Detecting and locating cancer for patients with CT-detected lung nodules

为 CT 检测到肺结节的患者检测和定位癌症

• 批准号: 10704494
• 负责人: XIANGHONG Jasmine ZHOU
• 金额: $ 63.82万
• 依托单位: UNIVERSITY OF CALIFORNIA LOS ANGELES
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-14 至 2027-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10704494
• 关键词: Address; Age; Algorithms; Base Pairing; Benign; Biological Assay; Biological Markers; Biopsy; Blood; Bypass; Cancer Detection; Cancer Patient; Chest; Clinical; Clinical Research; Cohort Studies; Collection; Complex; Copy Number Polymorphism; CpG Islands; DNA; DNA Methylation; DNA methylation profiling; Data; Diagnosis; Diagnostic; Diagnostic tests; Disease; Early identification; Epigenetic Process; Ethnic Origin; Etiology; Gender; Genetic; Genomics; Human; Image; Learning; Lesion; Life; Lung; Lung nodule; Malignant - descriptor; Malignant Neoplasms; Malignant neoplasm of lung; Methods; Methylation; Modeling; Names; Neoplasm Metastasis; Nodule; Organ; Pathogenesis; Patients; Plasma; Primary Neoplasm; Procedures; Race; Radiation; Risk; Sample Size; Sampling; Screening for cancer; Signal Transduction; Site; Source; Statistical Distributions; System; Systems Integration; Technology; Testing; Tissues; Training; Tumor-Derived; bisulfite sequencing; cancer diagnosis; cancer type; cell free DNA; chest computed tomography; cohort; comorbidity; computational platform; computer framework; cost; cost effective; former smoker; genome wide methylation; genome-wide; high risk; innovation; low dose computed tomography; lung cancer screening; methylation biomarker; methylome; microbial; microbial composition; microbiome; mortality; patient population; patient screening; psychologic; public health relevance; repository; screening; tool; tumor; tumor DNA; whole genome

PROJECT SUMMARY Low-Dose Computed Tomography (LDCT) has been demonstrated to reduce lung cancer mortality by 20% for high-risk current and former smokers. However, 25% of the subjects in the NLST demonstrated abnormalities and a large fraction of those lesions were determined to be false-positives. There is an unmet need to accurately and non-invasively identify early-stage aggressive lung cancers and distinguish lesions that are life threatening from those that are not. Recently cell-free DNA (cfDNA) in human blood has emerged as an ideal source for cancer detection. In this proposal, we develop an integrated system, CancerRadar, consisting of (1) an experimental assay, cfMethyl-Seq, for cost-effective genome-wide methylation profiling of cfDNA, offering >10 fold enrichment over Whole Genome Bisulfite Sequencing (WGBS) in profiling CpG islands; and (2) a computational framework to extract various information from cfMethyl-Seq data, including cfDNA methylation, cfDNA fragment size, copy number variation (CNV), and microbial composition, and perform multi-feature ensemble learning for detecting malignant lung nodule and locating its primary tumor sites. We will validate CancerRadar with several clinical cohorts. Compared to the commonly used small panels focusing on one type of markers, CancerRadar profiles and integrates genome-wide profiles of multiple genetic/epigenetic features, therefore can robustly capture the very small proportion of tumor-derived cfDNA fragments, comprehensively diagnose patients with heterogeneous cancer pathogenesis, and learn and exploit newly significant features as training sample size grow.

项目总结 低剂量计算机断层扫描(LDCT)已被证明可以将肺癌死亡率降低20% 现在和以前的吸烟者都是高危人群。然而，在NLST中，25%的受试者表现出异常 这些病变中有很大一部分被确定为假阳性。有一种未得到满足的需求 准确和非侵入性地识别早期侵袭性肺癌并区分有生命的病变 来自那些不是的威胁。最近，人类血液中的无细胞dna(Cfdna)已经成为一种理想的方法。 癌症检测的来源。在这项建议中，我们开发了一个集成系统，癌症雷达，包括(1) 一种用于经济有效的全基因组甲基化分析的实验性方法cfMethyl-Seq，提供 在分析CpG岛方面，比全基因组亚硫酸盐测序(WGBS)浓缩10倍；以及(2)a 从cf甲基序列数据中提取各种信息的计算框架，包括cfDNA甲基化、 CfDNA片段大小、拷贝数变异(CNV)和微生物组成，并执行多种功能 用于检测恶性肺结节并定位其原发肿瘤部位的集成学习。我们将验证 巨蟹座雷达和几个临床队列。与通常使用的专注于一种类型的小面板相比 在标记中，巨蟹座雷达描绘并整合了多种遗传/表观遗传特征的全基因组图谱， 因此可以很好地捕获很小比例的肿瘤来源的cfDNA片段，全面 诊断具有异质性癌症发病机制的患者，并学习和开发新的重要特征，如 训练样本量增长。

项目成果

cfSNV: a software tool for the sensitive detection of somatic mutations from cell-free DNA.

• DOI: 10.1038/s41596-023-00807-w
• 发表时间: 2023-05
• 期刊: NATURE PROTOCOLS
• 影响因子: 14.8
• 作者: Li, Shuo;Hu, Ran;Small, Colin;Kang, Ting-Yu;Liu, Chun-Chi;Zhou, Xianghong Jasmine;Li, Wenyuan
• 通讯作者: Li, Wenyuan