Gene Expression Patterns in Human Tumors Identified Using Transcript Sequencing
使用转录测序鉴定人类肿瘤中的基因表达模式
基本信息
- 批准号:8925212
- 负责人:
- 金额:$ 50万
- 依托单位:
- 依托单位国家:美国
- 项目类别:
- 财政年份:2009
- 资助国家:美国
- 起止时间:2009-09-29 至 2016-06-30
- 项目状态:已结题
- 来源:
- 关键词:Alternative SplicingBase SequenceBinding SitesBiological AssayBreastCancer EtiologyCharacteristicsChromatinClinicalCodeCoupledDNADNA MethylationDNA Microarray ChipDNA SequenceDNA copy numberDataDevelopmentDiseaseDistantEnhancersEpigenetic ProcessEventFormaldehydeGene ExpressionGene Expression ProfileGene Expression ProfilingGene StructureGenesGenomeGenomic DNAGenomicsGlioblastomaHead and neck structureHumanIndividualInfectious AgentInformaticsInstructionKnowledgeLeadLinkLocationLocus Control RegionMalignant NeoplasmsMalignant neoplasm of lungMammalian CellMapsMeasurementMessenger RNAMethodsMicroRNAsMolecular ProfilingMutateMutationNatureNormal tissue morphologyNucleosomesOligonucleotide MicroarraysOutcomeOutputPaintPathogen detectionPatientsPatternPersonsPhasePortraitsProceduresProtein IsoformsProteinsRNA SplicingRegulationRegulatory ElementRelative (related person)Research InfrastructureRoleSNP genotypingSolidTechnologyTestingThe Cancer Genome AtlasTimeTissuesTranscriptTumor BiologyTumor SubtypeTumor Suppressor GenesViralbasecancer genomechromatin remodelingcostdeep sequencingdisorder subtypeexperiencefusion genegene functiongenome wide association studygenome-widehistone modificationimprovedinfancyinsightnext generationnext generation sequencingnovelpathogenpromoterresearch studytooltranscription factortumor
项目摘要
Gene expression provides a snapshot of the cellular changes that promote tumor malignancy.
Quantitative gene expression analysis, especially as implemented by DNA microarrays, has proven to be an
extremely valuable tool for cancer genome characterization, and has lead to the development of new
genomic-based clinical tests. Our own experience with DNA microarrays to study gene expression patterns
for breast, head & neck, and lung cancers has lead to the identification of novel subtypes of tumors with
distinct patient outcomes and has identified new tumor suppressor genes. In the pilot phase of The Cancer
Genome Atlas (TCGA) project, multiple platforms were used including tools to study gene expression (our
role), tumor genomic DNA copy number alterations, SNP genotypes, DNA methylation and gene mutational
analyses. Our collaborative efforts identified new tumor subtypes of glioblastoma and painted an integrated
picture linking mutations to copy number changes to expression patterns, which identified biologically distinct
subtypes of disease with differences in patient outcomes.
For the second phase of TCGA project, we propose to continue to perform quantitative gene expression
profiling of all protein-coding genes, non-protein coding mRNAs(ncRNAs) and microRNAs, on -2000 tumors
per year. This approach has proven to be one of the most informative and comprehensive cancer genome
characterization tools available. In addition, we propose to generate global chromatin organization profiles of
cancer to identify regions of "open" chromatin domains (nucleosome-depleted regions). We will use FAIRE
(Formaldehyde-Assisted isolation of Regulatory Elements), a simple, low-cost method amenable to use on
small quantities of solid tissue, coupled to next-generation DNA sequencing. Since the function of most
histone modifications and chromatin remodeling activities is to regulate nucleosome occupancy, FAIRE
effectively summarizes the functional output of such epigenetic mechanisms in a single robust assay. Lastly,
we propose to perform integrated analyses of transcript levels with chromatin stoicture to map important
regulatory elements, which can be distant to the transcript(s) that they regulate. Our study of genome-wide
transcript regulation with chromatin organization will provide a critical portrait of the cancer genome that can
be integrated with (and indeed can sometimes generate) other important data, including mutations and copy
number events.
基因表达提供了促进肿瘤恶性的细胞变化的快照。
项目成果
期刊论文数量(0)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
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David N Hayes其他文献
David N Hayes的其他文献
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{{ truncateString('David N Hayes', 18)}}的其他基金
UNITS: The UNC / UT National Clinical Trials Network Group Integrated Translational Science Production and Consultation Center
单位:北卡罗来纳大学/德克萨斯大学国家临床试验网络集团综合转化科学生产和咨询中心
- 批准号:
9892991 - 财政年份:2019
- 资助金额:
$ 50万 - 项目类别:
UNITS: The UNC / UT National Clinical Trials Network Group Integrated Translational Science Production and Consultation Center
单位:北卡罗来纳大学/德克萨斯大学国家临床试验网络集团综合转化科学生产和咨询中心
- 批准号:
10581560 - 财政年份:2019
- 资助金额:
$ 50万 - 项目类别:
UNITS: The UNC / UT National Clinical Trials Network Group Integrated Translational Science Production and Consultation Center
单位:北卡罗来纳大学/德克萨斯大学国家临床试验网络集团综合转化科学生产和咨询中心
- 批准号:
10353405 - 财政年份:2019
- 资助金额:
$ 50万 - 项目类别:
Development of a Four-Class, Molecular Subtyping Diagnostic for HPV-negative Head and Neck Cancer
开发 HPV 阴性头颈癌的四类分子亚型诊断方法
- 批准号:
9752253 - 财政年份:2017
- 资助金额:
$ 50万 - 项目类别:
Development of a Four-Class, Molecular Subtyping Diagnostic for HPV-negative Head and Neck Cancer
开发 HPV 阴性头颈癌的四类分子亚型诊断方法
- 批准号:
10216187 - 财政年份:2017
- 资助金额:
$ 50万 - 项目类别:
Network Group Integrated Translational Science Centers Application
网络集团综合转化科学中心申请
- 批准号:
8840915 - 财政年份:2014
- 资助金额:
$ 50万 - 项目类别:
Network Group Integrated Translational Science Centers Application
网络集团综合转化科学中心申请
- 批准号:
9235259 - 财政年份:2014
- 资助金额:
$ 50万 - 项目类别:
Gene Expression Patterns in Human Tumors Identified Using Transcript Sequencing
使用转录测序鉴定人类肿瘤中的基因表达模式
- 批准号:
7942756 - 财政年份:2009
- 资助金额:
$ 50万 - 项目类别:
Gene Expression Patterns in Human Tumors Identified Using Transcript Sequencing
使用转录测序鉴定人类肿瘤中的基因表达模式
- 批准号:
8537844 - 财政年份:2009
- 资助金额:
$ 50万 - 项目类别:
Gene Expression Patterns in Human Tumors Identified Using Transcript Sequencing
使用转录测序鉴定人类肿瘤中的基因表达模式
- 批准号:
8117265 - 财政年份:2009
- 资助金额:
$ 50万 - 项目类别:
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