Genomic Miniarrays for HIV-1 Subtyping

用于 HIV-1 亚型分析的基因组微阵列

• 批准号: 6883469
• 负责人: DAVID A SHAFER
• 金额: $ 10万
• 依托单位: WEILIN BIOTECHNOLOGY, INC.
• 依托单位国家: 美国
• 财政年份: 2005
• 资助国家: 美国
• 起止时间: 2005-03-01 至 2006-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6883469
• 关键词: AIDS; AIDS /HIV test; HIV envelope protein; HIV infections; biotechnology; diagnosis design /evaluation; gag protein; gene mutation; genetic strain; genotype; human immunodeficiency virus 1; microarray technology; microprocessor /microchip; nucleic acid amplification techniques; nucleic acid hybridization; nucleic acid sequence; oligonucleotides; polymerase chain reaction; virus genetics

DESCRIPTION (provided by applicant): HIV/AIDS is an unprecedented viral pandemic with 42 million people infected worldwide and killing more than 3 million people per year. The high mutation rate of this virus has led to the evolution of multiple circulating genotypes, which confer variable disease outcomes, transmission rates, resistance to therapy, and responses to different vaccines. Worldwide efforts at vaccine development and trial evaluations depend on accurate information about which patient HIV-1 subtypes and circulating recombinant forms are present in the targeted populations. Current tests based on short sequencing, the heteroduplex mobility assay and realtime PCR are relatively expensive, can only detect a few targets, and are prone to error and misleading assessments. The PI has devised a novel miniarray and genomic probe set system for comprehensive SARS detection on a microarray platform. This new system can detect and distinguish the major genes of any viral species and provides a simplified profile of the genome structure. This grant Will adapt and extend this new technology to more accurate discrimination of HIV-1 subtypes by employing capture probe sets on the miniarray that parallel or duplicate essentially all the major gene targets which are presently employed in the above mentioned short-sequencing, HMA and real-time PCR assays. The proposed HIV-1 miniarrays will be populated with about 20 large and small probe sets for each of four reference subtypes, A1, B, C and D, with most targets in the conserved gag and the variable env gene regions. This system should therefore allow more exact and comprehensive subtype discrimination with a simple to use, inexpensive protocol, and with multiplex processing of patient samples. The proposed HIV-1 miniarrays will contain high specificity oligo-probes to selected consensus regions and larger target region probes that will be fault tolerant and will pick up new mutations and recombinant variations. The novel miniarrays and procedures are patent pending.

描述（由申请人提供）：艾滋病毒/艾滋病是一种前所未有的病毒性大流行病，全世界有4200万人感染，每年造成300多万人死亡。这种病毒的高突变率导致了多种循环基因型的进化，这赋予了可变的疾病结果、传播率、对治疗的抗性和对不同疫苗的反应。全世界在疫苗开发和试验评估方面的努力取决于关于目标人群中存在哪些患者HIV-1亚型和循环重组形式的准确信息。目前基于短测序、异源双链迁移率测定和实时PCR的测试相对昂贵，只能检测少数靶标，并且容易产生错误和误导性评估。PI设计了一种新的微阵列和基因组探针集系统，用于在微阵列平台上全面检测SARS。这种新系统可以检测和区分任何病毒物种的主要基因，并提供基因组结构的简化图谱。这项拨款将调整和扩展这项新技术，通过在微型阵列上使用捕获探针组，使其能够更准确地区分HIV-1亚型，这些探针组基本上平行或重复了目前在上述短测序、HMA和实时PCR检测中使用的所有主要基因靶标。拟议的HIV-1微型阵列将针对四种参考亚型A1、B、C和D中的每一种填充约20个大小探针组，其中大多数靶点位于保守的gag和可变的env基因区域。因此，该系统应允许更准确和全面的亚型歧视与简单易用，廉价的协议，并与患者样本的多重处理。所提出的HIV-1微阵列将包含针对选定的共有区域的高特异性寡核苷酸探针和更大的靶区域探针，这些探针将具有容错性，并将拾取新的突变和重组变异。新的微阵列和程序正在申请专利。