Computational tools for sequence-based large-scale epidemiology studies
基于序列的大规模流行病学研究的计算工具
基本信息
- 批准号:9901082
- 负责人:
- 金额:$ 41.8万
- 依托单位:
- 依托单位国家:美国
- 项目类别:
- 财政年份:2016
- 资助国家:美国
- 起止时间:2016-06-14 至 2021-03-31
- 项目状态:已结题
- 来源:
- 关键词:AddressBase SequenceBioinformaticsChromosome MappingCloud ComputingCodeCollectionComplexComputer softwareCopy Number PolymorphismCustomDataData AnalysesData QualityData SetDatabasesDevelopmentDiseaseDisease susceptibilityEnvironmentFactor AnalysisFamilyFutureGenesGenetic StructuresGenetic VariationGenomeGenotypeGoalsHealthHumanHybridsIndividualMethodologyMethodsModelingNamesNational Heart, Lung, and Blood InstitutePathway interactionsPhenotypePopulationQuality ControlReproducibilityResearch PersonnelResourcesRetrievalSamplingSourceStatistical MethodsSusceptibility GeneSystemTechnologyVariantanalysis pipelineanalytical methodbasebiological systemscomputerized toolscomputing resourcesdata accessdata managementepidemiologic dataepidemiology studyexomeexome sequencinggenetic analysisgenetic architecturegenetic epidemiologygenetic informationgenetic pedigreegenetic variantgenomic datahuman diseasenext generation sequencingonline resourcepublic health relevancerare variantrelational databasesuccessterabytetooltraituser-friendlyweb interfacewhole genome
项目摘要
DESCRIPTION (provided by applicant): We developed Variant Association Tools (VAT), which is a software application for the association analysis of disease susceptibility genes using next-generation sequencing (NGS) data. Unlike many other applications that specialize in certain aspects of rare variant association analysis, VAT aims to provide an effective and comprehensive solution to association analysis of genetic epidemiology studies. Although VAT has been successfully applied to a number of large-scale whole exome sequence (WES) association studies including the NHLBI Exome Sequencing Project, continued development is required to effectively analyze whole genome sequence (WGS) data from emerging large-scale genetic epidemiology studies. Such studies generate unprecedented amount of data and pose methodological and bioinformatics challenges including efficient storage, retrieval, and analysis of terabytes of genotype data, access to heterogeneous annotation resources, choices of appropriate statistical gene mapping methods, and applications to real-world studies with proper controls for errors and biases. To address these challenges, we propose to extend VAT with new capacity and new analytical methods. More specifically, in aim 1, we will remove a major bottleneck of VAT by implementing a highly efficient hybrid storage model to store WGS samples. In aim 2 we will implement recently developed and emerging statistical methods for sequence-based variant association analysis, with a programming interface to allow researchers to implement their own methods in VAT. In aim 3, we will provide user-friendly pipelines, online resources, tutorials, and web interfaces to facilitate the applications of VAT to real-world studie.
项目成果
期刊论文数量(3)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
Novel candidate genes and variants underlying autosomal recessive neurodevelopmental disorders with intellectual disability.
- DOI:10.1007/s00439-018-1928-6
- 发表时间:2018-09
- 期刊:
- 影响因子:5.3
- 作者:Santos-Cortez RLP;Khan V;Khan FS;Mughal ZU;Chakchouk I;Lee K;Rasheed M;Hamza R;Acharya A;Ullah E;Saqib MAN;Abbe I;Ali G;Hassan MJ;Khan S;Azeem Z;Ullah I;Bamshad MJ;Nickerson DA;Schrauwen I;Ahmad W;Ansar M;Leal SM
- 通讯作者:Leal SM
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SUZANNE M LEAL其他文献
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{{ truncateString('SUZANNE M LEAL', 18)}}的其他基金
Elucidating the Genetic Etiology of Intellectual Disability in African, Asian, and European Families
阐明非洲、亚洲和欧洲家庭智力障碍的遗传病因
- 批准号:
10660541 - 财政年份:2023
- 资助金额:
$ 41.8万 - 项目类别:
Gene discovery in multi-ethnic late-onset Alzheimer's disease families
多种族晚发性阿尔茨海默病家族的基因发现
- 批准号:
10640970 - 财政年份:2020
- 资助金额:
$ 41.8万 - 项目类别:
Gene discovery in multi-ethnic late-onset Alzheimer's disease families
多种族迟发性阿尔茨海默病家族的基因发现
- 批准号:
10186680 - 财政年份:2020
- 资助金额:
$ 41.8万 - 项目类别:
Gene discovery in multi-ethnic late-onset Alzheimer's disease families
多种族迟发性阿尔茨海默病家族的基因发现
- 批准号:
10434636 - 财政年份:2020
- 资助金额:
$ 41.8万 - 项目类别:
Identification and Functional Evaluation of Autosomal Recessive Nonsyndromic Hearing Impairment Genes in sub-Saharan Africans
撒哈拉以南非洲人常染色体隐性非综合征性听力障碍基因的鉴定和功能评估
- 批准号:
10468748 - 财政年份:2018
- 资助金额:
$ 41.8万 - 项目类别:
Identification and Functional Evaluation of Autosomal Recessive Nonsyndromic Hearing Impairment Genes in sub-Saharan Africans
撒哈拉以南非洲人常染色体隐性非综合征性听力障碍基因的鉴定和功能评估
- 批准号:
10238026 - 财政年份:2018
- 资助金额:
$ 41.8万 - 项目类别:
Computational tools for sequence-based large-scale epidemiology studies
基于序列的大规模流行病学研究的计算工具
- 批准号:
9078292 - 财政年份:2016
- 资助金额:
$ 41.8万 - 项目类别:
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