Cell-free DNA Analysis for Liquid Biopsy of Cancer

用于癌症液体活检的游离 DNA 分析

基本信息

批准号：
10818662
负责人：
Jordan C Cheng
金额：
$ 8.59万
依托单位：
STANFORD UNIVERSITY
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：
2023-09-01 至 2027-08-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10818662
关键词：
Address Animals Apoptosis Axilla Base Pairing Bioinformatics Biological Biological Markers Biological Models Biology CRISPR/Cas technology Cancer Center Cancer Detection Cancer Patient Cell Culture Techniques Cerebrospinal Fluid Circulation Clinical Complex Comprehensive Cancer Center DNA DNA analysis 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 Incisional Biopsy Inflammatory Response Jordan 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 Sampling School Dentistry Screening for cancer Selection Bias Single-Stranded DNA Testing Therapeutic Tissues Training Urine Validation Work anticancer research 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 professor saliva sample skills theories tumor tumor DNA tumor progression

项目摘要

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.

项目摘要/摘要循环肿瘤DNA（ctDNA），它反映了亲本肿瘤，存在于非小细胞肺的血浆中癌（NSCLC）患者。 CTDNA的液体活检分析允许早期检测和遗传监测。但是，由于低副本，当前基于PCR的液体活检方法通常很难检测到CTDNA 循环。相反，电场诱导的释放和测量液体活检（ELB）平台检测突变EGFR（L858R，EXON19DEL，T790M）ctDNA，<50ul <50ul <50ul的ctDNA ctDNA> 90％ NSCLC患者未经处理的血浆。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-Basepair对比核体核小体双链ctDNA。通过基于PCR的液体无法检测到这种新的亚群大小选择偏置引起的活检方法。 F99阶段的目标是使用USSSCTDNA-SEQ，一种新颖的NGS 管道，探索NSCLC等离子体是否含有大量的超短和单链的ctDNA。该管道由USSSCTDNA特定提取，库制备，深度测序和生物信息学组成分析。为了验证，80个晚期NSCLC EGFR突变的等离子体样品将接受USSSCTDNA-SEQ。这发现USSSCTDNA将开放大量以前未被注意到的信息，从而改善治疗 NSCLC患者的生存。之后，在K00阶段，学员希望探索生物学生物流体ctDNA的起源以及将USSSTDNA掺入现代多分析物方法中的起源癌症检测。这将涉及培训新技能，例如器官建模，甲基化和白细胞在世界领先的癌症研究所进行测序和生物信息学的机器学习。最终，目标在该拟议的F99/K00项目中，将为受训者做好准备，从事癌症研究职业的专业知识液体活检和无细胞DNA生物学。