15041 results for "cancer studies using rna-seq"

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• Mutational landscape of the transcriptome offers putative targets for immunotherapy of myeloproliferative neoplasms

  In this study, we aimed to comprehensively characterize in 113 myeloproliferative neoplasms (MPN) patients the mutational landscape of the granulocyte transcriptome using RNA sequencing data. We implemented workflows for fusion and variant calling, and differential splicing analysis for patients with hotspot SF3B1 mutations. Finally, we characterized the neoantigen landscape on individualized level taking each patient's HLA genotype (derived from the same RNA-seq dataset) into account.

  Study EGAS00001003486

• RNAseq of 76 samples from Uveal Melanoma tumors

  Hotspot mutations in the spliceosome gene SF3B1 are reported in 20% of uveal melanomas. SF3B1 is involved in 3'-splice site (3'ss) recognition during RNA splicing; however, the molecular mechanisms of its mutation have remained unclear. Here we show, using RNA-Seq analyses of uveal melanoma, that the SF3B1 R625/K666 mutation results in deregulated splicing at a subset of junctions, mostly by the use of alternative 3'ss

  Study EGAS00001002932

• Lung Cancer Genetic Study Among Asian Never Smokers

  The Lung Cancer Genetic Study Among Asian Never Smokers includes data from four population-based studies conducted among Asian women: the Shanghai Women's Health Study (SWHS), the Hwasun Cancer Epidemiology Study (HCES1 and HCES2), the Female Lung Cancer Consortium in Asia (FLCCA, including sFLCA), and the Guangzhou Lung Cancer Study (GLCS). Shanghai Women's Health Study (SWHS): The SWHS is a population-based prospective cohort study of approximately 75,000 adult women who were recruited between 1997 and 2000. The cohort has been followed by a combination of record linkage and active follow-ups. Lung cancer patients identified in the SWHS and non-cases were included in the current study.Hwasun Cancer Epidemiology Study-Lung Cancer (HCES1 and HCES2): The HCES is a hospital-based case-control study whose goal is to identify factors of the cancer development and clinical progression in a Korean population. Included in this project were 299 female lung cancer cases from HCES2, who were diagnosed between April 2004 and February 2013 at Chonnam National University Hwasun Hospital, a cancer specified hospital in Jeollanam-do province, South Korea. Controls were randomly selected from women with no previous cancer diagnosis at enrollment in the Namwon Study and the Dong-gu study, ongoing community-based cohort studies in South Korea. A total of 1,103 controls (273 from HCES1 and 830 from HCES2) were genotyped by MEGA. Guangzhou Lung Cancer Study (GLCS): The GLCS is a case-control study including never-smoking women lung cancer cases and controls from Guangzhou, China.In this study, the DNA samples of 1,195 subjects from SWHS and GLCS were genotyped using whole exome sequencing (WES), and the DNA samples of 7,174 subjects from SWHS, HCES1, HCES2, FLCCA, and sFLCA were genotyped using the Multi-Ethnic Global Array (MEGA).

  Study phs002366

• IgM heavy chain V(D)J library sequencing using varied PCR parameters

  When amplifying the rearranged V(D)J genes encoding antigen receptors during adaptive immune receptor repertoire sequencing (AIRR-seq), each cycle of the PCR can produce spurious “chimeric” hybrids of two or more different template sequences. To test the effects of PCR protocol variation on chimera formation in AIRR-seq, we produced IgM heavy chain V(D)J repertoire libraries under 8 conditions, varying the number of PCR cycles, indexing PCR template, input RNA, and extension time. Three donors were sequenced using all 8 conditions.

  Study EGAS50000001037

• PBL whole exome and transcriptome data

  Plasmablastic lymphoma (PBL) represents a clinically heterogeneous subtype of aggressive B-cell non-Hodgkin lymphoma. Although targeted sequencing studies and a single center whole exome sequencing (WES) study in HIV+ patients recently revealed several genes, associated with PBL pathogenesis, the global mutational landscape and transcriptional profile of PBL remain elusive. To inform on disease-associated mutational drivers, mutational patterns and perturbed pathways in HIV+ and HIV- PBL we performed WES and RNA-sequencing (RNA-seq) of 34 PBL tumors.

  Dataset EGAD00001006795

• RNA-Seq data from tumor samples collected from 12 UTSW translocation renal cell carcinoma (tRCC) patients.

  This study investigates differentially expressed genes associated with the progression of translocation renal cell carcinoma (tRCC) by analyzing RNA-Seq data from 23 tumor samples obtained from 12 patients. The samples were collected from affiliated hospitals of the University of Texas Southwestern Medical Center (UTSW), including Parkland Hospital and Children’s Medical Center. RNA isolated from tumor samples was sequenced using the Illumina platform.

  Dataset EGAD50000000172

• Small RNA-Seq of MicroRNA's in extracellular vesicles of Ushers Syndrome patients

  Small RNA-Seq dataset of MicroRNA's found in tear extracellular vesicles (EVs) and hiPSC-derived retinal pigment epithelium (RPE) cells of Ushers Syndrome patients and control samples. 14 samples were isolated and assessed for quality before preparing libraries using the miReasy and TruSeq Small RNA Library Preparation Kit. Sequencing was performed on the Illumina NextSeq 2000 platform, generating paired end FASTQ files.

  Dataset EGAD50000001709

• RNA-seq data

  This dataset contains 200 RNA-seq bam files (142 SLE, 58 healthy individuals). RNA libraries were prepared with the Illumina TruSeq sample preparation kit and were sequenced on Illumina HiSeq2000. 49 bp paired-end reads were mapped to the GRCh37 reference human genome using the GEM mapper.This dataset was generated as part of the following study: Panousis et al (2019). Combined genetic and transcriptome analysis of patients with SLE: Distinct, targetable signatures for susceptibility and severity

  Dataset EGAD00001005037

• DS-ALL RNA-Seq

  RNA-Seq was performed on 249 DS-ALL samples. Library preparation was carried out using TruSeq Stranded Total RNA Library Prep Kit. The libraries were sequenced on a NovaSeq platform with read length of 2×101.

  Dataset EGAD00001009403

• RNA-seq on patient-derived, stage II, CRC cell lines

  The gut microbiome is a key player in the immunomodulatory and pro-tumorigenic microenvironment in colorectal cancer (CRC). It is well established that Fusobacterium’s virulence factors are responsible for its pro-tumorigenic properties, however the role of its metabolic cross-talk with the tumor remains unexplored. Here we use in vitro, in vivo, and in silico methods to describe a novel microbe-host interaction keystone: formate. Omics data reveals molecular signatures, linking a metabolically driven CRC phenotype with Fusobacteria. We observed a metabolic shift towards increased F. nucleatum formate secretion in gut-on-chip model co-cultures with patient-derived CRC cells, along with an accelerated cancer glutamine metabolism. We show that high formate levels trigger AhR signaling, increase cancer stemness and cellular invasion. Finally, we observed an expansion of Th17 cells accompanying F. nucleatum-induced tumorigenesis. Moving beyond observational studies, we applied new experimental approaches for gaining ecosystem-level mechanistic understanding of F. nucleatum’s role in cancer pathogenesis.

  Study EGAS00001005948

• Illumina RNA-Seq paired of 10 different tumor samples from the Master program (H021)

  Fastq files of paired RNA-Seq of 10 different tumor samples, for which Nanopore and Illumina sequencing was compared. Illumina sequencing was carried out with HiSeq4000 or HiSeq X-Ten using the Illumina TruSeq stranded mRNA Kit.

  Dataset EGAD00001008971

• RNA-seq dataset: Short-term fasting before living kidney donation has an immune-modulatory effect

  This dataset contains 13 RNA-seq samples in CRAM format, generated using the Illumina NovaSeq 6000 platform. The Roche_mRNA_UniversalAdapterUniquePrime protocol was used for library preparation. The aim of the study is to determine the effect of Short-Term Fasting on the abundance and phenotype of different immune cell populations.

  Dataset EGAD00001015472

• Cancer Alliance RNA-Seq PolyA

  PolyA selection transcriptome profiling by high-throughput for individualized cancer interpretation

  Dataset EGAD00001006234

• ProstOmics: spatial and bulk multi-omics of prostate cancer

  In this ERC-funded ProstOmics project we have used spatial and bulk multi-omics on fresh frozen prostate cancer samples to investigate cancer biology and find for biomarkers to improve patient treatment. All tissue material were collected from prostate cancer patients undergoing radical prostatectomy who had not received any prior cancer-specific treatment.Of the 498 prostate tissue samples (114 patients) included in our project, 176 samples (N=37 patients) have been analyzed with bulk transcriptomics (RNA-seq). Some of these 176 samples were also analyzed with spatial transcriptomics (n=32, N=8, Visium 10x RNA-seq) and DNA methylomics (n=96, N=24, array). All datasets include metadata for histopathological evaluation. Patient metadata include information of age at surgery, time (months) until reported relapse, pre-surgery PSA and post-surgery T-stage.

  Study EGAS50000000413

• Human colorectal cancer single-cell RNA sequencing

  The aim was to investigate changes in transcriptomics following irradiation. This was studied in colorectal cancer-patient derived organoids. Analysis was performed with scRNA-seq.

  Study EGAS50000001348

• Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA) - OncoArray Genotypes

  The data come from 40 studies participating in the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA). CIMBA recruits individuals with pathogenic mutations in BRCA1 or BRCA2. The majority of carriers were recruited through cancer genetics clinics offering genetic testing, and were enrolled into national or regional studies. The remainder were identified by population-based sampling of cases, or community recruitment. Eligibility to participate is restricted to carriers of pathogenic BRCA1/2 mutations who were 18 years or older at recruitment. Information collected included amongst other variables: age at recruitment; ages at breast and ovarian cancer diagnosis; and estrogen receptor (ER) status. Samples were genotyped using the Illumina OncoArray beadchip 500K SNP custom array. Details of the genotyping process and sample selection are included in Phelan et al, Identification of twelve new susceptibility loci for different histotypes of epithelial ovarian cancer, Nat Genet. 2017 May;49(5):680-691 (PMID:28346442), and Milne et al, Identification of ten variants associated with risk of estrogen receptor negative breast cancer, Nat Genet (in press).

  Study phs001321

• QSEA – modelling of genome-wide DNA methylation from sequencing enrichment experiments

  We describe a new method, QSEA, for analyzing methylation enrichment data. We generated a benchmark experiment consisting of MeDIP-seq enrichment data, targeted BS-seq validation data, and RNA-seq data on five pairs of tumor and adjacent normal samples of non-small cell lung cancer patients. Details of the method and its performance on the data have been described in Lienhard et al. (2016).

  Study EGAS00001001822

• GENCORD2_RNAseq

  GENCORD2 RNA-seq BAM files using BWA

  Dataset EGAD00001000425

• National Cancer Institute (NCI) Non-Hodgkin Lymphoma Genome-wide Association Study (GWAS)

  Within the framework of the International Lymphoma Epidemiology Consortium (InterLymph) Consortium and NCI-sponsored Cohort Consortium, investigators from 22 studies came together to conduct a genome-wide association study (GWAS) of non-Hodgkin lymphoma (NHL). The goal of the study was to identify common genetic variants associated with the risk of NHL. As described previously (Berndt SI et al., Nature Genetics, 2013, PMID: 23770605 ), cases and controls from 22 studies, including nine prospective cohort studies, eight population-based case-control studies, and five clinic or hospital-based case-control studies were included in this effort. Cases of NHL were ascertained from cancer registries, clinics or hospitals, or through self-report verified by medical and pathology reports. The phenotype information for all NHL cases was reviewed centrally at the InterLymph Data Coordinating Center and harmonized according to the hierarchical classification proposed by the InterLymph Pathology Working Group based on the World Health Organization (WHO) classification (2008). Controls were frequency matched to cases on age and gender by study, and the study was limited to subjects of European ancestry. Participants were genotyped using the Illumina Omni Express. The NCI Non-Hodgkin Lymphoma GWAS is utilized in the following dbGaP sub-studies. To view genotypes and derived variables collected in these sub-studies, please click on the following sub-studies below or in the "Sub-studies" box located on the right hand side of this top-level study page phs000801 NCI Non-Hodgkin Lymphoma GWAS. phs000802 NCI Non-Hodgkin Lymphoma GWAS: CLL phs000818 NCI Non-Hodgkin Lymphoma GWAS: Controls phs000889 NCI Non-Hodgkin Lymphoma GWAS: DLBCL phs000890 NCI Non-Hodgkin Lymphoma GWAS: FL phs000891 NCI Non-Hodgkin Lymphoma GWAS: MZL

  Study phs000801

• Whole Genome Sequencing of Skull-Based Chordoma

  Chordoma is a rare bone tumor, which is believed to originate from notochordal remnants. Based on the United States Surveillance Epidemiology and End Results (SEER) data, the incidence of chordoma varies by gender and race; however, little is known about the etiologic factors that predispose to it. Genomic profiling studies of chordoma are limited, particularly in the Chinese population. We therefore conducted a detailed molecular characterization of paired chordoma tumor/normal tissues using fresh frozen tissues and blood collected from skull-based Chinese chordoma patients. These analyses included whole exome sequencing and RNA sequencing analyses.

  Study phs002301