Development of an automated, point of care DNA methylation cartridge blood test for colorectal cancer detection in LMICs- an academic-industrial partnership

开发用于中低收入国家结直肠癌检测的自动化护理点 DNA 甲基化盒血液检测 - 学术与工业合作伙伴关系

• 批准号: 10635412
• 负责人: SARASWATI SUKUMAR
• 金额: $ 61.88万
• 依托单位: JOHNS HOPKINS UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-06-06 至 2028-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10635412
• 关键词: 2019-nCoV; Actins; Affect; Africa; African; Age; Aliquot; Asia; Attention; Benign; Biological Assay; Blood Tests; Body mass index; Breast Cancer Detection; Cells; Cessation of life; Characteristics; Classification; Clinical; Clinical Research; Collaborations; Colonoscopy; Colorectal Cancer; Communicable Diseases; Community Health; Cost Savings; DNA; DNA Methylation; DNA Modification Process; Data; Detection; Development; Diagnosis; Diagnostic; Disease; Early Diagnosis; Ensure; Equilibrium; Future; Genes; Goals; Hour; Hypermethylation; Industrialization; Infrastructure; Intervention; Knowledge; Laboratories; Lead; Lesion; Malignant - descriptor; Malignant Neoplasms; Manuals; Measures; Memorial Sloan-Kettering Cancer Center; Methods; Methylation; Modification; Molecular; Nigeria; Oncology Group; Outcome; Pathology; Patient Care; Patient Selection; Patients; Performance; Persons; Plasma; Predictive Value; Prospective Studies; Publishing; Reproducibility; Research; Resource-limited setting; Resources; Sampling; Sensitivity and Specificity; Signs and Symptoms; Specificity; System; Technology; Testing; Tissues; Training; Triage; Tumor Subtype; Validation; biomarker panel; bisulfite; cancer biomarkers; cell free DNA; clinical practice; colon cancer patients; colorectal cancer screening; colorectal cancer treatment; commercialization; cost; detection assay; diagnostic tool; financial toxicity; flu; improved; industry partner; innovation; liquid biopsy; low and middle-income countries; methylation biomarker; mortality; patient subsets; point of care; point of care testing; product development; programs; prospective; prototype; rapid detection; rapid diagnosis; sex; success; tumor; underserved area

ABSTRACT Colorectal cancer (CRC) is diagnosed at advanced stages in many low- and middle-income countries (LMICs). The lack of knowledge of CRC signs and symptoms by patients and community health practitioners frequently leads to delayed presentation with Stage 3-4 disease. This initial delay, paired with limited colonoscopy facilities, leads to prolonged diagnostic delays. The result is a 5-year mortality rate in LMIC up to 5 times higher than that in USA. An innovative solution to this problem could be an affordable, easily deployable, “point of care” molecular test to identify and prioritize patients likely to have a malignancy for expedited colonoscopy and pathology review leading to better outcomes. Continuing our established collaboration with our industrial partner, Cepheid, we propose to build on our strong published data on hypermethylated markers in CRC to develop an affordable, <3- hour, automated CRC-methylation detection blood test that analyzes a panel of five hypermethylated genes in cell free DNA from 1 ml of plasma. The proposed innovations could lead to a single-cartridge assay for quick CRC detection with a 3-fold reduction in cost. In Aim 1a, we will optimize a cartridge-less bisulfite DNA conversion method for plasma and test its efficiency in Patient Set 1 plasma (N= 20 malignant, 20 normal). In Aim 1b we will select one optimal 5-marker panel out of 20 CRC markers using DNA from FFPE samples from the U.S and Nigeria (N= 30 malignant, 30 benign), and one optimal “pan” set will be confirmed in plasma using U.S Patient Set 2 and Nigeria Set 3 (N=35 malignant, 35 benign). In Aim 1c, we will evaluate analytical performance of the CRC-MD assay. Intra-assay reproducibility will be assessed on multiple aliquots of U.S Patient Set 4 plasma (N=35 malignant, 35 benign). Inter-operator reproducibility will be determined using replicate aliquots of plasma from Patient Set 4 (N= 35 malignant, 35 benign). The goal of Aim 2a is to technically validate the CRC-MD assay using prospectively collected samples in Nigeria. We will first select a threshold in a Training set of plasma from Patient Set 4 (N=90 malignant, 90 benign) to optimally balance sensitivity and specificity, and validate performance of the selected threshold in a Test set of plasma from Patient Set 5 (N= 90 malignant, 90 benign). Accuracy (sensitivity, specificity, and positive- and negative-predictive value) of CRC- MD-based diagnosis to distinguish benign versus malignant disease will be measured using histopathological diagnosis of the lesion as the gold standard. Lastly, in Aim 2b, to determine whether the performance of the CRC-MD assay is altered by select patient characteristics, we will test its clinical accuracy among specific patient subgroups classified by age, sex, BMI, and tumor characteristics. Our prior success in developing automated cell-based/liquid biopsy assays with Cepheid has established the path ensuring an accurate and reliable test. This intervention could be cost saving by hastening colonoscopy for those who need it urgently, thus expediting detection and treatment of CRC in LMICs. This will save thousands of lives yearly. This study will also facilitate further development of the CRC-MD assay moving toward future commercialization and access globally.

抽象的 在许多低收入和中等收入国家（LMIC）的高级阶段诊断结直肠癌（CRC）。 经常缺乏患者和社区卫生从业人员的CRC标志和符号的知识 导致延迟出现3-4期疾病。最初的延迟与有限的结肠镜检查设施配对， 导致诊断延迟。结果是LMIC的5年死亡率高达5倍 在美国。解决此问题的创新解决方案可能是负担得起的，易于部署的“护理点”分子 测试以识别和确定可能患有加快结肠镜检查和病理审查的恶性肿瘤的患者 导致更好的结果。继续与我们的工业合作伙伴Cepheid建立合作，我们 提出基于我们关于CRC中高甲基化标记的大量发布的数据，以开发负担得起的，<3- 小时，自动化的CRC-甲基化检测血液测试，分析了一个五个高甲基化基因的面板 从1 ml血浆中的无细胞DNA。拟议的创新可能会导致单核测定法以进行快速 CRC检测，成本降低了3倍。在AIM 1A中，我们将优化无弹药纤维的Bisulfite DNA 血浆的转化方法并测试其在患者集1血浆中的效率（n = 20个恶性肿瘤，20正常）。 AIM 1B我们将使用来自FFPE样品的DNA从20个CRC标记中选择一个最佳5标记面板 美国和尼日利亚（n = 30个恶性，30个良性）和一套最佳的“ PAN”集将在血浆中使用 美国患者套2和尼日利亚套装3（n = 35个恶性，35良性）。在AIM 1C中，我们将评估分析 CRC-MD测定法的性能。在美国的多个等分试样将评估测定内的可重复性 患者组4个血浆（n = 35个恶性肿瘤，35良性）。操作员的可重复性将使用 从患者组4（n = 35个恶性，35良性）中复制血浆的等分试样。 AIM 2A的目标是技术上 使用前瞻性收集的样品在尼日利亚验证CRC-MD分析。我们将首先选择一个阈值 患者组4（n = 90个恶性，90良性）的血浆训练集以最佳平衡灵敏度和 特异性和验证在患者组5的血浆中选定阈值的性能（n = 90） 恶性，90良性）。 CRC-的准确性（灵敏度，特异性以及正面和负面预测值） 基于MD的诊断将使用组织病理学来测量以区分良性疾病与恶性疾病 诊断病变为黄金标准。最后，在AIM 2B中，确定是否表现 CRC-MD分析因某些患者特征而改变，我们将测试特定患者的临床精度 按年龄，性别，BMI和肿瘤特征分类的亚组。我们先前在发展自动化方面的成功 基于细胞/液体活检测定法已建立了路径，确保了准确可靠的测试。 这种干预措施可以通过为紧急需要的人加速结肠镜检查来节省成本，从而加快其加快 LMIC中CRC的检测和处理。这将每年挽救数千人的生命。这项研究也将有助于 CRC-MD主张的进一步发展朝着未来的商业化和全球访问发展。