15034 results for "cancer studies using rna-seq"

in 19.06 milliseconds.

• Whole exome sequencing of two BPDCN patients for tracing clonal evolution

  Whole exome sequencing data was mapped to GRCh38 using bwa-mem2 as implemented in the nfcore sarek workflow.

  Dataset EGAD50000000309

• H3Africa ACEGID Omni 2.5M and 5M Genotype

  SNP Genotyping for Lassa Fever cases and population controls from Nigeria and Sierra Leone using Illumina Omni 2.5M and 5M

  Dataset EGAD00010002509

• H3Africa EPIGEN EWAS

  Data from 59 whole blood samples from pregnant mothers, unexposed and exposed to the Rwandan genocide, was generated using Infinium MethylationEPIC BeadChip Kit.

  Dataset EGAD00010002383

• Tissue Site

  Tissue site for RNAsequencing data. Tissue site is associated with the clinical biomarker data and be linked to the biomarker data using the SAMPLE and PAT identifiers.

  Dataset EGAD50000000931

• H3Africa ACEGID Array Phenotype

  Phenotype data for Lassa Fever cases and population controls from Nigeria and Sierra Leone associated with genotype data generated using Illumina H3Africa array version 1.

  Dataset EGAD00001010923

• Dataset of Clonal Evolution of PPM1D Mutations in the Spectrum of Myeloid Disorders

  This dataset contains genomic profiles of 7 PPM1D-mutated patients across the spectrum of myeloid disorders using single-cell analyses (Tapestri technology) on diagnostic and longitudinal samples.

  Dataset EGAD50000001229

• Tumor Whole-exome sequencing

  20 tumor tissue WES data with paired cfDNA sWGS data. This data is used for concordance analysis between cfDNA-based and tissue-based CNA. The WES libraries were sequenced across 3 independent runs using multiple lanes.

  Dataset EGAD50000001864

• Repertoire sequencies from three different protocols

  This dataset contains sequencing data from Bulk RNAseq, PCR-based RepSeq and SMRT sequencing to compare immunoglobulin repertoire profiling strategies using matched human B-cell samples

  Dataset EGAD50000002217

• Whole Genome Sequencing of Normal Singaporean Volunteers

  Whole-genome sequencing (WGS) data for 546 Singaporean volunteers used to estimate WGS-LTL in the study. Samples were sequenced using Illumina Hiseq X to a mean coverage of 30X.

  Dataset EGAD00001005480

• HV31 - MGI single-tube long fragment read (stLFR) linked-read sequencing

  MGI single-tube long fragment read (stLFR) linked-read sequencing data for individual HV31 generated using DNA from CD14+ monocytes, to a sequencing depth of ~51×.

  Dataset EGAD00001007045

• Trio Sequencing results for the AnkyrinG MIPS screening study

  Approximately 1000 trio's with varying degrees of cognitive disorders. All samples have been sequenced for the AnkyrinG interactome using MIPS technology. Data is presented as BAM and unfiltered VCF files.

  Dataset EGAD00001006823

• Whole-genome sequencing (Illumina HiSeq X-Ten) of tumor-stage mycosis fungoides

  This dataset contains whole-genome sequencing data of tumors from 9 patients with mycosis fungoides. The data was generated using the Illumina HiSeq X-Ten platform.

  Dataset EGAD00001003982

• 10xscRNA sequencing of 2 samples RRMM (multiple myeloma)

  Paired scRNA sequencing using 10xgenomics library preparation and Illumina HiSeq4000 for sequencing of 2 samples RRMM (relapsed refractory multiple myeloma)

  Dataset EGAD00001009681

• Targeted sequencing of healthy bone marrow without antibodies

  Targeted sequencing using BD Rhapsody with 462 mRNA of healthy young adult bone marrow mononuclear cells from iliac crest aspirations (BM3/Young3).

  Dataset EGAD00001008184

• Nanopore medulloblastoma data

  Nanopore data from 3 medulloblastoma samples of which 2 are tumor-normal pairs sequenced with the MinIon and one is tumor only data sequenced on the PromethIon. The data consists of BAM files aligned using minimap2

  Dataset EGAD00001010851

• ARIC

  Bam files are from matched normal + "very early" plasma (diagnostic) samples, sequenced on Illumina NovaSeq 6000 instrument. After bwa alignment, duplicates were removed by picard markduplicate, and base quality scores recalibrated using gatk baserecalibrator + apply bqsr.

  Dataset EGAD00001015603

• GWAS in African Americans, Latinos and Japanese

  The Multiethnic Cohort Study is a population-based prospective cohort study (n=215,251) that was initiated between 1993 and 1996 and includes subjects from various ethnic groups - African Americans and Latinos primarily from Californian (great Los Angeles area) and Native Hawaiians, Japanese-Americans, and European Americans primarily from Hawaii. State drivers' license files were the primary sources used to identify study subjects in Hawaii and California. Additionally, in Hawaii, state voter's registration files were used, and, in California, Health Care Financing Administration (HCFA) files were used to identify additional African American study subjects. In the cohort, incident cancer cases are identified annually through cohort linkage to population-based cancer Surveillance, Epidemiology, and End Results (SEER) registries in Hawaii and Los Angeles County as well as to the California State cancer registry. Information on estrogen receptor status is also obtained through these registries. Blood sample collection in the MEC began in 1994 and targeted incident breast cancer cases and a random sample of study participants to serve as controls for genetic analyses. Subjects are frequency matched on age at blood draw and ethnicity. The following number of breast cancer cases and controls were genome-wide scanned as part of this study: African Americans, 473 cases and 464 controls; Japanese: 885 cases and 822 controls; Latinos, 520 cases and 544 controls.

  Study phs000517

• The neo-open reading frame peptides that comprise the tumor framome are a rich source of neoantigens for cancer immunotherapy

  Identification of immunogenic cancer neoantigens as targets for therapy is challenging. Here, we integrate whole genome and long-read transcript sequencing of cancers to identify the collection of neo-open reading frame peptides (NOPs) expressed in tumors. We termed this collection of NOPs the tumor framome. NOPs represent tumor-specific peptides that are different from wild-type proteins and may be strongly immunogenic. We describe a class of hidden NOPs that derive from structural genomic variants involving an upstream protein coding gene driving expression and translation of non-coding regions of the genome downstream of a rearrangement breakpoint, i.e. where no gene annotation or evidence for transcription exists. The entire collection of NOPs represents a vast number of possible neoantigens particularly in tumors with many structural genomic variants and a low number of missense mutations. We show that NOPs are immunogenic and epitopes derived from NOPs can bind to MHC class I molecules. Finally, we provide evidence for the presence of memory T cells specific for hidden NOPs in peripheral blood from a patient with lung cancer. This work highlights NOPs as a major source of possible neoantigens for personalized cancer immunotherapy and provides a rationale for analyzing the complete cancer genome and transcriptome as a basis for detection of NOPs.

  Study EGAS00001006021

• Dynamic Evolution of Fibroblasts Revealed by Single Cell RNA Sequencing of Human Pancreatic Cancer

  Understanding the constituents of the pancreatic ductal adenocarcinoma (PDAC) microenvironment may illuminate more efficacious targets for treating this aggressive malignancy. However, the compositional changes occurring in untreated and treated PDAC relative to both normal and inflamed pancreas have not been well characterized. To provide a more comprehensive understanding of the PDAC tumor microenvironment relative to the non-cancerous pancreas, we performed single-cell expression profiling (10X Genomics Chromium) on samples of upfront resectable PDAC, FOLFIRINOX-based treated PDAC, chronic pancreatitis, and normal pancreas specimens from 19 patients. Spatial gene expression profiling (10X Genomics Visium) was performed to gain additional insight into cell populations. Our analysis revealed that fibroblasts are central mediators of cell-cell communication in both inflamed and malignant settings and defined unique roles for these cell populations in different disease contexts.

  Study phs003751

• Single-Cell Analysis of Somatic Mutations in Human Bronchial Epithelial Cells in Relation to Aging and Smoking

  While lung cancer risk among smokers is dependent on smoking dose, it remains unknown if this increased risk reflects an increased rate of somatic mutation accumulation in normal lung cells. Here we applied single-cell whole genome sequencing of proximal bronchial basal cells from 33 subjects, aged between 11 and 86 years, with smoking histories varying from never smoking to 116 pack years. We found an increase in the frequency of single-nucleotide variants and small insertions and deletions with chronological age in never-smokers, with mutation frequencies significantly elevated among smokers. However, when plotted against smoking pack-years, mutations were found to follow the linear increase in cancer risk only until about 23 pack years, after which no further increase in mutation frequency was observed, pointing towards individual selection for mutation avoidance. Known lung cancer-defined global mutation signatures tracked with both age and smoking. Within study power limits, no significant enrichment for somatic mutations in lung cancer driver genes was observed.

  Study phs002758

• Epigenomics Studies in Acute Myeloid Leukemia (AML)

  Acute Myeloid Leukemia (AML) remains a clinical challenge since most patients diagnosed with AML will die from the disease. Some patients harbor treatment-refractory disease and many others relapse with disease that in many cases is resistant to treatments. Our study was designed to understand the molecular basis of disease progression in AML through assessing genomics signatures in patient specimens collected through an international collaboration which assembled samples from 138 AML patients which experienced disease relapse and normal hematopoietic cells (n=15). It is hoped that this resource will help researchers understand mechanisms of disease relapse in AML and contribute to the general pool of data available for analyses for this disease and general research use.

  Study phs001027

• Dual spatially resolved transcriptomics for human host-pathogen colocalization studies in FFPE tissue sections

  Technologies to study localized host-pathogen interactions are urgently needed. Here, we present a spatial transcriptomics approach to simultaneously capture host and pathogen transcriptome-wide spatial gene expression information from human formalin-fixed paraffin-embedded (FFPE) tissue sections at a near single-cell resolution. We demonstrate this methodology in lung samples from COVID-19 patients and validate our spatial detection of SARS-CoV-2 against RNAScope and in situ sequencing. Host-pathogen colocalization analysis identified putative modulators of SARS-CoV-2 infection in human lung cells. Our approach provides new insights into host response to pathogen infection through the simultaneous, unbiased detection of two transcriptomes in FFPE samples.

  Study EGAS00001006186

• 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 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