A Rapid and Comprehensive Approach for Clinical Genomic Profiling in Lung Cancer

肺癌临床基因组分析的快速综合方法

基本信息

  • 批准号:
    10613055
  • 负责人:
  • 金额:
    $ 38.8万
  • 依托单位:
  • 依托单位国家:
    美国
  • 项目类别:
  • 财政年份:
    2023
  • 资助国家:
    美国
  • 起止时间:
    2023-05-01 至 2026-04-30
  • 项目状态:
    未结题

项目摘要

ABSTRACT The long-term goal of this project is to advance precision medicine by developing a simple, rapid, and comprehensive approach to molecular diagnostic testing that can be easily performed on any cancer subtype. In lung adenocarcinoma and many other solid tumor types, optimal treatment relies on the identification of specific genomic alterations. These include single nucleotide variants and small insertions and deletions, as well as larger copy number alterations and chromosomal translocations. Currently, clinical testing for these mutations requires multiple assays and significant amounts of tissue so that both DNA and RNA can be obtained for analysis. As a result, many samples fail or simply cannot be tested. At our cancer center 38% of lung cancer patient biopsies sent for comprehensive molecular evaluation either fail or result in incomplete results. More robust and streamlined diagnostic methods are therefore needed to provide truly comprehensive mutational profiling for all cancer patients. We have developed a novel approach for whole-genome sequencing (ChromoSeq) that provides rapid, unbiased evaluation of all mutation types in a single assay. ChromoSeq leverages recent advances in high-throughput sequencing methods to deliver a complete genomic profile in as little as 3 days using minimal DNA input. We have previously shown that ChromoSeq can provide rapid comprehensive genomic profiles from blood or marrow of patients with myeloid malignancies and that ChromoSeq has increased sensitivity to detect clinically significant genomic alterations compared to conventional methods. However, obtaining similar performance from solid tumors with limited amounts of degraded DNA typically obtained from formalin-fixed paraffin-embedded (FFPE) tissue biopsies is challenging. We hypothesize that with substantial methodologic pre-analytic improvements and rigorous clinical validation testing, ChromoSeq can also be used for the comprehensive genomic profiling of solid tumors. In this application, we propose to measure and optimize DNA changes that occur during pre-analytic tissue processing of routine clinical biopsies (Aim 1) and then establish the clinical performance of the assay using retrospectively and prospectively collected patient samples (Aim 2). These Aims will be performed in a CLIA-licensed, CAP- accredited laboratory with the overall objective of producing a CLIA-compliant assay for future use in clinical studies and to improve the diagnosis and treatment of patients with lung cancer. Tools and protocols developed in this application will enable other laboratories to benefit from this simplified approach to cancer genomic profiling.
摘要 该项目的长期目标是通过开发一种简单,快速, 这是一种全面的分子诊断检测方法,可以轻松地对任何癌症亚型进行检测。 在肺腺癌和许多其他实体瘤类型中,最佳治疗依赖于识别 特定的基因组改变这些包括单核苷酸变异和小的插入和缺失,以及 更大的拷贝数改变和染色体易位。目前,对这些突变的临床测试 需要多次检测和大量的组织,以便可以获得DNA和RNA, 分析.因此,许多样品不合格或根本无法测试。在我们的癌症中心, 送去进行综合分子评价的患者活组织检查失败或导致不完整的结果。更 因此,需要稳健和简化的诊断方法来提供真正全面的突变检测。 对所有癌症患者进行分析。我们开发了一种新的全基因组测序方法 (ChromoSeq),其在单个测定中提供所有突变类型的快速、无偏评估。ChromoSeq 利用高通量测序方法的最新进展, 用最少的DNA输入只需要3天我们之前已经证明,ChromoSeq可以提供快速的 来自骨髓恶性肿瘤患者血液或骨髓的全面基因组图谱, 与对照组相比,ChromoSeq检测临床显著基因组改变的灵敏度增加。 常规方法。然而,从具有有限量的实体瘤中获得类似的性能 通常从福尔马林固定的石蜡包埋(FFPE)组织活检中获得的降解的DNA是具有挑战性的。 我们假设,随着大量的方法学分析前的改进和严格的临床验证, 通过测试,ChromoSeq也可用于实体瘤的全面基因组分析。在本申请中, 我们建议测量和优化DNA的变化,发生在分析前的组织处理的常规, 临床活检(目标1),然后使用回顾性和 前瞻性采集患者样本(目标2)。这些目标将在CLIA许可的CAP- 经认证的实验室,总体目标是生产符合CLIA要求的检测试剂盒,供未来临床使用 肺癌的诊断和治疗是肺癌患者的重要治疗手段。开发的工具和协议 将使其他实验室受益于这种简化的癌症基因组学方法, 侧写

项目成果

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ERIC J DUNCAVAGE其他文献

ERIC J DUNCAVAGE的其他文献

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{{ truncateString('ERIC J DUNCAVAGE', 18)}}的其他基金

Genome sequencing for evaluating the efficacy, specificity, and safety of human genome editing
用于评估人类基因组编辑的有效性、特异性和安全性的基因组测序
  • 批准号:
    10667893
  • 财政年份:
    2023
  • 资助金额:
    $ 38.8万
  • 项目类别:
Whole Genome Sequencing for Genomic Evaluation and Risk Stratification of Patients with Myelodysplastic Syndromes
全基因组测序用于骨髓增生异常综合征患者的基因组评估和风险分层
  • 批准号:
    10506155
  • 财政年份:
    2022
  • 资助金额:
    $ 38.8万
  • 项目类别:

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