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.

抽象的 亚急性肺部感染越来越被认为是导致部分人群症状控制不佳的原因 患有慢性肺病的人（估计有超过 200 万哮喘和慢性阻塞性肺病患者）。什么时候 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变 从中度/重度到较轻的疾病表型，需要较少的药物来实现更好的健康 成本显着降低。目前亚急性感染的金标准诊断依赖于数十年的历史 技术可能需要数周时间才能完成，灵敏度有限，并且在类型和数量上也受到限制 通过一次测试即可筛选出的微生物。因此，由于当前无法 诊断全面、快速、准确地检测微生物病原体，低负担临床 样本，这是改善慢性肺病临床结果的重大障碍。我们开发了一个 全面的 NGS 靶向扩增子组，用于 a) 检测和分析相关微生物 治疗耐药性数据和 b) 分析人类免疫系统宿主反应基因。我们的 NGS 诊断 (Dx) 面板是对当前方法的重大技术创新，因为它结合了 有针对性的 NGS 方法的固有技术特征、我们针对的特定扩增子集以及我们的 专有的实验室和分析工作流程。该项目的长期目标是提供一种新颖的临床 用于检测驱动疾病病理学、症状学和低负担微生物感染的工具 慢性肺病人群的恶化，如慢性阻塞性肺病、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) 直接利用患者样本而不是需要 b) 提供比 qPCR 或宏基因组更高几个数量级的灵敏度和准确性 方法，以及 c) 在一次测定中全面筛选细菌、真菌和病毒物种。我们的具体 目的旨在测试我们的 NGS Dx 方法的可行性，以提供实质性增强 准确性、灵敏度、特异性和速度超过当前的临床标准。这项研究的第一个目的是 确定目标 NGS Dx 组合的检测限和特异性，以在以下情况下检测微生物物种： 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 panel 识别严重慢性肺病受试者亚急性感染的可行性 疾病。成功完成这些目标后，第二阶段研究将以这些和其他早期目标为基础 在 CLIA 认证的实验室中展示临床验证和实用性的研究活动，使 将患者样本用于临床诊断测试。该诊断的总市场是 症状不受控制的慢性肺病患者可以进行亚急性感染筛查。 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、 在一次检测中进行微生物分析、简化分析和治疗效果洞察。