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

摘要 该项目的长期目标是通过开发一种简单、快速和 全面的分子诊断测试方法，可轻松对任何癌症亚型进行检测。 在肺腺癌和许多其他实体肿瘤类型中，最佳治疗依赖于对 特定的基因组改变。这包括单核苷酸变异和小插入和小缺失。 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 需要多次化验和大量的组织才能同时获得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，38%的肺癌患者 送去进行全面分子评估的患者活组织检查要么失败，要么结果不完整。更多 因此，需要强大和简化的诊断方法来提供真正全面的突变 为所有癌症患者做侧写。我们开发了一种新的全基因组测序方法 (ChromoSeq)，在一次检测中提供对所有突变类型的快速、公正的评估。ChromoSeq 利用高通量测序方法的最新进展在AS中提供完整的基因组图谱 使用最少的DNA输入仅需3天。我们之前已经证明，ChromoSeq可以提供快速 髓系恶性肿瘤患者血液或骨髓的全面基因组图谱 ChromoSeq在检测临床上有意义的基因组变化方面的敏感性比 传统的方法。然而，从实体肿瘤中获得类似的表现，并使用有限的 通常从福尔马林固定石蜡包埋(FFPE)组织活检中获得的降解DNA是具有挑战性的。 我们假设，通过大量的方法学分析前改进和严格的临床验证 经过测试，ChromoSeq还可用于实体肿瘤的全面基因组图谱分析。在此应用程序中， 我们建议测量和优化在常规分析前组织处理过程中发生的DNA变化 临床活组织检查(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- 获得认可的实验室，总体目标是生产符合CLIA标准的分析方法，供未来临床使用 研究并提高肺癌患者的诊断和治疗水平。开发的工具和协议 这一应用将使其他实验室从这种简化的癌症基因组检测方法中受益 侧写。

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.