banked for future correlative studies.

  Study phs002973

• Genomic and transcriptomic characterization of chordoma

  In this study, we performed paired tumor/normal whole exome and shallow long insert whole genome sequencing, as well as tumor RNAseq, from archival chordoma specimens collected from four patients at the Barrow Neurological Institute in Phoenix, AZ. The purpose of this analysis was to identify potential therapeutic targets. In three patients, we observed that although different DNA and RNA changes were present in each tumor, alterations fell on converging pathways. In the fourth patient, constitutional DNA demonstrated potentially pathogenic alterations that may have predisposed the patient to chordoma.

  Study phs001643

• Genetic measurement of memory B-cell recall using antibody repertoire sequencing

  We developed an improved high throughput sequencing approach to measure the quantities and sequences of the repertoire of antibody heavy chain RNA in a blood sample. Using this approach we analyzed the antibody repertoire in response to yearly vaccinations with influenza vaccines TIV and LAIV in healthy adults in two subsequent years. We determined vaccine response patterns specific to LAIV and TIV and found antibody sequences that were shared between two samples of the same individuals following influenza vaccination in subsequent years, thereby providing a genetic measurement of B-cell memory recall.

  Study phs000656

• Single-Cell Analysis of the Multiple Myeloma Microenvironment after Gamma-Secretase Inhibition and CAR T-Cell Therapy

  We examined the effects of gamma-secretase inhibition (GSI) on the bone marrow microenvironment in multiple myeloma patients before anti-B-cell maturation antigen (BCMA) CAR T-cell therapy. Single-nuclei RNA and ATAC sequencing revealed significant changes in gene expression and chromatin accessibility, especially in monocytes and tumor cells, following exposure to GSI. The findings suggest that GSI influences not only BCMA signaling but also broader cellular interactions within the tumor microenvironment. De-identified sequencing data from the study is available through dbGaP.

  Study phs003741

• Epigenetic landscape reorganization and reactivation of embryonic development genes are associated with malignancy in IDH-mutant astrocytoma

  Accurate grading of IDH-mutant gliomas is crucial for determining patient prognosis and guiding treatment decisions. However, histological grading can be challenging, so we aimed to identify objective molecular markers. To this end, we conducted bulk RNA sequencing on primary IDH-mutant astrocytomas (n=138) from the prospective CATNON trial, which evaluated the prognostic impact of adjuvant and concurrent temozolomide. Using this data, we sought to identify molecular markers linked to increased malignancy in IDH-mutant astrocytomas to establish objective grading criteria.

  Study EGAS50000000381