Enabling comprehensive diagnosis of sub-acute infection in chronic respiratory disease via high sensitivity next generation sequencing

通过高灵敏度下一代测序实现慢性呼吸道疾病亚急性感染的全面诊断

• 批准号: 10021480
• 负责人: Tasha E. Fingerlin
• 金额: $ 30万
• 依托单位: PEAK DIAGNOSTIC PARTNERS LLC
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-04-17 至 2021-07-21
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10021480
• 关键词: Acute; Acute respiratory infection; Asthma; Automobile Driving; Biological Assay; CLIA certified; Characteristics; Chronic; Chronic Obstructive Airway Disease; Chronic lung disease; Clinical; Clinical Data; Complex Mixtures; Cystic Fibrosis; DNA; Data; Detection; Diagnosis; Diagnostic; Diagnostic tests; Disease; Dose; Effectiveness; Environment; Evaluation; Future; Genes; Goals; Gold; Health; Hospitalization; Human; Immune response; Immune system; In Vitro; Individual; Infection; Knowledge; Laboratories; Lung; Lung diseases; Lung infections; Medical Care Costs; Metagenomics; Methodology; Methods; Microbe; National Heart, Lung, and Blood Institute; Nucleic Acids; Organism; Outcome; Pathogen detection; Pathology; Patients; Performance; Pharmaceutical Preparations; Phase; Population; Quality of life; RNA; Research; Research Activity; Sampling; Sensitivity and Specificity; Series; Small Business Technology Transfer Research; Source; Specificity; Speed; Stream; Symptoms; Technology; Testing; Tissue Sample; Tissues; Treatment Effectiveness; United States Food and Drug Administration; United States National Institutes of Health; Validation; Viral; acute infection; antimicrobial drug; base; burden of illness; clinical diagnostics; commercial application; cost; design; diagnosis standard; diagnostic panel; disease phenotype; disorder control; experience; experimental study; follower of religion Jewish; improved; insight; metagenomic sequencing; microbial; next generation sequencing; novel; novel diagnostics; novel strategies; nucleic acid detection; pathogen; pathogenic microbe; patient engagement; phase 2 study; respiratory; side effect; targeted treatment; technological innovation; therapy resistant; tool

ABSTRACT Sub-acute lung infections are increasingly recognized as drivers of poor symptom control among a subset of individuals with chronic lung disease (estimated more than 2 million for Asthma and COPD patients). When these sub-acute infections are diagnosed and treated appropriately, chronic lung disease patients can convert from moderate/severe to a milder disease phenotype, requiring lower medication to achieve better health at a significantly lower cost. Current gold-standard diagnostics for sub-acute infection rely on decades-old technology that can take weeks to complete, have limited sensitivity, and are limited in the type and number of microbes that can be screened by a single test. Thus, a critical gap exists due to the inability of current diagnostics to comprehensively, quickly, and accurately detect microbial pathogens in low-burden clinical samples, which is a significant barrier to improved clinical outcomes in chronic lung disease. We developed a comprehensive NGS targeted amplicon panel for a) detection and profiling of microbes with associated treatment resistance data and b) profiling human immune system host response genes. Our NGS diagnostics (Dx) panel is a significant technological innovation over current methodology due to the combination of the inherent technical characteristics of a targeted NGS approach, the specific set of amplicons we target and our proprietary laboratory and analysis workflows. The long-term goal of this project is to provide a novel clinical tool for the detection of low-burden microbial infections driving disease pathology, symptomology, and exacerbations in chronic lung disease populations such as COPD, cystic fibrosis, and moderate to severe Asthma. Our preliminary studies demonstrate an ability to a) utilize patient samples directly vs. requiring cultures, b) provide orders of magnitude greater sensitivity and accuracy than qPCR or metagenomic approaches, and c) comprehensively screen bacterial, fungal and viral species in a single assay. Our specific aims are designed to test the feasibility of our NGS Dx approach to provide substantial enhancements in accuracy, sensitivity, specificity, and speed over current clinical standards. The first aim of this study is to establish the limits of detection and specificity of the targeted NGS Dx panel to detect microbial species when most of the DNA/RNA in the sample comes from a human host. The second aim of the study is to demonstrate the feasibility of the NGS Dx panel to identify sub-acute infections among subjects with severe chronic lung disease. After successful completion of these aims, Phase II studies will build off of these and other early research activities to demonstrate clinical validation and utility in a CLIA certified laboratory, enabling engagement of patient samples for clinical diagnostic testing. The total market for this diagnostic is the set of chronic lung disease patients with uncontrolled symptoms who could be screened for sub-acute infections. Our competitive advantages include vastly improved sensitivity, speed, comprehensive microbe detection, microbe profiling, stream-lined analysis, and treatment effectiveness insights within a single assay.

摘要 亚急性肺部感染越来越多地被认为是一个子集中症状控制不良的驱动因素， 慢性肺病患者（估计超过200万哮喘和COPD患者）。当 这些亚急性感染得到适当的诊断和治疗，慢性肺病患者可以转换为 从中度/重度到轻度疾病表型，需要更少的药物来实现更好的健康， 大大降低成本。目前亚急性感染的黄金标准诊断依赖于数十年前的 可能需要数周才能完成的技术，具有有限的灵敏度，并且在类型和数量上受到限制。 微生物可以通过一个单一的测试筛选。因此，由于电流的不可能， 诊断，以全面，快速，准确地检测微生物病原体在低负担的临床 样本，这是改善慢性肺部疾病临床结局的重要障碍。我们开发了一个 用于a）检测和分析具有相关联的微生物的综合NGS靶向扩增子组 治疗抗性数据和B）分析人类免疫系统宿主应答基因。NGS诊断 (Dx)面板是一个重大的技术创新，目前的方法，由于结合 靶向NGS方法的固有技术特征，我们靶向的特定扩增子组和我们的 专有实验室和分析工作流程。该项目的长期目标是提供一种新型的临床 用于检测低负荷微生物感染的工具，驱动疾病病理学、病理学和 慢性肺病人群的急性加重，如COPD、囊性纤维化和中度至重度 哮喘我们的初步研究表明，能够a）直接利用患者样本， B）提供比qPCR或宏基因组培养高几个数量级的灵敏度和准确度 方法，和c）在单一测定中全面筛选细菌、真菌和病毒物种。我们的具体 目的是测试我们的NGS Dx方法的可行性，以提供实质性的增强， 准确性、灵敏度、特异性和速度超过当前临床标准。本研究的第一个目的是 确定目标NGS Dx试剂盒的检测限和特异性，以检测微生物菌种， 样本中的大部分DNA/RNA来自人类宿主。研究的第二个目的是证明 NGS Dx试剂盒用于识别重度慢性肺部疾病受试者中亚急性感染的可行性 疾病在成功完成这些目标后，第二阶段研究将在这些目标和其他早期目标的基础上进行。 在CLIA认证的实验室中展示临床验证和实用性的研究活动， 参与患者样本的临床诊断测试。这种诊断的总市场是一套 症状不受控制的慢性肺病患者，可以筛查亚急性感染。 我们的竞争优势包括大大提高的灵敏度，速度，全面的微生物检测， 微生物分析、流线型分析和治疗有效性见解。