Advanced development and validation of targeted molecular counting methods for precise and ultrasensitive quantitation of low prevalence somatic mutations

先进的开发和验证靶向分子计数方法，用于低流行体细胞突变的精确和超灵敏定量

• 批准号: 9061644
• 负责人: Stephen J Salipante
• 金额: $ 37.59万
• 依托单位: UNIVERSITY OF WASHINGTON
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-05-01 至 2018-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9061644
• 关键词: Acute Myelocytic Leukemia; Address; Advanced Development; Alleles; Basic Science; Biological Assay; Biological Markers; Blood Circulation; CLIA certified; Cancer Detection; Cancer Diagnostics; Cancer Patient; Cataloging; Catalogs; Cell Line; Cells; Characteristics; Clinical; Consensus; DNA Sequence; Detection; Detection of Minimal Residual Disease; Diagnosis; Diagnostic; Disease; Drug resistance; Early Diagnosis; Event; Exons; Flow Cytometry; Frequencies; Gene Frequency; Genes; Genetic screening method; Goals; Gold; Haploidy; Health; Hereditary Disease; Individual; Laboratories; Low Prevalence; Malignant Neoplasms; Massive Parallel Sequencing; Measurement; Measures; Mediating; Methodology; Methods; Mind; Molecular; Molecular Analysis; Molecular Target; Monitor; Monitoring for Recurrence; Mutate; Mutation; Non-Invasive Cancer Detection; Outcome; Patient Care; Patients; Performance; Prognostic Marker; Property; Reaction; Reading; Reagent; Recurrence; Recurrent disease; Relapse; Reproducibility; Residual Neoplasm; Residual state; Sampling; Screening for cancer; Site; Somatic Mutation; Specificity; Specimen; Technology; Time; Validation; actionable mutation; anticancer research; base; cancer genome; cancer recurrence; cancer therapy; cell free DNA; clinical application; clinical practice; clinically relevant; combinatorial; cost; cost effective; cost effectiveness; design; diagnostic assay; exome sequencing; genome sequencing; genomic biomarker; insertion/deletion mutation; meetings; multiplex detection; mutant; neoplastic cell; novel; outcome forecast; personalized medicine; progenitor; prognostic; research clinical testing; resistance mutation; targeted sequencing; technology validation; tool; tumor; tumor DNA; whole genome

DESCRIPTION (provided by applicant): The ultrasensitive detection of clinically relevant somatic alterations in cancer genomes has great potential for impacting patient care, e.g. for early detection, establishing diagnoses, refining prognoses, guiding treatment, and monitoring recurrence. However, current technologies are poorly suited to the robust detection of somatic mutations present at very low frequencies (<1%). Massively parallel sequencing represents an advantageous path forward, but its sensitivity to detect very rare events is fundamentally constrained by the sequencing error rate. We have recently developed a new experimental paradigm that overcomes this limitation. In our approach, each copy of a target sequence that is present in a sample is molecularly tagged during the first cycle of a multiplex capture reaction with a unique random sequence. After amplification, target amplicons and their corresponding molecular tags are subjected to massively parallel sequencing. During analysis, the molecular tags are used to associate sequence reads sharing a common origin. Through oversampling, reads bearing the same molecular tag error-correct one another to yield an independent haploid consensus for each progenitor molecule. Furthermore, the collapsing of commonly derived reads inherently corrects for any allele-specific bias during amplification, such that estimates of mutant allele frequency can be accompanied by precise confidence bounds ("molecular counting"). Among other benefits, the approach is sensitive to at least 1 mutated sequence in a background of 10,000 unmutated copies. Here we propose the advanced development and validation of this approach for use as a clinical diagnostic. In our first aim, we will develop a multiplexed panel to broadly target common cancer associated mutations using this technology. In our second aim, we will apply the panel to the detection of minimal residual disease in acute myeloid leukemia as a prognostic marker of disease relapse. In our third aim, we will apply the panel to detection of ultra-rare mutations in circulating cell-free DNA, which is released into circulation from dying tumor cells, as a robust and non-invasive cancer diagnostic. The panel will be rigorously validated for clinical use in both aims, with performance metrics appropriately designed for the two separate analytes. The availability of robust, cost-effective, quantitative, and generically applicable tools for the ultrasensitive, multiplex detection of rare somatic events in the clinical setting will provide enhanced, transformative capabilities in the diagnosis and monitoring of cancers. The methodology will also have application to basic science cancer research.

描述（由申请人提供）：癌症基因组中临床相关体细胞改变的超灵敏检测具有影响患者护理的巨大潜力，例如用于早期检测、建立诊断、完善诊断、指导治疗和监测复发。然而，目前的技术不太适合于以非常低的频率（<1%）存在的体细胞突变的稳健检测。大规模并行测序代表了一条有利的前进道路，但其检测非常罕见事件的灵敏度从根本上受到测序错误率的限制。我们最近开发了一种新的实验范式，克服了这一限制。在我们的方法中，样品中存在的靶序列的每个拷贝在多重捕获反应的第一个循环期间用独特的随机序列进行分子标记。扩增后，对靶扩增子及其相应的分子标签进行大规模平行测序。在分析期间，分子标签用于关联共享共同起源的序列读段。通过过采样，带有相同分子标签的读段彼此纠错以产生每个祖分子的独立单倍体共有序列。此外，通常衍生的读段的折叠固有地校正扩增期间的任何等位基因特异性偏差，使得扩增产物的估计值与等位基因特异性偏差的估计值之间的关系是不一致的。 突变等位基因频率可伴随有精确的置信界限（“分子计数”）。在其他益处中，该方法对10，000个未突变拷贝的背景中的至少1个突变序列敏感。在这里，我们提出了先进的开发和验证这种方法作为临床诊断。在我们的第一个目标中，我们将开发一个多路复用的面板，使用该技术广泛靶向常见的癌症相关突变。在我们的第二个目标中，我们将应用该小组检测急性髓性白血病的微小残留病，作为疾病复发的预后标志物。在我们的第三个目标中，我们将应用该小组检测循环无细胞DNA中的超罕见突变，该DNA从垂死的肿瘤细胞释放到循环中，作为一种强大的非侵入性癌症诊断。将对该试剂盒进行严格验证，以用于两种目标的临床应用，并为两种单独的分析物适当设计性能指标。可靠的、经济的、定量的和通用的工具的可用性，用于罕见体细胞事件的超灵敏、多重检测 在临床环境中，将在癌症的诊断和监测方面提供增强的变革能力。该方法也将应用于基础科学癌症研究。