Streamlined Genotyping for HIV-1 Recombinants

简化 HIV-1 重组体的基因分型

• 批准号: 8951265
• 负责人: Ming Zhang
• 金额: $ 7.5万
• 依托单位: UNIVERSITY OF GEORGIA
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-06-15 至 2017-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8951265
• 关键词: AIDS/HIV problem; Address; Antiviral Therapy; Central Africa; China; Classification; Collection; Complex; Computational Biology; Computer software; Databases; Detection; Development; Drug resistance; Elements; Ensure; Epidemic; Epidemiologic Studies; Epidemiology; Event; Evolution; Foundations; Genbank; Generations; Genetic Recombination; Genome; Genomics; Genotype; Geographic Locations; Goals; HIV; HIV-1; Healthcare; Human; Individual; Infection; Investigation; Knowledge; Methods; Molecular Epidemiology; Organism; Pathogenesis; Pattern; Plague; Population; Prevalence; Procedures; Production; Publishing; Recombinants; Records; Research; Selection Criteria; Staging; Structure; System; Technical Expertise; Time; Vaccine Design; Validity and Reliability; Viral; Virulence; Virus; Work; base; design; epidemiology study; fitness; genome sequencing; improved; meetings; public health relevance; repository; skills; surveillance study; virus classification

 DESCRIPTION (provided by applicant): This proposal addresses a critical issue in HIV-1 global surveillance and epidemiology study: how do we ensure the validity and reliability of virus genotyping information? Such information has frequently proven inconsistent, even erroneous, from public genome repositories (such as, GenBank). This situation will continue to deteriorate with the growing list of identified HIV sequences, as a result of increased sequencing and surveillance efforts, and in the face of lack of reliable genotyping reference sequences. Hence, developing strategies to ensure viral genotyping quality should be considered high priority in HIV research, particularly given the importance of genotyping information in regards to epidemiological surveillance, genomic research, and genomic health care. The overall goal of this project is to develop a platform for reliable HIV-1 genotyping, in particular for recombinant cases, which are more difficult than pure subtypes to be genotyped due to the complexity of recombination events. Additionally, we aim to develop a high-throughput and systematic platform that meets current research needs in the era of advanced genome sequencing. We plan to implement the following elements within such a platform: 1) an efficient computational pipeline for reliable HIV-1 genotyping; and 2) a reliable collection of HIV-1 recombinant sequences and a list of recombinants that can be used as valid and reliable genotyping references. Through this first of its kind, systematic investigation of genotyping quality of all published HIV sequences, our results will lay a robust foundation for HIV genomic research to help improve current knowledge of HIV evolutionary patterns under different epidemiological settings. More broadly, this proposed research strategy would also contribute to research in other organisms that similarly require reliable classifications for case definition and treatment options.

 描述（由申请人提供）：该提案解决了 HIV-1 全球监测和流行病学研究中的一个关键问题：我们如何确保公共基因组存储库中的病毒基因分型信息的有效性和可靠性？ （例如 GenBank），由于测序和监测工作的增加以及缺乏可靠的基因分型参考序列，这种情况将继续恶化。在艾滋病毒研究中，应高度重视制定确保病毒基因分型质量的策略，特别是考虑到基因分型信息在流行病学监测、基因组研究和基因组医疗保健方面的重要性。该项目的总体目标是开发一个可靠的平台。 HIV-1 基因分型，特别是重组病例，由于重组事件的复杂性，比纯亚型更难进行基因分型。此外，我们的目标是开发一个满足当前研究需求的高通量和系统化平台。在先进的基因组测序时代，我们计划在这样的平台中实现以下要素：1）用于可靠的 HIV-1 基因分型的高效计算管道；2）可靠的 HIV-1 重组序列集合和重组体列表。通过对所有已发表的 HIV 序列的基因分型质量进行首次系统性调查，我们的结果将为 HIV 基因组研究奠定坚实的基础，以帮助提高当前对 HIV 进化模式的了解。不同的更广泛地说，这项拟议的研究策略也将有助于对其他同样需要可靠分类的病例定义和治疗方案的生物体进行研究。