Predoctoral to Postdoctoral Research Training in ctDNA Biology for Liquid Biopsy of Cancer

癌症液体活检 ctDNA 生物学博士前至博士后研究培训

• 批准号: 10470351
• 负责人: Jordan C Cheng
• 金额: $ 4.12万
• 依托单位: UNIVERSITY OF CALIFORNIA LOS ANGELES
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-01 至 2023-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10470351
• 关键词: Address; Animals; Apoptosis; Axilla; Bioinformatics; Biological; Biological Markers; Biological Models; Biology; Blood Circulation; CRISPR/Cas technology; Cancer Center; Cancer Detection; Cancer Patient; Cell Culture Techniques; Cerebrospinal Fluid; Clinical; Complex; Comprehensive Cancer Center; DNA; DNA purification; DNA sequencing; Data; Detection; Development; Disease Progression; Disseminated Malignant Neoplasm; Doctor of Philosophy; Early Diagnosis; Elements; Epidermal Growth Factor Receptor; Excision; Exclusion; Genetic; Genomics; Genotype; Goals; Head and neck structure; Inflammatory Response; Institutes; Jordan; Lead; Length; Leukocytes; Libraries; Machine Learning; Malignant Neoplasms; Malignant neoplasm of brain; Malignant neoplasm of lung; Malignant neoplasm of pancreas; Measurement; Mentorship; Methodology; Methods; Methylation; Modeling; Modernization; Monitor; Mutate; Mutation; Nature; Non-Small-Cell Lung Carcinoma; Oncogenic; Oncology; Oral; Organoids; Outcome; Patients; Pharmacotherapy; Phase; Plasma; Population; Positioning Attribute; Postdoctoral Fellow; Preparation; Process; Protocols documentation; Regulatory Pathway; Research; Research Project Grants; Research Training; Sampling; School Dentistry; Screening for cancer; Selection Bias; Testing; Therapeutic; Tissues; Training; Urine; Validation; Work; anticancer research; base; cancer cell; cancer genetics; cancer type; career; cell free DNA; cohort; deep sequencing; design; ds-DNA; electric field; experimental study; extracellular; improved; insight; interest; liquid biopsy; methylation pattern; mutant; next generation sequencing; novel; pre-doctoral; professor; saliva sample; skills; tumor; tumor DNA; tumor progression

PROJECT SUMMARY/ABSTRACT Circulating tumor DNA (ctDNA) which mirrors the parental tumor, is present in the plasma of non-small cell lung carcinoma (NSCLC) patients. Liquid biopsy analysis of ctDNA allows early detection and genetic monitoring. However, current PCR-based liquid biopsy methods often have difficulty detecting ctDNA due to low copies in circulation. In contrast, the electric field-induced release and measurement liquid biopsy (eLB) platform, detects mutant EGFR (L858R, exon19del, T790M) ctDNA with a >90% tissue-genotype concordance in <50ul of unprocessed plasma of NSCLC patients. Preliminary data demonstrate that the ctDNA detected by eLB may be ultrashort single-stranded ctDNA (usssctDNA) which contrasts the typically described 160-basepair internucleosomal double-stranded ctDNA. This new subpopulation is undetectable through PCR-based liquid biopsy methods due to size-selection bias. The goal of the F99 Phase is to use usssctDNA-seq, a novel NGS pipeline, to explore if NSCLC plasma contains high quantities of ctDNA that are ultrashort and single-stranded. This pipeline consists of a usssctDNA-specific extraction, library preparation, deep sequencing, and bioinformatic analysis. To verify, 80 late-stage NSCLC EGFR-mutated plasma samples will undergo usssctDNA-seq. The discovery of usssctDNA will open up a wealth of previously unnoticed information leading to improved treatment and survival of NSCLC patients. Afterward, during the K00 Phase, the trainee hopes to explore the biological origins of biofluid ctDNA and the incorporation of usssctDNA into modern multi-analyte approaches for pan- cancer detection. This will involve training in new skills such as organoid modeling, methylation and leukocyte sequencing, and bioinformatic machine learning at a world-leading cancer-oriented institute. Ultimately, the goal of this proposed F99/K00 project will to prepare the trainee for a career in cancer research with an expertise in liquid biopsy and cell-free DNA biology.

项目概要/摘要 反映亲本肿瘤的循环肿瘤 DNA (ctDNA) 存在于非小细胞肺的血浆中 癌症（非小细胞肺癌）患者。 ctDNA 液体活检分析可实现早期检测和基因监测。 然而，目前基于 PCR 的液体活检方法通常难以检测 ctDNA，因为 ctDNA 的拷贝数较低。 循环。相比之下，电场诱导释放和测量液体活检 (eLB) 平台可检测 突变型 EGFR（L858R、外显子 19del、T790M）ctDNA 在 <50ul 的组织中具有 >90% 的组织基因型一致性 NSCLC 患者的未处理血浆。初步数据表明，eLB检测到的ctDNA可能是 超短单链 ctDNA (usssctDNA)，与通常描述的 160 个碱基对形成鲜明对比 核小体间双链 ctDNA。这种新的亚群无法通过基于 PCR 的液体检测到 由于尺寸选择偏差而导致的活检方法。 F99 阶段的目标是使用 usssctDNA-seq，一种新型 NGS 管道，探索 NSCLC 血浆是否含有大量超短单链 ctDNA。 该流程包括 usssctDNA 特异性提取、文库制备、深度测序和生物信息学 分析。为了验证，80 个晚期 NSCLC EGFR 突变血浆样本将接受 usssctDNA-seq。这 usssctDNA 的发现将揭示大量以前未被注意到的信息，从而改善治疗 和 NSCLC 患者的生存率。之后，在K00阶段，学员希望探索生物 生物流体 ctDNA 的起源以及将 usssctDNA 纳入现代多分析方法以进行泛 癌症检测。这将涉及新技能的培训，例如类器官建模、甲基化和白细胞 世界领先的癌症研究所的测序和生物信息机器学习。最终，目标 拟议的 F99/K00 项目的一部分将为受训者准备从事癌症研究的职业，并具有以下方面的专业知识： 液体活检和无细胞 DNA 生物学。