Academic-Industrial Partnership for Non-invasive Barrett's Esophagus Detection

Barrett食管（BE）是食管癌前病变的一种， 腺癌（EAC）是美国增长最快和最致命的恶性肿瘤之一， 欧洲（3）。EAC在成为侵袭性和不可治疗之前很少被检测到，95%的EAC发生在 既往未诊断为BE的患者（19）（20）。与此相反，被诊断为BE的患者具有极好的 预后，因为定期内窥镜监测可以很早发现肿瘤。然而，没有 目前可用的BE筛查试验。微创、低成本生物标记物为基础的临床翻译 BE诊断的方法将改善早期EAC检测并提高总生存率。通过结合我们 由我们的工业生产的可吞咽、可回收的食管样本收集海绵（EsophaCapTM） 合作伙伴Capnostics，凭借我们的专利BE DNA甲基化标记和我们的增强处理 技术，珠上甲基化（MOB），以最大限度地提取和亚硫酸氢盐转化DNA;以及 在我们的工业合作伙伴MyGenetx的CLIA合规实验室中建立这种检测方法，我们现在可以 该测定广泛可用。初步数据表明，我们的海绵为基础的诊断准确性高 生物标志物检测我们将通过追求以下具体目标来实施这一战略：目标1。分析地 验证我们基于EsophaCapTM的BE诊断分析。目标1a。首先，使用技术复制EsophaCapTM 从42名新招募的BE患者和42名非BE对照的标本中，我们将确认准确性， 我们的BE诊断测定的稳健性和可靠性。这方面的初步结果也令人鼓舞 (see表2，技术重复）。目标1b。接下来，在同样的42名已知BE患者和42名对照组中， 如果没有BE，我们将建立基于EsophaCapTM的数据与匹配的组织活检的分析一致性 样本数据目标2.进行试点研究，以验证基于EsophaCapTM的多变量模型 BE的诊断基于我们已经收集的EsophaCapTM衍生样本训练数据集（见图5）， 我们构建了BE的3-标记预测模型（图6）。我们将应用这个模型和选择的切割- 关闭阈值到新收集的一组50个未测试样本（独立于目标1样本）。目标3。到 在BE测试集队列中前瞻性测试组合的海绵甲基化生物标志物策略 患者与对照组。我们的测定将在来自前瞻性研究的EsophaCapTM衍生样品中进行- 收集80例BE患者和240例对照组。目标2中验证的多变量模型将应用于 这个测试集的患者群体很大。目标4。使我们的EsophaCapTM检测方案工业化。并行 与目标1 - 3同时，我们将建立基于MOB的DNA提取的所有步骤，亚硫酸氢盐 在符合CLIA的实验室中进行修改和定量甲基化特异性PCR（qMSP）方案， MyGenetx将通过从相同患者获得重复海绵来重复目标3中进行的测定， 这一次是在CLIA实验室，并通过与Aim 3结果进行比较来检查准确性。

Barrett’s esophagus (BE) is the dangerous obligate premalignant precursor lesion of esophageal adenocarcinoma (EAC), one of the most rapidly increasing and lethal malignancies in the United States and Europe(3). EAC is rarely detected before it becomes invasive and untreatable, and 95% of EACs develop in patients not previously diagnosed with BE(19)(20). Patients diagnosed with BE, in contrast, have an excellent prognosis, since neoplasia is detected very early by periodic endoscopic surveillance. There is, however, no currently available screening test for BE. Clinical translation of minimally invasive, low-cost biomarker-based approaches to BE diagnosis will improve early EAC detection and increase overall survival. By combining our swallowable, retrievable esophageal sample collection sponge (EsophaCapTM) manufactured by our industrial partner, Capnostics, with our patented BE DNA methylation markers and our enhanced processing technique, Methylation-On-Beads (MOB) to maximize extraction and bisulfite conversion of DNA; and by establishing this assay in the CLIA-compliant laboratory of our industrial partner, MyGenetx, we can now make this assay widely available. Preliminary data demonstrate high diagnostic accuracy of our sponge-based biomarker test for BE. We will apply this strategy by pursuing the following Specific Aims: Aim 1. To analytically validate our EsophaCapTM-based BE diagnostic assay. Aim 1a. First, using technical replicate EsophaCapTM specimens from 42 newly recruited BE patients and 42 non-BE controls, we will confirm the accuracy, robustness, and reliability of our BE diagnostic assay. Preliminary results in this context are also encouraging (see Table 2, Technical replicates). Aim 1b. Next, in these same 42 patients with known BE vs. 42 controls without BE, we will establish analytical concordance of EsophaCapTM-based data with matched tissue biopsy sample data. Aim 2. To conduct a pilot study to validate a multivariate model for EsophaCapTM-based diagnosis of BE. Based on our already-collected EsophaCapTM-derived specimen training dataset (see Fig. 5), we have constructed a 3-marker prediction model for BE (Fig. 6). We will apply this model and the chosen cut- off threshold to a newly collected set of 50 untested samples (independent of the Aim 1 samples). Aim 3. To prospectively test the combined sponge-methylation biomarker strategy in a test set cohort of BE patients vs. controls. Our assay will be performed in EsophaCapTM-derived samples from a prospectively- collected cohort of 80 BE patients and 240 controls. The multivariate model validated in Aim 2 will be applied to this test set of large patient population. Aim 4. To industrialize our EsophaCapTM assay protocol. In parallel and simultaneously with Aims 1-3, we will establish all steps in our MOB-based DNA extraction, bisulfite modification and quantitative methylation-specific PCR (qMSP) protocol in the CLIA-compliant laboratory at MyGenetx. Assays performed in Aim 3 will be repeated by obtaining repeat sponges from the same patients, this time in the CLIA lab, and checked for accuracy by comparison to Aim 3 results.