Blood biopsy test for pan-cancer mutations with error-checking probes

使用错误检查探针进行泛癌突变的血液活检测试

• 批准号: 9404829
• 负责人: DAVID A SHAFER
• 金额: $ 24.26万
• 依托单位: GENETAG TECHNOLOGY, INC.
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-18 至 2018-09-17
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9404829
• 关键词: BRAF gene; Binding; Biological Assay; Biopsy; Blood; Blood Circulation; Blood specimen; CTNNB1 gene; Cancer Patient; Colorectal Cancer; Communicable Diseases; Companions; DNA amplification; Data; Detection; Development; Diagnostic; Diagnostic tests; Discrimination; Distal; Doctor of Philosophy; Drug resistance; Epidermal Growth Factor Receptor; FDA approved; Fluorescence; Frequencies; Genomic DNA; Goals; Grant; Health Benefit; High-Risk Cancer; Journals; Label; Legal patent; Malignant Neoplasms; Malignant neoplasm of lung; Malignant neoplasm of ovary; Malignant neoplasm of prostate; Methods; Mutate; Mutation; Neoplasm Circulating Cells; Neuroblastoma; Nucleic Acid Amplification Tests; Patients; Phase; Physicians; Plasma; Preparation; Prevalence; Primary carcinoma of the liver cells; Probability; Public Health; Publishing; Research; Sampling; Scanning; Screening for cancer; Series; Specificity; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Speed; Statistical Methods; System; Technology; Temperature; Testing; The Cancer Genome Atlas; Time; Tissues; Variant; actionable mutation; base; cancer biomarkers; cancer risk; cancer type; cell free DNA; cost; diagnostic assay; digital; follow-up; improved; liquid biopsy; malignant breast neoplasm; molecular diagnostics; mutant; neoplastic cell; next generation sequencing; phase 1 study; phase 2 study; prevent; prototype; rare variant; screening; success; targeted treatment; tumor; tumor DNA; validation studies; web site

Blood biopsy test for pan-cancer mutations with error-checking probes Confidential PI: Shafer, David A., PhD PROJECT SUMMARY GeneTAG Technology (www.genetagtech.com) has developed a series of molecular diagnostic assays for cancer and infectious diseases based on DNA amplification and proprietary detection methods. Our primary system, internal DDS (iDDS) probes, comprises two interacting components, a fluor-labeled probe and a quencher-labeled antiprobe nearly complementary to the probe. In the absence of the intended target, paired probes and antiprobes bind together, quenching fluorescence and preventing off-target detection. This unique system provides highly specific single-base discrimination over a wide temperature range (10–30ºC). Recently, we merged iDDS probe technology with Wild Terminator (WTx) methods to enable detection of low-abundance mutants by blocking amplification of the wild-type sequence (patent pending). By combined these technologies, we can reliably detect single-base variants of numerous targets at trace levels (0.01%) in a background of wild type genomic DNA. This enhanced qPCR sensitivity meets or exceeds the sensitivity of specialized platforms (such as droplet digital PCR, next-generation sequencing [NGS], and MALDI-TOF), which have been used to study rare mutations in the plasma of cancer patients. Our primary goal is to develop a pan-cancer screening test based on this combined method. This new method should enable the detection of low frequency diagnostic driver mutations in the blood that derive from a somatic tumor located elsewhere in the body. Our probes can reliably detect specific mutations that are indicative of a particular cancer or of a drug resistant variant. By covering ten or more of the common cancer-specific mutations in one assay we can identify the presence of an unknown cancer at an early stage, and in some cases, we can pin-point which cancer is likely. The Specific Aims of this Phase I grant are: 1, to test and compare selective-amplification methods for detecting low- abundance, pan-cancer driver mutations and 2, to develop and test a prototype assay for pan-cancer driver mutations in plasma based on iDDS probes and selective amplification. To demonstrate feasibility, we will study pan-cancer mutations in plasma samples from early- and late-stage patients with cancers that show high levels of ctDNA, such as neuroblastoma, prostate, ovarian, colorectal, hepatocellular, and breast cancer. Our long-range goal by the end of Phase II is to market a generalized test for ~100 circulating cancer biomarkers (actionable and drug-resistant variants), based on a synthesis between WTx, iDDS, NGS, and statistical methods. Such information would guide physicians in follow-up testing and selecting appropriate first-line targeted therapy. This, in turn, would provide a public health benefit by enabling early cancer detection through a non-invasive approach.

带错误检查问题的Pan-Cancer突变的血液活检测试机密PI：Shafer，David A.，PhD 项目摘要 Genetag技术（www.genetagtech.com）开发了一系列分子诊断测定 基于DNA扩增和专有检测方法的癌症和传染病。我们的主要 系统，内部DDS（IDD）问题，包括两个相互作用的组件，一个荧光标记的探针和一个 淬灭者标记的抗验型几乎是对探针的完整性。在没有预期目标的情况下 探针和抗植物结合在一起，淬灭荧光并防止脱靶检测。这个独特 系统在较宽的温度范围内（10–30ºC）提供高度特异性的单基础歧视。最近， 我们将IDDS探测技术与野生终结器（WTX）方法合并，以实现低丰度的检测 通过阻止野生型序列的扩增（申请专利）来扩增突变体。通过结合这些技术， 我们可以可靠地检测到野生背景下痕量水平（0.01％）的众多靶标的单基数变体 型基因组DNA。这种增强的QPCR灵敏度满足或超过了专用平台的灵敏度 （例如液滴数字PCR，下一代测序[NGS]和MALDI-TOF），它们已用于 研究癌症患者血浆中的罕见突变。我们的主要目标是开发泛伴侣筛查 基于此组合方法的测试。这种新方法应能够检测低频诊断 血液中的驱动突变是从体内其他地方的体细胞肿瘤衍生而来的。我们的问题可以 可靠地检测指示特定癌症或耐药性变体的特定突变。经过 在一个测定中覆盖十个或更多的癌症特异性突变，我们可以确定存在 在早期阶段未知的癌症，在某些情况下，我们可以限定可能的癌症。具体 该阶段I授予的目的是：1，测试和比较用于检测低 - 的选择性放大方法 抽象，Pan-Canter驱动器突变和2 基于IDD的问题和选择性扩增的血浆中的突变。为了证明可行性，我们将 来自早期和晚期癌症患者的血浆样品中的研究Pan-Cancer突变显示 高水平的ctDNA，例如神经母细胞瘤，前列腺，卵巢，结直肠癌，肝细胞和乳房 癌症。第二阶段结束时，我们的远程目标是销售约100个循环癌的广义测试 基于WTX，IDD，NGS和 统计方法。这些信息将指导医生进行后续测试并选择适当的 一线目标治疗。反过来，这将通过实现早期癌症检测来提供公共卫生的益处 通过非侵入性方法。