15080 results for "cancer studies using rna-seq"

in 19.88 milliseconds.

• Deciphering RBP - alternative splicing networks in ALS iPSC-MN: TDP-43, NOVA1, NOVA2 and RBFOX2 eCLIP-seq

  We produced enhanced cross-linking immunoprecipitation (eCLIP) sequencing data of the RNA binding proteins (RBP) TDP-43, NOVA1, NOVA2 and RBFOX2 in iPSC motor neurons of two healthy control individuals, respectively.

  Study EGAS00001005880

• DNA WGS Long Read Sequence (PromethION) for manuscript titled: "Performance of Somatic Structural Variant Calling in Lung Cancer using Oxford Nanopore Sequencing Technology"

  DNA WGS Long Read Sequence (PromethION) for manuscript titled: "Performance of Somatic Structural Variant Calling in Lung Cancer using Oxford Nanopore Sequencing Technology"

  Dataset EGAD00001015400

• Childhood Cancer Model Atlas

  we establish a single-site collection of 243 cell lines, including 207 paediatric cancer cell lines representing 14 distinct extracranial and brain childhood tumour types. We subjected 164 paediatric cancer cell lines to multi-omic analyses across three dimensions (DNA-sequencing, RNA-sequencing, DNA methylation) to classify them based on clinically relevant molecular subtypes.

  Study EGAS00001006320

• Genomic Characterization of Head and Neck Squamous Cell Carcinoma Cell Lines

  Head and neck squamous cell carcinoma (HNSCC) is the sixth leading cancer by incidence worldwide(1). Various chemical carcinogens (tobacco, alcohol and betel nut), human papillomavirus (HPV) infection, and genetic predisposition contribute to the etiology of HNSCC, and to the complex genetic alterations in tumor subsets that differ in prognosis and response to therapies (2). Recently, a comprehensive landscape of genomic and transcriptomic alterations in HNSCC tumors has emerged from The Cancer Genome Atlas (TCGA) Network (3). TCGA revealed novel and previously recognized gene and chromosomal region copy number alterations (CNAs), mutations, and expression clusters, and defined their frequency, co-occurrence, and relationship to common and rare subtypes of HPV(-) and (+) tumors that vary in prognosis. To identify cell line models for determining the functional role and therapeutic importance of these alterations, we are performing whole exome and RNA sequencing and bioinformatic analysis of an expanded panel of 15 HPV(-) and 11 HPV(+) HNSCC cell lines and primary oral keratinocytes. We find that the recurrent genomic alterations in cell lines are remarkably consistent with those found in more aggressive tumors, from which cell lines have traditionally been most readily adapted to culture (4). Genome-wide correlation of CN (copy number) with expression identified a suite of potential drivers or modifier genes that differ by HPV status, and are of potential biologic and therapeutic relevance. Further, our findings elucidate and validate genomic alterations underpinning numerous discoveries made with these widely-used and recently derived HNSCC lines, and provide a roadmap for their potential use as models for future studies of tumor subtypes with worse prognosis. References Torre LA, Bray F, Siegel RL, Ferlay J, Lortet-Tieulent J, Jemal A. Global cancer statistics, 2012. CA Cancer J Clin. 2015;65(2):87-108. Van Waes C, Musbahi O. Genomics and advances towards precision medicine for head and neck squamous cell carcinoma. Laryngoscope Investig Otolaryngol. 2017;2(5):310-9. Cancer Genome Atlas N. Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature. 2015;517(7536):576-82. White JS, Weissfeld JL, Ragin CC, Rossie KM, Martin CL, Shuster M, et al. The influence of clinical and demographic risk factors on the establishment of head and neck squamous cell carcinoma cell lines. Oral Oncol. 2007;43(7):701-12.

  Study phs001581

• The dataset for Early detection of ovarian cancer using cell-free DNA fragmentomes and protein biomarkers

  The dataset for “Early detection of ovarian cancer using cell-free DNA fragmentomes and protein biomarkers” includes 409 cram 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 EGAD50000000695

• Whole Mitochondrial Sequencing of Gingivo-buccal Cancer: ICGC-India Project

  As a part of the ICGC, India has undertaken genomic studies on gingivobuccal cancer of the oral cavity, which is the most prevalent form of cancer among men in India. There are various known environmental (life-style) correlates of this cancer, the most important of which are tobacco chewing and HPV infection. Detailed clinical characterization of the patients, collection of data on demographic and environmental exposures, and isolation of DNA samples from blood and tumor tissues collected from each patient are being done at the Advanced Centre for Research, Treatment and Education on Cancer, Mumbai. Whole genome and other sequencing experiments are being performed at the National Institute of Biomedical Genomics, Kalyani. Whole mitochondria sequencing of 89 patients was performed in this study. The mean depth of sequencing was at least 2500X, but variable across platforms, 2689X and 9894X for amplicon sequencing in Ion Torrent PGM (Tumor-blood pairs=16) and Illumina HiSeq 2500 (Tumor-blood pairs =48), respectively; and, 14,190X for whole genome sequencing in Illumina HiSeq 2500 (Tumor-blood pairs =25). Associations of mutation data with important clinical aspects have been found.

  Study EGAS00001002425

• Transcriptomic Analysis of HIV-Infected Cells

  Defining the attributes of rare CD4 T cells that harbor latent HIV under therapy with anti-retroviral agents has been challenging due to difficulties in identifying and isolating these cells. These cells represent an important barrier to cure, and characterizing them would aid the design and development of novel HIV cure strategies. In this study, we addressed this challenge using a custom microfluidic technology named Focused Interrogation of cells by Nucleic acid Detection and Sequencing (FIND-seq) that isolates HIV-infected cell transcriptomes, based on HIV DNA detection. We applied this method to HIV DNA+ memory CD4 T cells isolated from blood from five persons with HIV who were receiving anti-retroviral agents. After curating samples based on data quality, we proceeded with bioinformatics analysis from three persons. This analysis identified six transcriptomic pathways that were inhibited in HIV DNA+ cells compared to HIV DNA- cells. These included death receptor signaling, necroptosis signaling, and anti-proliferative G-alpha12/13 signaling. Furthermore, we identified two gene clusters, including 60 and 85 genes, that were significantly associated with HIV DNA+ cells identified by co-expression network analysis. These genes included negative regulators of HIV transcription that were higher in HIV DNA+ cells, positive regulators of HIV transcription that were lower in HIV DNA+ cells, and other genes involved in the negative regulation of mRNA translation, additional RNA processing functions, and the regulation of cellular state and fate. We further examined these signatures in transcriptomic data from CD4 T cell subsets sorted by flow cytometry from nine persons with HIV. We found a partial similarity between the smaller cluster of genes and the signature of CCR6- peripheral TFH cells. Raw sequencing data from all eleven human participant samples included in the study are available. These include samples from two participants who were studied only by FIND-seq, three participants who were studied by both FIND-seq and flow cytometry and six participants who were studied only by flow cytometry.

  Study phs003095

• Identification of High-Risk PHF19 Expressing Cells in Myeloma Single-Cell Multiomics

  The aim of this study is to identify novel subsets of cells that are associated with progression and response to treatment. In this project, we study the tumor fraction from 49 myeloma patients across stages of progression. Samples were collected from 10 smoldering multiple myeloma (SMM), 22 newly diagnosed multiple myeloma (NDMM), and 17 relapsed refractory multiple myeloma (RRMM) patients. These samples were then sorted using magnetic-activated cell sorting (MACS) for CD138+ cells that represent the tumor fraction of each sample. The CD138+ fraction then underwent whole genome sequencing (WGS), where possible, and single-cell multiomics. Single-cell multiomics can now measure scRNA-seq and scATAC-seq simultaneously, which we use in this project. Using single-cell multiomics, we will study subclonal changes in gene expression, chromatin accessibility, and identify novel regulatory relationships within myeloma tumors. Furthermore, we will apply state of the art single-cell and single-cell multiomic techniques to better identify the more high-risk components of myeloma.

  Study phs003220

• Single nuclei ATAC-Seq data from the human ganglionic eminences

  Data generated through single nuclei ATAC sequencing on whole ganglionic eminences from 3 human fetuses (two of 16 and one of 17 gestational weeks). Tissue was acquired from the MRC-Wellcome Trust Human Developmental Biology Resource with ethical approval. snATAC-Seq libraries were prepared from ~8,000 nuclei per sample using Chromium Next GEM Single Cell ATAC (v1.1) reagents (10X Genomics). Quality control of libraries was performed using the Agilent 5200 Fragment Analyzer before sequencing on an Illumina NovaSeq 6000 to a depth of at least 617 million read pairs per library. Raw sequencing data were converted into FASTQ files. For a full description of data generation, please see Cameron et al, Schizophrenia Bulletin 2024, https://doi.org/10.1093/schbul/sbae083. Please note that 10X generated BAM files, rather than FASTQ files, have been uploded. FASTQ files can be regenerated using the 10X Genomics bamtofastq tool. https://support.10xgenomics.com/docs/bamtofastq

  Dataset EGAD50000000601

• Omic Studies in Children's Respiratory and Environmental Workgroup (CREW) Cohorts

  Children's Respiratory Research Workgroup (CREW) is an NIH-funded project consisting of multiple individual U.S. cohorts and three scientific centers working together to identify phenotypes and causes of childhood asthma. CREW will include data from a large number of children and their families, with broad diversity in terms of ethnicity, family characteristics, neighborhoods and geographic locations. One of the primary goals of CREW is to put together sets of data and samples of participating cohorts to identify phenotypes of childhood asthma (i.e. specific subtypes of asthma that can be distinguished by clinical features such as natural history, triggers, exacerbation frequency, concurrent allergies, lung function, sex, etc). Omics studies will include genotyping, methylation, and RNA sequencing. By integrating the DNA genotyping with the expression, immunologic and clinical data, we will identify eQTL, inflammation QTL, and lung function QTL, as well as QTL associated with other biomarkers. Analyses will identify genetic, epigenetic, transcriptional and protein/metabolite profiles that are associated with specific exposures or phenotypes. As we obtain mechanistic insights about personal and early life risk factors, we will connect asthma phenotypes with underlying causes and pathogenic mechanisms to define endotypes of childhood asthma.

  Study phs004036

• Integrative genomic analysis reveals cancer-associated mutations at diagnosis of CML in patients with high risk disease

  Genomic events associated with poor outcome in chronic myeloid leukemia (CML) are poorly understood. We performed whole exome sequencing, copy number variation and/or RNA-Seq for 65 patients to discover mutations at diagnosis and blast crisis (BC). Forty-six chronic phase patients with the extremes of outcome were studied at diagnosis. Cancer gene variants were detected in 15/27 patients (56%) with subsequent BC or poor outcome and in 3/19 optimal responders (16%), P=.007. Frequently mutated genes at diagnosis were ASXL1, IKZF1 and RUNX1. The methyltransferase SETD1B was a novel recurrently mutated gene. A novel class of variant associated with the Philadelphia translocation was detected at diagnosis in 11/46 patients (24%) comprising fusions and/or rearrangement of genes on the translocated chromosomes, with evidence of fragmentation, inversion and imperfect sequence reassembly. These were more frequent at diagnosis in patients with poor outcome: 9/27 (33%) versus 2/19 optimal responders (11%), P=.07. Thirty-nine patients were tested at BC and all had cancer gene variants, including ABL1 kinase domain mutations in 58%. However, ABL1 mutations co-occurred with other mutated cancer genes in 89% of cases, and these predated ABL1 mutations in 62% of evaluable patients. Gene fusions not associated with the Philadelphia translocation occurred in 42% of patients at BC and commonly involved fusion partners that were known cancer genes (78%). Genomic analysis revealed numerous relevant variants at diagnosis in patients with poor outcome and all patients at BC. Future refined biomarker testing of specific variants will likely provide prognostic information to facilitate a risk-adapted therapeutic approach.

  Study EGAS00001003071

• RNA sequencing of BCP-LBL patients samples

  In order to perform comprehensive transcriptomics and gene fusion analyses of a cohort of BCP-LBL patients, we performed RNA sequencing of 49 tissue samples from BCP-LBL patients. Because the material was available as FFPE, and had a relative low quality, we used a capture-based approach, where NGS libraries obtained from total RNA were captured in 4-plex, using a whole exome capture panel.

  Dataset EGAD50000000419

• RNAseq profiles from the CheckMate-142 clinical trial

  The dataset contains RNAseq profiles of 57 patients from the CheckMate-142 clinical trial. The Allprep DNA/RNA FFPE kit was used to simultaneously purify genomic DNA and RNA from formalin-fixed, paraffin embedded (FFPE) tissue sections. Baseline tumor tissue samples were processed using the Illumina TruSeq RNA Access in-solution hybrid capture panel and underwent subsequent NGS on the Illumina NovaSeq platform. Fastq files are included.

  Dataset EGAD50000000609

• Targeted sequencing of breast cancer susceptibility genes for 1,995 Japanese breast cancer patients

  In this study, we investigated pathogenic germline variants in 11 genes implicated in hereditary breast cancer, including BRCA1, BRCA2, TP53, PTEN, CDH1, STK11, NF1, PALB2, ATM, CHEK2, NBN1, in a total of 1,995 unselected Japanese women with breast cancer using targeted-capture sequencing of pooled DNA (n = 106).

  Study EGAS00001004630

• Total RNA sequencing of 32 chronic lymphocytic leukemia (CLL) patients

  Peripheral blood mononuclear cells (PBMC) of CLL patients were isolated by density-gradient centrifugation over Linfosep (Biomedics, Madrid, Spain). B cells were purified with a CD19+ magnetic-bead system (MidiMACS, Miltenyi Biotec, Bergish Gladbash, Germany) according to the manufacturers’ instructions. Mean B-cell purity was >99% and the mean percentage of CD5+/CD19+ cells after purification was >98%, as measured by flow cytometry. Total RNA was extracted from purified cells in a single step using TriPure Isolation Reagent (Roche Applied Science, Vilvoorde, Belgium).Whole transcriptome sequencing libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina). Libraries underwent 2 × 76 bp paired-end sequencing on a HiSeq 2500 instrument (Illumina). The median number of paired-end reads was 60.5 million (range, 49.7-79.7 million).

  Dataset EGAD00001004047

• Longitudinal 3'RNA-Seq data from MEMORI trial

  80 bam files generated from 3'RNAseq of tumour biopsies from oesophageal adenocarcinoma. Samples were collected within the clinical MEMORI trial.

  Dataset EGAD50000000357

• Single-cell RNA-seq of immune cells sorted from human melanoma tumors

  Tumor immune cell compositions play a major role in response to immunotherapy but the heterogeneity and dynamics of immune infiltrates in human cancer lesions remain poorly characterized. Here we identify conserved intratumoral CD4 and CD8 T cell behaviors in scRNA-seq data from 25 melanoma patients. We discover a large population of CD8 T cells showing continuous progression from an early effector "transitional" into a dysfunctional T cell state. CD8 T cells that express a complete cytotoxic gene set are rare, and TCR sharing data suggest their independence from the transitional and dysfunctional cell states. Notably, we demonstrate that dysfunctional T cells are the major intratumoral proliferating immune cell compartment and that the intensity of the dysfunctional signature is associated with tumor-reactivity. Our data demonstrate that CD8 T cells previously defined as exhausted, are in fact a highly proliferating, clonal and dynamically differentiating cell population within the human tumor microenvironment.

  Study EGAS00001003363

• cHCC-ICC RNAseq

  The RNA-seq data of 97 tumor samples from 77 cHCC-ICC cases, data of two other HCC tumor samples were also included.

  Dataset EGAD00001005182

• RCC transcriptomic data

  RNA-seq data. 287 Japanese RCC cases.

  Dataset EGAD00001010003

• Transcriptome Profiling of human AT2 cells in COPD

  RNA-seq of FACS sorted AT2 cells from ex-smokers with (n=6) and without (n=3) COPD at different disease stages. Fastq files are provided.

  Dataset EGAD00001011115

• Nivolumab plus chemotherapy or ipilimumab in gastroesophageal cancer: CheckMate 649 biomarker analyses

  First-line nivolumab-plus-chemotherapy demonstrated superior overall survival (OS) versus chemotherapy for advanced gastroesophageal adenocarcinoma (CheckMate 649). Nivolumab-plus-ipilimumab provided durable responses and higher survival rates versus chemotherapy; however, the prespecified OS significance boundary was not met. To identify biomarkers predictive of differential efficacy outcomes, exploratory analyses were performed using whole-exome sequencing and RNA sequencing. Nivolumab-based therapies demonstrated improved efficacy versus chemotherapy in hypermutated and, to a lesser degree, Epstein Bar Virus-positive tumors compared with chromosomally unstable and genomically stable tumors. Within the KRAS-altered subgroup, only patients treated with nivolumab-plus-chemotherapy demonstrated improved OS benefit versus chemotherapy. Low stroma gene expression signature scores were associated with OS benefit with nivolumab-based regimens; high regulatory T-cell signatures were associated with OS benefit only with nivolumab-plus-ipilimumab. Our analyses suggest that distinct and overlapping pathways contribute to the efficacy of nivolumab-based regimens in gastroesophageal adenocarcinoma.

  Study EGAS50000000747

• CXCL8 secreted by immature granulocytes inhibits wildtype hematopoiesis in chronic myelomonocytic leukemia

  CXCL8 secreted by immature granulocytes inhibits wildtype hematopoiesis in chronic myelomonocytic leukemia [Abstract] In chronic myelomonocytic leukemia, blocking CXCL8 produced by clonal dysplastic granulocytes is a potential therapeutic strategy to slow disease progression. [Data provided] Exome-sequencing, bulk mRNA-seq and single-cell RNA-seq of iGRAN, monocytes and PBMC of CMML patients and controls.

  Dataset EGAD50000000789

• Sequence data for "An allele-resolved nanopore-guided tour of the human placental methylome" (Kindlova et al 2025)

  Sequence data generated for the study "An allele-resolved nanopore-guided tour of the human placental methylome" includes Illumina WGS, Illumina RNA-seq, Illumina EM-seq, and Oxford Nanopore Technologies PromethION sequence data.

  Dataset EGAD50000001850

• Genome-Wide Association Studies of Prematurity and Its Complications (African American)

  Preterm delivery resulting in the birth of a premature infant is a complex problem with a devastating impact on individuals, families and society. The prevalence of preterm birth has increased steadily in developed countries over the last 20 years and more than three million children die of preterm birth worldwide each year. Despite the importance of the problem and its disproportionate occurrence in poor and minority populations, the underlying causes have been difficult to identify. Spontaneous preterm labor has as its suspected triggers infection, stress, poor nutrition and inherited factors. The single best predictor for preterm delivery is a previous preterm birth. Studies of twins and of recurrences within families provide evidence that genetic factors underlie a substantive component of the risk for prematurity. One major challenge in studying genetic factors in prematurity is that the risk case is not truly established. The genetic risk could reside either in the mother and her uterus or in the infant/placenta. Identification of genetic factors in the mother and/or infant could provide insights into identifying relevant environmental covariates that may be more amenable to rapid interventions but difficult to find using standard epidemiology alone. A comprehensive genome-wide association study (GWAS) is the ideal way to identify those genes that would not be suspected based on our current understanding of the biology of parturition. We are using 2200 African American samples with term or preterm labor. A subset of these (~800) are infant samples recruited by the Neonatal Research Network as part of a study on cytokines and infection in extremely low birth weight infants (Schelonka RL, et al., 2011. PMID: 21145756). Therefore, this group consists of infants <1,000 grams with clinical outcome data for the infant allowing study of the genetic contributors for not only preterm birth but also the complications that often accompany preterm birth. The result will enable a better understanding of the biology of parturition and suggest environmental modifications that can prolong gestations to improve neonatal and adult outcomes. This study is part of the Gene Environment Association Studies initiative (GENEVA, http://www.genevastudy.org) funded by the trans-NIH Genes, Environment, and Health Initiative (GEI). The overarching goal is to identify novel genetic factors that contribute to preterm birth through large-scale genome-wide association studies of African-American cases and controls from multiple sites in the United States. Genotyping was performed at the Johns Hopkins University Center for Inherited Disease Research (CIDR). Data cleaning and harmonization were done at the GEI-funded GENEVA Coordinating Center at the University of Washington.

  Study phs000353

• RNA-Sequencing of cervical cancers

  Question: Can we identify cervical cancer patients who are at risk for distant metastatic (DM) recurrence following treatment with radiotherapy, concurrent weekly cisplatin and brachytherapy (RTCT). Findings: An immune-based 55 gene risk score was developed using a cohort of 81 patients treated with RTCT that was strongly predictive of DM and cause-specific survival (CSS). The risk score was validated in two independent patient cohorts. A high immune metastatic risk score was associated with a high tumor mutational burden and a ‘cold’, immune-excluded tumor microenvironment at diagnosis. Meaning: The immune gene expression risk score may help to identify patients at risk of DM and potential targets for mitigating this risk.

  Study EGAS50000000087