GTEx engagement with the CFDE-CC and other DCCs towards building a data ecosystem spanning the Common Fund projects
GTEx 与 CFDE-CC 和其他 DCC 合作,构建涵盖共同基金项目的数据生态系统
基本信息
- 批准号:10905807
- 负责人:
- 金额:$ 77.92万
- 依托单位:
- 依托单位国家:美国
- 项目类别:
- 财政年份:2020
- 资助国家:美国
- 起止时间:2020-09-23 至 2024-09-22
- 项目状态:已结题
- 来源:
- 关键词:AddressAdultAreaBenchmarkingCalendarChIP-seqChildCollaborationsCollectionCommunitiesComplexDNA MethylationDNA sequencingDataData AnalysesData ProtectionData SetDeoxyribonuclease IDevelopmentDiseaseEducation and OutreachEducational workshopEnrollmentExonsFundingGene ExpressionGene Expression RegulationGenerationsGenesGenetic VariationGenetic studyGenotypeGenotype-Tissue Expression ProjectGoalsHistologyHistonesHumanHuman BioMolecular Atlas ProgramHypersensitivityImageInheritedJointsLinkMass Spectrum AnalysisMeasurementMetadataMolecularNormal tissue morphologyOrganPaperPediatric NeoplasmPlayPredispositionProcessProductionProtein IsoformsProteomicsPublishingQuantitative Trait LociRNA SequencesRNA SplicingResourcesRoleSamplingSiteTestingThe Cancer Genome AtlasTissue SampleTissuesTrainingTrans-Omics for Precision MedicineTranscriptUnited States National Institutes of HealthVisualizationWorkanalysis pipelinebiobankcloud platformcohortcomputing resourcescostdata accessdata ecosystemdata explorationdata resourcedata toolsdatabase of Genotypes and Phenotypesexomeexome sequencingexperimental studyhuman tissueinsightinterestlarge datasetstooltranscriptome sequencingtumorwhole genome
项目摘要
Detailed Engagement Plan
The National Institutes of Health Common Fund’s Genotype-Tissue Expression (GTEx) project was
launched in 2010 with a goal of providing the scientific community with a resource for the study of human
gene expression and regulation across multiple tissues, to specifically provide insights into the mechanisms
of gene regulation and disease-related perturbations, and to further our understanding of the role that
inherited genetic variation plays in susceptibility to complex diseases. The project enrolled 960 recently
deceased, adult donors and collected close to 49,000 tissue samples. Core data generation was
completed at the end of 2017, with the primary data types including whole genome (WGS, 30X) and whole
exome (WES, 100X) sequence data on all donors, and RNA-sequence data from at least 25,000 samples
spanning 53 human tissues/organs. This dataset constitutes the largest multi-tissue RNA sequence data
resource generated to date (a previous study of genetic effects on gene expression, TwinsUK/EUROBATS,
generated ~2,700 RNA-seq samples from four accessible tissue sites). The GTEx resource also includes
a rich and well annotated collection of donor, sample, and experiment metadata. Furthermore, additional
molecular data types, aimed at enhancing the core data sets, are still being produced, including mass
spectrometry-based proteomics, measurements of DNA methylation, histone marks (ChIP-seq), somatic
DNA sequencing, and DNase I hypersensitivity sites.
The GTEx resource includes both protected-access and open-access data (Fig. 1). The protected-access
data include extensive sample, subject and technical metadata and raw sequence BAM files from RNAseq,
whole genome (WGS) and whole exome (WES) sequencing, ChIP-seq and m6A RNA-seq, as well as
protected data derived from these such as genotype calls in VCF format. An approved dbGaP application
is required to obtain all protected-access data, including access to the raw sequence data, which are
accessible on the AnVIL platform (on Google Cloud Platform; GCP). The GTEx data also include a large
amount of open-access data, such as gene and transcript expression quantifications, cis- and trans-expression
and splicing QTLs, histology images of every tissue, some eGTEx data summaries, the sample
biobank, and a very limited set of de-identified sample and subject metadata. All of these public data are
available for download, and as interactive visualizations and summary tables on the GTEx portal.
The GTEx project has developed an extensive suite of tools and analysis pipelines that have been
benchmarked, optimized and implemented in GCP for the project (such as the RNA-seq alignment,
quantification, and QC pipeline, and the QTL analysis pipeline). These pipelines were also selected by the
TOPMed project to produce a harmonized resource of RNA sequence data across the large number of
cohorts being sequenced for that project (>20,000 samples to date); our team was involved in initial
benchmarking and harmonization tests of our pipeline across TOPMed sequencing centers and are actively
involved in ongoing data production and analyses. Moreover, very similar pipelines are used by the
ENCODE project, thus facilitating comparisons across large datasets that would be prohibitive in terms of
costs and computational resources in the absence of harmonized pipelines. We have also created
numerous visualizations developed specifically for the open access data on the GTEx portal. The GTEx
project has a very large user community: the GTEx data have the second largest number of Data Access
Requests for protected data in dbGaP (behind TCGA), and it is the most frequently downloaded dbGaP
project. An even larger number of users access the data, tools and interactive visualizations on the GTEx
portal: in the 2019 calendar year, the GTEx portal had 135,000 users (~12,000-18,000/month) worldwide,
with users spiking in October 2019 following the release of the V8 data. The GTEx consortium has published
numerous papers describing the dataset and analyses of the data, and two additional data releases are
still planned.
业务业务详细计划
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)
数据更新时间:{{ journalArticles.updateTime }}
{{
item.title }}
{{ item.translation_title }}
- DOI:
{{ item.doi }} - 发表时间:
{{ item.publish_year }} - 期刊:
- 影响因子:{{ item.factor }}
- 作者:
{{ item.authors }} - 通讯作者:
{{ item.author }}
数据更新时间:{{ journalArticles.updateTime }}
{{ item.title }}
- 作者:
{{ item.author }}
数据更新时间:{{ monograph.updateTime }}
{{ item.title }}
- 作者:
{{ item.author }}
数据更新时间:{{ sciAawards.updateTime }}
{{ item.title }}
- 作者:
{{ item.author }}
数据更新时间:{{ conferencePapers.updateTime }}
{{ item.title }}
- 作者:
{{ item.author }}
数据更新时间:{{ patent.updateTime }}
KRISTIN ARDLIE其他文献
KRISTIN ARDLIE的其他文献
{{
item.title }}
{{ item.translation_title }}
- DOI:
{{ item.doi }} - 发表时间:
{{ item.publish_year }} - 期刊:
- 影响因子:{{ item.factor }}
- 作者:
{{ item.authors }} - 通讯作者:
{{ item.author }}
{{ truncateString('KRISTIN ARDLIE', 18)}}的其他基金
Whole Individual Comprehensive KnowlEDge: Somatic Mosaicism across Human Tissues (WICKed SMaHT)
整体综合知识:人体组织的体细胞镶嵌(WICKed SMaHT)
- 批准号:
10662869 - 财政年份:2023
- 资助金额:
$ 77.92万 - 项目类别:
Developmental GTEx Laboratory, Data Analysis and Coordination Center
GTEx发展实验室、数据分析与协调中心
- 批准号:
10662497 - 财政年份:2021
- 资助金额:
$ 77.92万 - 项目类别:
Developmental GTEx Laboratory, Data Analysis and Coordination Center
GTEx发展实验室、数据分析与协调中心
- 批准号:
10302863 - 财政年份:2021
- 资助金额:
$ 77.92万 - 项目类别:
Developmental GTEx Laboratory, Data Analysis and Coordination Center
GTEx发展实验室、数据分析与协调中心
- 批准号:
10492761 - 财政年份:2021
- 资助金额:
$ 77.92万 - 项目类别:
GTEx engagement with the CFDE-CC and other DCCs towards building a data ecosystem spanning the Common Fund projects
GTEx 与 CFDE-CC 和其他 DCC 合作,构建涵盖共同基金项目的数据生态系统
- 批准号:
10444364 - 财政年份:2020
- 资助金额:
$ 77.92万 - 项目类别:
GTEx engagement with the CFDE-CC and other DCCs towards building a data ecosystem spanning the Common Fund projects
GTEx 与 CFDE-CC 和其他 DCC 合作,构建涵盖共同基金项目的数据生态系统
- 批准号:
10683507 - 财政年份:2020
- 资助金额:
$ 77.92万 - 项目类别:
GTEx engagement with the CFDE-CC and other DCCs towards building a data ecosystem spanning the Common Fund projects
GTEx 与 CFDE-CC 和其他 DCC 合作,构建涵盖共同基金项目的数据生态系统
- 批准号:
10468521 - 财政年份:2020
- 资助金额:
$ 77.92万 - 项目类别:
A portal and integrative collaborative analysis platform for GTEx
GTEx 的门户和综合协作分析平台
- 批准号:
10181004 - 财政年份:2017
- 资助金额:
$ 77.92万 - 项目类别:
相似海外基金
History of Community and Adult Education in Old Coal Mining Area in Northern Kyushu
九州北部老煤矿区社区与成人教育的历史
- 批准号:
26780447 - 财政年份:2014
- 资助金额:
$ 77.92万 - 项目类别:
Grant-in-Aid for Young Scientists (B)
High Risk Adult Hepatitis B Vaccination Pilot -Program Area 7
高危成人乙型肝炎疫苗接种试点 - 计划领域 7
- 批准号:
8506903 - 财政年份:2012
- 资助金额:
$ 77.92万 - 项目类别:
The San Francisco Bay Area Adult Glioma Survival Study
旧金山湾区成人神经胶质瘤生存研究
- 批准号:
7253800 - 财政年份:2007
- 资助金额:
$ 77.92万 - 项目类别:
San Francisco Bay area adult glioma survival study
旧金山湾区成人神经胶质瘤生存研究
- 批准号:
6686704 - 财政年份:2002
- 资助金额:
$ 77.92万 - 项目类别:
The San Francisco Bay Area Adult Glioma Survival Study
旧金山湾区成人神经胶质瘤生存研究
- 批准号:
8258656 - 财政年份:
- 资助金额:
$ 77.92万 - 项目类别:
San Francisco Bay area adult glioma survival study
旧金山湾区成人神经胶质瘤生存研究
- 批准号:
7550487 - 财政年份:
- 资助金额:
$ 77.92万 - 项目类别:
The San Francisco Bay Area Adult Glioma Survival Study
旧金山湾区成人神经胶质瘤生存研究
- 批准号:
8099448 - 财政年份:
- 资助金额:
$ 77.92万 - 项目类别:
San Francisco Bay area adult glioma survival study
旧金山湾区成人神经胶质瘤生存研究
- 批准号:
7550482 - 财政年份:
- 资助金额:
$ 77.92万 - 项目类别:
The San Francisco Bay Area Adult Glioma Survival Study
旧金山湾区成人神经胶质瘤生存研究
- 批准号:
7885642 - 财政年份:
- 资助金额:
$ 77.92万 - 项目类别:
San Francisco Bay area adult glioma survival study
旧金山湾区成人神经胶质瘤生存研究
- 批准号:
7550492 - 财政年份:
- 资助金额:
$ 77.92万 - 项目类别: