DEVELOPMENT OF AN AUTOMATED CARTRIDGE-BASED BREAST CANCER DETECTION ASSAY- AN ACADEMIC-INDUSTRIAL PARTNERSHIP

抽象的。在许多低收入和中等收入国家（LMIC），乳腺癌在晚期被诊断出来。 许多妇女目前与一个可触及的乳房肿块，这是罕见的社区，乳房筛查是 available.除了有限的成像设施外，部分由于 病理学家的极度短缺（每百万人口只有1名）导致5年死亡率高达 是美国的4倍。一个创新的解决方案，这个问题可能是一个负担得起的，易于部署 分子检测，以识别和优先考虑可能患有恶性肿瘤的女性，以进行快速活检和病理学检查 审查.众所周知，早期发现乳腺癌可以提高生存率。与我们的工业合作伙伴， Cepheid，我们建议在我们已发布的乳腺癌检测原型的基础上，开发一种经济实惠的<3- 小时，自动乳腺癌检测（aBCD）分析，分析乳腺癌中的一组高甲基化基因， 细针抽吸（FNA）。拟议的创新将减少一半的分析时间，并降低成本， 以提供用于快速癌症检测的单盒测定。在目标1a中，我们将优化 体外亚硫酸氢盐介导的DNA转化方法，并在患者组1 FNA（N= 29）中测试其效率 恶性，25例良性）。在目标1b中，我们将选择一个最佳的5标记面板，并使用第一， 金标准，FFPE样本（N= 30个恶性，30个良性），然后，患者组2 FNA（N=35个恶性， 35例良性）。在目标1c中，我们将对aBCD检测试剂盒进行技术验证。试验内重现性将 在患者集3 FNA的多个样本采集中进行评估（N=30例恶性，30例良性）。跨网 将使用来自患者组2（N= 35恶性，35良性）的重复FNA载玻片来确定再现性。 目标2a的目标是对aBCD检测试剂盒进行临床验证。我们将首先在 FNA训练集：患者集4（N=100例恶性，100例良性），以最佳平衡灵敏度和特异性， 并验证FNA测试组中所选阈值的性能：患者组5（N= 180例恶性，180例 良性）。我们将测量以下指标的准确性（灵敏度、特异性、阳性和阴性预测值）： 基于aBCD的诊断，使用组织病理学诊断区分良性与恶性病变， 核心活检作为金标准。最后，在目标2b中，为了确定选择的患者特征是否改变 为了验证aBCD检测试剂盒的性能，我们将根据以下指标在特定患者亚组中检测其临床准确性： 年龄、种族、BMI和肿瘤特征（分级、分期、肿瘤亚型）。所有这些步骤都是必要的，以确保 准确可靠的测试。这种干预是范式转变，并可能彻底改变目前的检测 通过加快治疗，在世界上服务不足的地区减少了乳腺癌的发病率， 每年生活。本研究还将促进aBCD检测的进一步商业化发展， 使其可以在全球范围内使用。

Abstract. In many low- and middle-income countries (LMICs) breast cancer is diagnosed at advanced stages. Many women present with a palpable breast mass, which is rare in communities where breast screening is available. In addition to limited imaging facilities, prolonged diagnostic delays (76-630 days) due in part to the extreme shortage of pathologists (as few as 1 per million/population) contribute to a 5-year mortality rate up to 4 times higher than that in the US. An innovative solution to this problem could be an affordable, easily deployable molecular test to identify and prioritize women likely to have a malignancy for expedited biopsy and pathology review. It is well established that early detection of breast cancer improves survival. With our industrial partner, Cepheid, we propose to build on our published breast cancer detection prototype to develop an affordable, <3- hour, automated breast cancer detection (aBCD) assay that analyzes a panel of hypermethylated genes in breast fine needle aspirates (FNAs).The proposed innovations will cut the assay time in half, and reduce costs by at least 3-fold to provide a single-cartridge assay for quick cancer detection. In Aim 1a, we will optimize the Offboard bisulfite-mediated DNA conversion method and test its efficiency in Patient Set 1 FNAs (N= 29 malignant, 25 benign). In Aim 1b we will select one optimal 5-marker panel and test its performance using first, the gold standard, FFPE samples (N= 30 malignant, 30 benign), and then, Patient Set 2 FNAs (N=35 malignant, 35 benign). In Aim 1c, we will perform technical validation of the aBCD assay. Intra-assay reproducibility will be assessed on multiple sample collections of Patient Set 3 FNAs (N=30 malignant, 30 benign). Inter-operator reproducibility will be determined using replicate FNA slides from Patient Set 2 (N= 35 malignant, 35 benign). The goal of Aim 2a is to perform clinical validation of the aBCD assay. We will first select a threshold in a Training set of FNAs: Patient Set 4 (N=100 malignant, 100 benign) to optimally balance sensitivity and specificity, and validate performance of the selected threshold in a Test set of FNAs: Patient Set 5 (N= 180 malignant, 180 benign). We will measure the accuracy (sensitivity, specificity, and positive- and negative-predictive value) of aBCD-based diagnosis to distinguish benign versus malignant lesions using histopathological diagnosis of the core biopsy as the gold standard. Lastly, in Aim 2b, to determine whether select patient characteristics alter the performance of the aBCD assay, we will test its clinical accuracy among specific patient subgroups based on age, race, BMI, and tumor characteristics (grade, stage, tumor subtype). All these steps are necessary to ensure an accurate and reliable test. This intervention is paradigm shifting, and could revolutionize the current detection of breast cancer in underserved regions of the world by expedited treatment and, in turn, saving thousands of lives yearly. This study will also facilitate further development of the aBCD assay toward commercialization, making it accessible globally.