11805 results for "cancer rna-seq"

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• CIDR: The Role of Rare Coding Variation in Prostate Cancer in Men of African Ancestry - RESPOND Project 2

  In RESPOND Project 2, we seek to identify rare genetic factors that are associated with prostate cancer (PCa) risk and aggressiveness in men of African ancestry (AA). We will conduct exome sequencing of 15,000 prostate cancer cases and 5,000 controls from the RESPOND cohort and the African Ancestry Prostate Cancer Consortium (AAPC) with cases selected based on risk categories: high-risk (stage T3/T4 or Gleason 8+ or PSA>20 ng/ml), intermediate-risk (stage T2b/T2c or Gleason 7 or PSA 10-20 ng/ml) and low-risk disease (stage T1/T2a and Gleason ≤ 6 and PSA<10 ng/ml). We expect the findings from this Project to significantly advance knowledge of susceptibility to aggressive PCa and racial/ethnic disparities in PCa risk, and to guide the development of future preventive, early detection and prognostic measures for AA men. The first phase of the study will include exome sequence data for approximately 7,500 cases and 5,000 controls from AAPC. The second phase of the study will include exome data for 5,000 cases from RESPOND and AAPC.ACKNOWLEDGMENTS and CONTRIBUTING SITES Multiethnic Cohort (MEC): The MEC and the genotyping in this study were supported by National Institutes of Health (NIH) grants CA63464, CA54281, CA1326792, CA148085, and HG004726. Cancer incidence data for the MEC and Los Angeles Study of Aggressive Prostate Cancer (LAAPC) studies have been collected by the Los Angeles Cancer Surveillance Program of the University of Southern California with federal funds from the National Cancer Institute (NCI)/NIH/Department of Health and Human Services (DHHS) under Contract No. N01-PC-35139, and the California Department of Health Services as part of the state-wide cancer reporting program mandated by California Health and Safety Code Section 103885, and grant 1U58DP000807-3 from the Centers for Disease Control and Prevention (CDC). Ghana Prostate Study (GPS): The Ghana Prostate Study was funded by the Intramural Program of the NCI/NIH/DHHS under Contract No. HHSN261200800001E. Men of African Descent and Carcinoma of the Prostate (MADCaP): We thank all MADCaP study participants. This work is a product of the MADCaP network. This work was supported by NCI/NIH grant U01CA184374 to Timothy Rebbeck and National Institute of General Medical Sciences (NIGMS) MIRA grant R35GM133727 to Joseph Lachance. Additional funding includes a seed grant from the Integrated Cancer Research Center at Georgia Institute of Technology. UGANDA: The UGANDA study was supported by NIH grant R01CA165862. Southern Community Cohort (SCCS) is funded by NIH grant CA092447. SCCS sample preparation was conducted at the Epidemiology Biospecimen Core Lab that is supported in part by the Vanderbilt Ingram Cancer Center (CA68485). Data on SCCS cancer cases were provided by Alabama Statewide Cancer Registry, Kentucky Cancer Registry, Office of Cancer Surveillance at Tennessee Department of Health, Florida Cancer Data System, Central Cancer Registry at North Carolina Division of Public Health, Georgia Comprehensive Cancer Registry, Louisiana Tumor Registry, Mississippi Cancer Registry, South Carolina Central Cancer Registry, Virginia Cancer Registry at Virginia Department of Health, and Cancer Registry at Arkansas Department of Health. The Arkansas Central Cancer Registry is fully funded by a grant from National Program of Cancer Registries (NPCR)/Centers for Disease Control and Prevention (CDC). Data on SCCS cancer cases from Mississippi were collected by the Mississippi Cancer Registry which participates in the NPCR/CDC. The contents of this publication are solely the responsibility of the authors and do not necessarily represent the official views of the CDC or the Mississippi Cancer Registry. Karuprostate: The Karuprostate study was supported by the French National Health Directorate and by the Association pour la Recherche sur les Tumeurs de la Prostate. Séverine Ferdinand, Marc Romana. The North Carolina - Louisiana Prostate Cancer Project (PCaP) is carried out as a collaborative study supported by the Department of Defense contract DAMD 17-03-2-0052. The authors thank the staff, advisory committees and research subjects participating in the PCaP study for their important contributions. We would also like to acknowledge the UNC BioSpecimen Facility and the LSUHSC Pathology Lab for our DNA extractions, blood processing, storage and sample disbursement (https://genome.unc.edu/bsp). Gene-Environment Interaction in Prostate Study (GECAP) was supported by NIH grant ES011126. King County Prostate Cancer Study (KCPCS) was supported by NIH grants CA056678, CA082664, and CA092579, with additional support from the Fred Hutchinson Cancer Research Center. We thank the participants in these studies, and Ms. Suzanne Kolb for help with study management. The Los Angeles Study of Aggressive Prostate Cancer (LAAPC) was funded by grant 99-00524V-10258 from the Cancer Research Fund, under Interagency Agreement #97-12013 (University of California contract #98-00924V) with the Department of Health Services Cancer Research Program. Cancer incidence data for the MEC and LAAPC studies have been collected by the Los Angeles Cancer Surveillance Program of the University of Southern California with Federal funds from the NCI/NIH/DHHS under Contract No. N01-PC-35139, and the California Department of Health Services as part of the state-wide cancer reporting program mandated by California Health and Safety Code Section 103885, and grant 1U58DP000807-3 from the CDC. Prostate Cancer Studies at MD Anderson (MDA) was supported by grants CA68578, ES007784, DAMD W81XWH-07-1-0645, and CA140388.

  Study phs002637

• The Prostate, Lung, Colon, Ovary Screening Trial (PLCO)

  The Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial is a large population-based randomized trial designed and sponsored by the National Cancer Institute (NCI) to determine the effects of screening on cancer-related mortality and secondary endpoints in over 150,000 men and women aged 55 to 74. The screening component of the trial was completed in 2006. However, participants have been under follow-up for cancer incidence and mortality since that time. In addition, PLCO included a large biological sample biorepository which has served as a unique resource for cancer research, particularly for etiologic and early-marker studies. As part of these efforts, PLCO has been used for a large number of genome-wide association and exome sequencing studies for different types of cancer. Recently, a blood DNA methylation analysis was conducted in annexes case-controls study of breast cancer.

  Study phs001286

• High volume culture initiating in vitro evolution in neuroblastoma cell lines

  Despite the advent of advanced molecular prognostic tools, it is still difficult to predict the course of disease for cancer patients at the individual level. This lack of predictability is also reflected in many experimental cancer model systems, begging the question of whether certain biological aspects of cancer (eg. growth, evolution etc.) can ever be anticipated or if there remains an inherent unpredictability to cancer, similar to other complex biological systems. We demonstrate by a combination of agent-based mathematical modelling, analysis of patient-derived xenograft systems from multiple cancer types, and in-vitro culture that certain conditions may invoke chaotic fluctuations in the clonal landscape of cancer growth. Our findings indicate that under those conditions, the cancer genome may behave as a complex dynamic system, making its long-term evolution inherently unpredictable.

  Study EGAS00001007962

• README-for-EGAS00001004349-linking-HIPO-K09R-RNA-files

  Dataset EGAD00001006785

• RNA-sequençing of 21 inflammatory hepatocellular adenomas and 1 non-tumoral sample

  Dataset EGAD00001005284

• ADARIO Dataset

  RNA editing analyses of BRCA-isogenic cell lines and patient-derived xenografts (PDX)

  Dataset EGAD50000000739

• Adrenal scRNA sequencing data access

  Raw sequencing datasets for manuscript "Hybrid untargeted and targeted RNA sequencing facilitates genotype-phenotype associations at single-cell resolution".

  Dac EGAC50000000869

• The Genetic Basis of Aggressive Prostate Cancer, The Role of Rare Variation

  In this study, we will apply a multi-staged approach to reveal genes harboring rare variants that are associated with aggressive PCa. Whole-exome sequencing (Aim 1a) of 2,774 aggressive cases and 2,776 non-aggressive cases of European ancestry will be conducted followed by rare variant analysis of single sites and gene burden testing to identify novel susceptibility loci/genes for aggressive disease. We will validate the most significantly associated genes (~500) through targeted sequencing in an additional 6,415 aggressive and 5,586 non-aggressive cases and 1,890 controls (Aim 1b). Next, we will investigate the clinical predictive utility of the genes/variants identified in 2,291 cases in the STHM3 trial who are undergoing biopsy based on PSA and genetic risk score stratification (Aim 2). Through this tiered approach we expect to significantly advance knowledge of aggressive PCa etiology and health disparities as well as guide the development of early detection and prognostic strategies for the subset of men who are most susceptible to this fatal form of disease. In this case-case study of aggressive vs non aggressive prostate cancer, aggressive cases are defined as prostate cancer as cause of death, (T4 disease or T3 disease) and Gleason 8+. Non-aggressive cases are men with T1/2 disease and Gleason ACKNOWLEDGMENTS and CONTRIBUTING SITES CAPS, PROCAP, STHM1, STHM2: Swedish Cancer Society (CAN 2016/818), Swedish Research Council (2014/2269).STHM3: Stockholm County Council (Stockholms Läns Landsting).MEC: Funding provided by the National Cancer Institute: Understanding Ethnic Differences in Cancer, 2U01CA164973 and The Genetic Basis of Aggressive Prostate Cancer, The Role of Rare Variation, 5R01CA196931-02.ATBC: The ATBC Study is supported by the Intramural Research Program of the U.S. National Cancer Institute, National Institutes of Health, and by U.S. Public Health Service contract HHSN261201500005C from the National Cancer Institute, Department of Health and Human Services.COSM: The Swedish Research Council/National Research Infrastructure Grant (VR 2014/6397; VR 2015/5997) The Swedish Cancer Foundation (CAN 2013/456; CAN 2016/727)CPSII: The authors express sincere appreciation to all Cancer Prevention Study II participants and to each member of the study and biospecimen management group. The American Cancer Society funds the creation, maintenance, and updating of the Cancer Prevention Study-II cohort.MCCS/APCS/PCFS: The Melbourne Collaborative Cohort Study (MCCS) recruitment was funded by VicHealth and Cancer Council Victoria and further supported by Australian National Health and Medical Research Council (NHMRC) grants 209057 and 396414. The Aggressive Prostate Cancer Case-Control Study (APCS) was funded by NHMRC grant 623204. The Prostate Cancer Family Study (PCFS) was fully funded by Cancer Council Victoria. Cancer Council Victoria funds the continuing maintenance and updating of the MCCS, APCS and PCFS. Cases and their vital status are ascertained and followed up through the Victorian Cancer Registry and the Australian Institute of Health and Welfare, including the National Death Index and the Australian Cancer Database.PLCO: The Prostate Lung Colorectal Ovarian Cancer Screening Trial (PLCO) was supported by the Intramural Research Program of the Division of Cancer Epidemiology and Genetics and by contracts from the Division of Cancer Prevention, National Cancer Institute, US National Institutes of Health, Department of Health and Human Services. EPIC: The coordination of EPIC is financially supported by International Agency for Research on Cancer (IARC) and also by the Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London which has additional infrastructure support provided by the NIHR Imperial Biomedical Research Centre (BRC). The national cohorts are supported by: Danish Cancer Society (Denmark); Ligue Contre le Cancer, Institut Gustave Roussy, Mutuelle Générale de l'Education Nationale, Institut National de la Santé et de la Recherche Médicale (INSERM) (France); German Cancer Aid, German Cancer Research Center (DKFZ), German Institute of Human Nutrition Potsdam- Rehbruecke (DIfE), Federal Ministry of Education and Research (BMBF) (Germany); Associazione Italiana per la Ricerca sul Cancro-AIRC-Italy, Compagnia di SanPaolo and National Research Council (Italy); Dutch Ministry of Public Health, Welfare and Sports (VWS), Netherlands Cancer Registry (NKR), LK Research Funds, Dutch Prevention Funds, Dutch ZON (Zorg Onderzoek Nederland), World Cancer Research Fund (WCRF), Statistics Netherlands (The Netherlands); Health Research Fund (FIS) - Instituto de Salud Carlos III (ISCIII), Regional Governments of Andalucía, Asturias, Basque Country, Murcia and Navarra, and the Catalan Institute of Oncology - ICO (Spain); Swedish Cancer Society, Swedish Research Council and County Councils of Skåne and Västerbotten (Sweden); Cancer Research UK (14136 to EPIC-Norfolk; C8221/A19170 and C8221/A29017 to EPIC-Oxford), Medical Research Council (1000143 to EPIC-Norfolk; MR/M012190/1 to EPIC-Oxford). (United Kingdom). DFCI: Linda and Arthur Gelb and Rebecca and Nathan Milikowsky. HPFS and PHS: The Health Professionals Follow-up Study was supported by U01 167552 and P01 CA228696 from the National Cancer Institute, and with support from the Prostate Cancer Foundation. The Physicians' Health Study was supported by grants CA34944, CA40360, CA097193, HL26490 and HL34595.Northwestern: P50CA180995 (Catalona) 08/01/15 – 07/31/20 NIH/NCI SPORE in Prostate Cancer; The Urological Research FoundationPROMPT: MRC UK - Project reference G0500966, Cambridge BRC infrastructure funding, Cambridge Biomedical Research Campus (BRC-1215-20014), CRUK Cambridge Cancer Centre infrastructure funding (they are requesting this statement is written in blue for publications).ICR: This work was supported by the NIH R01 grant 5R01CA196931-02. The samples from the UK were from UKGPCS and PrompT. The UKGPCS study was supported by Cancer Research UK (grant numbers C5047/A7357, C1287/A10118, C1287/A5260, C5047/A3354, C5047/A10692, C16913/A6135 and C16913/A6835). We would like to acknowledge the NCRN nurses and Consultants for their work in the UKGPCS study. We thank all the patients who took part in this study. We also acknowledge The Institute of Cancer Research, The National Cancer Research Network UK, The National Cancer Research Institute (NCRI) UK for their ongoing support. We are grateful for support of NIHR funding to the NIHR Biomedical Research Centre at The Institute of Cancer Research and The Royal Marsden NHS Foundation Trust.Funding:CIDR grant X01HG008336

  Study phs001524

• ATAC Dataset for 19 T-ALL patient samples and 1 normal control sample

  19 ATAC-seq from T-ALL patient samples and one healthy normal control sample. Reads were aligned to HG38 reference

  Dataset EGAD50000000024

• ChIPseq data for Glioblastoma (EGAS00001003953, H016)

  ChIPseq data for human glioblastoma patients, EGAS00001003953. Mix of input, H3K27ac, H3K27me1, H3K27me3, H3K36me3, H3K4me1, H3K4me3, H3K9me3 and BRD, 20 human samples, 2 cell lines (LN229, ZH487).

  Dataset EGAD00001006548