14977 results for "cancer studies using rna-seq"

in 126.33 milliseconds.

• 1__Fanconi_Anemia_transformation_to_AML

  Genomic libraries (500 bps) will be generated from total genomic DNA derived from 7 Fanconi anemia (FA) derived Acute myeloid leukemia samples and subjected to total of two lanes of 50 bp, paired end sequencing on the llumina HiSeq. 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 EGAS00001000033

• CML_blast_phase_rearrangement_screen

  Genomic libraries (500 bps) will be generated from total genomic DNA derived from 10 Chronic Myeloid Leukemia in blast phase samples and subjected to a total of two lanes of 50 bp, paired end sequencing on the llumina HiSeq. 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 EGAS00001000191

• Genetic subclone heterogeneity of tumor-initiating cells in human colorectal cancer

  A subset of tumor-initiating cells (TIC) drives colorectal cancer (CRC) progression in serial mouse xenografts. The TIC compartment itself is heterogeneous and comprises hierarchically organized long-term TIC, tumor transient amplifying cells, and delayed contributing TIC. To address the genomic heterogeneity of the CRC TIC compartment, genome-wide high-coverage whole genome sequencing was performed on patient tumors (n=3), corresponding serially passaged TIC-enriched spheres, and serial xenografts.HIPO P002

  Study EGAS00001001857

• MutWP5__CRUK_Mutographs_of_Cancer__Breast__BRCA_Carriers__Exome_

  Sequencing of LCM-derived microbiopsies from 20 women who underwent risk-reducing reduction mastectomies due to germline BRCA1/2. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Exome data will be used as a driver and clonality screen, highly clonal or driver-containing samples will subsequently be sent for whole-genome sequencing. Results from this portion of the study will be compared to women who had cosmetic breast reduction surgeries and those with cancer.

  Study EGAS00001003316

• MutWP5__CRUK_Mutographs_of_Cancer__Breast__BRCA_Carriers__Targeted_

  Sequencing of LCM-derived microbiopsies from 20 women who underwent risk-reducing reduction mastectomies due to germline BRCA1/2. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Targeted data will be used as a driver and clonality screen, highly clonal or driver-containing samples will subsequently be sent for whole-genome sequencing. Results from this portion of the study will be compared to women who had cosmetic breast reduction surgeries and those with cancer.

  Study EGAS00001003315

• Circulating tumor cell copy-number heterogeneity in ALK-rearranged non-small-cell lung cancer resistant to ALK inhibitors

  Gatekeeper mutations are identified in only 50% of the cases at resistance to Anaplastic Lymphoma Kinase (ALK)-tyrosine kinase inhibitors (TKIs). Circulating tumor cells (CTCs) are relevant tools to identify additional resistance mechanisms and can be sequenced at the single-cell level. Here, we provide in-depth investigation of copy number alteration (CNA) heterogeneity in phenotypically characterized CTCs at resistance to ALK-TKIs in ALK-positive non-small cell lung cancer.

  Study EGAS00001005301

• MutWP5__CRUK_Mutographs_of_Cancer__Breast__Cancer_Mastectomy__Targeted_

  Sequencing of LCM-derived microbiopsies from 30 women who mastectomies due to Breast Cancer. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Targeted data will be used as a driver and clonality screen, highly clonal or driver-containing samples will subsequently be sent for whole-genome sequencing. Results from this portion of the study will be compared to women who had cosmetic breast reduction surgeries and those with germline BRCA 1/2 mutations.

  Study EGAS00001003318

• To_profile_the_landscape_of_sebaceous_tumours_WES

  Sebaceous tumours are a rare cutaneous cancer with potential for aggressive behaviour. However, limited information is available on these cancers with few published cases. Here we wish to exome sequence these cancers to define the first genomic landscape for this malignancy. We will extract DNA from formalin-fixed, paraffin-embedded (FFPE) cores. Cores may be obtained from lesional and non-lesional tissues of primaries as well as matching metastases. The extracted DNA will be used for exome sequencing.

  Study EGAS00001003553

• Preservation of stemness in high-grade serous ovarian cancer organoids requires low Wnt environment

  High-grade serous ovarian cancer (HGSOC) likely originates from the fallopian tube (FT) epithelium, but advanced stages are mostly found outside the FT. We used ex-vivo cultures of HGSOC and knock-out of tumor suppressors in FT organoids to study changes in epithelial cells and niche requirements for normal and transformed FT cells. We found that transformed cells require BMP signaling and are growth arrested in Wnt rich medium.

  Study EGAS00001003821

• Genomic landscape of Neutrophilic Leukemias of Ambiguous Diagnosis

  Chronic neutrophilic leukemia (CNL), atypical chronic myeloid leukemia (aCML), and unclassified myelodysplastic syndrome/myeloproliferative neoplasms (MDS/MPN-U) are a group of rare, heterogeneous myeloid disorders. There is strong morphologic resemblance amongst these distinct diagnostic entities as well as lack of specific molecular markers and limited understanding of disease pathogenesis, which has made their diagnosis challenging. Treatment has remained empirical, resulting in dismal outcomes. We, therefore, performed whole exome and RNA-sequencing on a cohort of over 100 cases of these rare hematologic malignancies and present the most complete survey of the genomic landscape of these diseases to date. [Abstract from manuscript currently under review so copyright not yet determined]

  Study phs001799

• Transcriptomic profiling of granulosa cells from IVF patients at different ages

  Two major factors contributing to reduced fertility is use of exogenous hormones and old age. Here, we sequenced RNA from granulosa cell samples from human patients undergoing in vitro fertilization to test how hormonally stimulated cells' transcriptional profiles change with age. All patients were normal responders referred for male infertility and were grouped into two age groups. The gene expression differences in aging were compared to mouse data (previous experiments, see ArrayExpress E-MTAB-13479) and the results are published in the article "Granulosa cell transcription is similarly impacted by superovulation and aging and predicts early embryonic trajectories". Corresponding count tables are available in ArrayExpress (E-MTAB-13496).

  Study EGAS50000000824

• Pathologically Expanded Peripheral B Cell-Helper T Cells in Rheumatoid Arthritis

  PROSET-HD aims to identify and study immune cell populations altered in patients with autoimmune and inflammatory diseases. We have identified a population of PD-1hi CXCR5- 'peripheral helper' T (Tph) cells that are expanded in the joints and circulation of patients with seropositive rheumatoid arthritis. This T cell population uniquely combines potent B cell-helper function with a migratory program that directs homing to inflamed tissues. RNA sequencing was performed on sorted memory CD4+ T cell subpopulations to compare the global gene expression profiles of PD-1hi CXCR5- CD4+ T cells, PD-1hi CXCR5+ follicular helper T cells, and other T cell populations obtained from blood of rheumatoid arthritis patients.

  Study phs001262

• Whole blood RNAseq from a large ALS case-control study at Univ of Michigan

  Patients with amyotrophic lateral sclerosis (ALS), a rare fatal neurodegenerative disease, face a lengthy diagnostic process, and, although most survive only 2 to 4 years from diagnosis, lack information regarding their specific anticipated disease course due to a lack of prognostic tools. Although ALS is a heterogeneous disease of varied etiology, peripheral immune system dysfunction is ubiquitous, reflected in altered whole blood transcriptome. Herein, we profiled whole blood gene expression by RNA sequencing in a large cohort of ALS cases versus controls. Several machine learning classifiers trained on our gene expression dataset predicted case-control status and survival, and integration analysis with external cohorts led to the identification of drug candidates.

  Study EGAS50000001019

• Host-microbe interactions in a novel SARS-CoV-2 human challenge model

  This research leverages previously collected clinical data and samples from a first-in-human SARS-CoV-2 challenge study conducted in healthy adults without serological evidence of prior infection or vaccination. We performed shotgun metagenomic and RNA sequencing of serially collected mid-turbinate nasal and throat swab samples from 34 adults who were inoculated with a wild-type virus, 18 (53%) of whom developed PCR-confirmed infection. By integrating microbiome and host transcriptome data, this research will provide insight into the complex interplay between the upper respiratory microbiota and the host immune system, offering a deeper understanding of factors that influence susceptibility to and severity of SARS-CoV-2 and other respiratory viral infections.

  Study EGAS50000001440

• Transcriptomic profiling of proximal and distal regions of human long head biceps tendon

  Tendinopathy is a prevalent musculoskeletal disorder marked by extracellular matrix disorganization, collagen remodeling, vascular ingrowth, and pain, yet its underlying molecular mechanisms remain insufficiently defined. The long head of the biceps tendon (LHBT) is particularly prone to mechanical overload and early degenerative changes, making it a relevant model for studying tendon pathology. In this study, we aimed to characterize region-specific gene expression changes along the LHBT to better understand the molecular basis of degeneration. We collected paired proximal and distal LHBT tissue from patients undergoing rotator cuff repair surgery and performed bulk RNA sequencing. This approach enables the identification of degeneration-associated transcriptional signatures while minimizing inter-patient variability.

  Study EGAS50000001454

• Origins and timing of emerging lesions in advanced renal cell carcinoma

  Renal cell carcinoma (RCC) with venous tumor thrombus (VTT) arising from the primary tumor occurs in ~10% of cases and is thought to represent more advanced disease. RCC with VTT and distant metastasis provides unique opportunities to examine the origins and relative timing of tumor lesion emergence and to identify molecular correlates with disease state. We performed multi-region exome and RNA sequencing analysis of a clinical cohort of 16 RCC patients with VTT, with eight patients also having sequenced metastasis, to examine which genomic alterations, biological pathways, and evolutionary processes contribute to VTT and metastasis, and to ask whether metastasis typically arises directly from VTT or is independent of VTT.

  Study EGAS00001005897

• Genomic profiling of IBC

  We collected matched pretreatment blood and tumor samples from 19 patients with primary TN-IBC enrolled in a phase II clinical trial (NCT02876107). Patients were treated with neoadjuvant chemotherapy (NAC) or the anti-EGFR antibody panitumumab (PmAb) plus NAC (PmAb/NAC). We conducted whole-exome sequencing, RNA sequencing, and CIBERSORT analyses for these TN-IBC samples and compare the genetic and molecular profiles with similarly analyzed stage III TN-non-IBC patient samples. We also compared the genetic and molecular characteristics of TN-IBC in patients who had a pathologic complete response (pCR) to NAC or PmAb/NAC treatment, a suitable surrogate endpoint for IBC, with those who did not have pCR (non-pCR).

  Study EGAS00001007520

• Using NGS to Sequence Whole Genomes to Identify Genes Underlying ALS

  Our ALS Consortium - a partnership of clinicians, basic scientists, geneticists, and computational biologists from 48 institutions (4 of which are industry partners) across 5 countries - establishes a framework to apply whole genome sequencing (WGS) and functional genomics to the study of amyotrophic lateral sclerosis (ALS). Because ALS-causing mutations tend to be of moderate impact and are relatively rare in the population (reviewed in Al-Chalabi et al., 2017, PMID: 27982040), identification of new mutations require several thousand samples, which need to be obtained from multiple sites (even the busiest ALS clinics see only 200-400 patients per year). ALS Consortium is using genomics technologies to study the causes and mechanisms underlying neurodegenerative disease, and the contribution of various cell types within the brain and spinal cord. Much of this work is done and continues to be done in collaboration with the members of the NYGC ALS Consortium.

  Study phs003067

• Targeted Mutational Analysis of Intestinal T-cell Lymphomas, Using a Customized Targeted Amplicon Panel on the Ion Torrent PGM

  Intestinal T-cell lymphomas (ITCL) are rare, aggressive T-cell lymphomas that are composed primarily of enteropathy-associated lymphomas Type 1 and type 2, and a small fraction of cases not classifiable as EATL that are classified as peripheral T-cell lymphoma, not otherwise classifiable. The molecular pathogenesis of these rare lymphomas is largely unknown. We studied a series of 34 ITCL cases using a combination of amplicon based targeted next generation sequencing and pyrosequencing for mutations in 34 genes previously reported to be mutated in other types of T-cell lymphomas and other genes known to have significant roles in normal T-cell proliferation. We identified a high percentage of cases with mutations in JAK/STAT signaling pathway members, and also in RAS family members. Notably, we did not detect GNAI-2 mutations in our North American cases of EATL type 2 by targeted pyrosequencing, which had been reported previously in Asian cases.

  Study phs001126

• The University of Hong Kong Gastric Cancer Exome Sequencing Project Data Access Committee

  Dac EGAC00001000032

• Cancer genomics project, the University of Tokyo Data Access Committee

  Dac EGAC00001000087

• DAC for the study of response to EGFR Blockade in Colorectal Cancer

  Dac EGAC00001000360

• Data access committee of the Prostate Cancer Research Center, University of Tampere, Finland.

  Dac EGAC00001000423

• UT MD Anderson Cancer Center Department of Genomic Medicine Lipoasarcoma Data Access Committee

  Dac EGAC00001000821

• The evolutionary history of human colitis-associated colorectal cancer

  Dac EGAC00001000917

• DAC for study: Frequent mutation of the FOXA1 untranslated region in prostate cancer

  Dac EGAC00001000962

• Age-related remodeling of apparently normal esophageal epithelia by common cancer drivers

  Dac EGAC00001001067

• DAC for study: Evaluation of commercial Guardant360 ctDNA test in metastatic prostate cancer

  Dac EGAC00001001082

• Immune and Metabolic Features of Brain Metastases Melanoma (Cancer Discovery) Data Access Committee

  Dac EGAC00001001216

• Mutational Study Committee of a Taiwanese Lung Cancer Cohort (MSCTLCC)

  Dac EGAC00001001614