Development and Validation of Liquid Biopsy ddPCR and Next Generation Sequencing Assays for Diffuse Midline Glioma, K27M Variant

弥漫性中线胶质瘤 K27M 变体液体活检 ddPCR 和下一代测序测定的开发和验证

• 批准号: 9909098
• 负责人: D. Ashley Hill
• 金额: $ 22.47万
• 依托单位: RESOURCEPATH, LLC
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-09-11 至 2021-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9909098
• 关键词: Accreditation; Adult; Advocacy; Affect; American; Biological Assay; Biopsy; Blood; Blood Tests; Brain Stem; Brain Stem Glioma; Caring; Cerebrospinal Fluid; Characteristics; Chemistry; Child; Childhood Brain Neoplasm; Clinical; Clinical Management; Clinical Trials; Communities; DNA; Detection; Development; Diagnosis; Diagnosis Clinical Trials; Diagnostic; Diagnostic tests; Diffuse; Diffuse intrinsic pontine glioma; Discrimination; Documentation; Eligibility Determination; Europe; Event; Gene Frequency; Genes; Genotype; Glioma; Goals; Gold; Histone Deacetylase; Histone H3; Histones; Immunotherapy; Individual; International; Knowledge; Laboratories; Lead; Location; Magnetic Resonance; Malignant - descriptor; Malignant Childhood Neoplasm; Malignant Glioma; Malignant Neoplasms; Malignant neoplasm of brain; Measurement; Measures; Missense Mutation; Monitor; Mutation; Needle biopsy procedure; Neurologist; Nucleic Acid Probes; Oncologist; Outcome; Pathologic; Pathologist; Patients; Pediatric Neoplasm; Pediatric Oncologist; Phase; Plasma; Publishing; Radiation necrosis; Radiation therapy; Recovery; Relapse; Reproducibility; Research; Resistance; Sampling; Scanning; Sensitivity and Specificity; Services; Signal Transduction; Small Business Innovation Research Grant; Specialized Center; Specificity; Specimen; Symptoms; Testing; Tumor Volume; United States; United States Centers for Medicare and Medicaid Services; United States Food and Drug Administration; Validation; Variant; World Health Organization; base; childhood cancer mortality; college; commercial application; design; digital; effective therapy; experimental study; improved; liquid biopsy; locked nucleic acid; mutant; next generation sequencing; noninvasive diagnosis; novel; novel diagnostics; outcome forecast; outreach; pediatric drug development; personalized diagnostics; prognostic assays; reconstruction; response; response biomarker; standard measure; technological innovation; tool; treatment response; tumor; tumor DNA; tumor progression; tumorigenic

PROJECT SUMMARY/ABSTRACT Diffuse intrinsic pontine glioma (DIPG), affecting an estimated 200-300 children in the United States per year, is one of the deadliest cancers of any type. The median survival for children with DIPG is less than one year from diagnosis; which has not changed in three decades. The diagnosis of DIPG is typically made using clinical symptoms and magnetic resonance (MR) scans. Because of the location of the tumors in the brainstem, diagnostic biopsies are typically avoided, although MR-guided, stereotactic needle biopsies are available in a few specialized centers. Missense mutations in Histone 3 genes H3.3 (H3F3A K27M) or H3.1 (HIST1H3B K27M) are present in most DIPGs and represent an early tumorigenic event. The World Health Organization (WHO) now classifies DIPG and non-pontine midline gliomas together as a distinct pathologic group known as diffuse midline glioma, H3K27 mutant (DMG). Children with H3F3A mutant tumors are more resistant to radiotherapy and relapse earlier than HIST1H3B/C mutant tumors. Documentation of either H3K27 mutation determines eligibility for clinical trial use of H3-K27 demethylase and histone deacetylases. Further, a preliminary study published by collaborators in this proposal showed that 16/20 (80%) of children with H3K27 mutant tumors had detectable circulating tumor DNA (ctDNA) in plasma and mutant allele frequency in plasma correlated with tumor volume measured by MR scans, decreased with initial response to therapy, and increased upon tumor progression. ResourcePath is developing DMG-Dx, a digital droplet PCR (ddPCR) assay for diagnosis, genotyping and monitoring of midline malignant glial neoplasms of childhood in cerebrospinal fluid and/or plasma samples, i.e. liquid biopsy. The ddPCR assay uses advanced, locked-nucleic-acid probe chemistry to achieve exquisitely sensitive and specific histone H3.3 (H3F3A K27M) or histone H3.1 (HIST1H3B/C K27M) hotspot mutations which define DMG. Our long-term goal is to develop DMG-Dx as non-invasive and precise diagnostic tests that will improve clinical management and support drug development for pediatric brainstem gliomas. This liquid biopsy will serve three unmet needs: 1) obtain diagnostic information without having to perform invasive and risky biopsies available only at special centers; 2) determine eligibility for clinical trials and 3) serve as a therapeutic response biomarker providing objective information important to clinical trial of novel agents including immunotherapy. In this SBIR Phase I the aims are: 1) Perform analytic validation of DMG-Dx ddPCR assays for sensitive detection of H3K27 mutations for diagnosis and 2) Determine reliability of these assays for quantitative measurement in tumor monitoring indications. In Phase II we will clinically validate the DMG-Dx in the context of multiple clinical trials. DMG-Dx will be marketed by direct outreach to the international community of pediatric oncologists and neurologists who care for individuals with diffuse midline gliomas.

项目摘要/摘要 弥漫性内在庞然神经胶质瘤（DIPG），每年影响美国200-300名儿童， 是任何类型的最致命的癌症之一。 DIPG儿童的中位生存期不到一年 诊断；三十年来没有改变。通常使用DIPG的诊断 临床症状和磁共振（MR）扫描。由于肿瘤在 脑干，诊断活检通常是避免的，尽管MR引导，即立体定向的针刺活检是 有一些专业中心可供选择。组蛋白3基因H3.3（H3F3A K27M）或H3.1中的错义突变 （Hist1H3b K27M）存在于大多数DIPG中，代表了早期的肿瘤性事件。世界健康 组织（WHO）现在将DIPG和非胰的中线神经胶质瘤分类为一种独特的病理学 被称为弥漫性中线神经胶质瘤，H3K27突变体（DMG）。 H3F3A突变肿瘤的儿童更多 比Hist1h3b/c突变肿瘤更早地对放疗和复发。任何H3K27的文档 突变确定了H3-K27脱甲基酶和组蛋白脱乙酰基酶的临床试验使用资格。此外， 合作者在该提案中发表的初步研究表明，有16/20（80％）的H3K27儿童 突变肿瘤在等离子体中具有可检测的循环肿瘤DNA（CTDNA） 与通过MR扫描测量的肿瘤体积相关，随着对治疗的初始反应而减少，并且 肿瘤进展时增加。 ResourcePath正在开发DMG-DX，一种用于诊断，基因分型和的数字液滴PCR（DDPCR）测定 监测脑脊液和/或血浆样品中的儿童中期恶性神经肿瘤，即 液体活检。 DDPCR分析使用先进的，锁定的核酸探针化学来实现精美的 敏感和特异性组蛋白H3.3（H3F3A K27M）或组蛋白H3.1（Hist1h3b/c K27M）热点突变 定义DMG。我们的长期目标是将DMG-DX作为无创和精确的诊断测试开发 将改善临床管理并支持小儿脑干神经胶质瘤的药物开发。这个液体 活检将满足三个未满足的需求：1）获取诊断信息，而无需执行侵入性和 风险的活检仅在特殊中心可用； 2）确定临床试验的资格，3）用作 治疗反应生物标志物为新型药物的临床试验提供了重要的目标信息 包括免疫疗法。在SBIR I期中，目的是：1）执行DMG-DX DDPCR的分析验证 对H3K27突变的敏感检测测定法和2）确定这些测定的可靠性 肿瘤监测指示中的定量测量。在第二阶段，我们将在临床上验证DMG-DX 多个临床试验的背景。 DMG-DX将通过直接推广国际销售 小儿肿瘤学家和神经科医生社区，他们照顾弥漫性中线神经胶质瘤的人。