PO.CL01.09 · 临床研究
检测晚期癌前病变的cfDNA释放
Detection of cfDNA shedding from advanced precancerous lesions
作者与单位 Authors & Affiliations
摘要 Abstract
中文摘要
用于检测结直肠癌（CRC）和晚期癌前病变（APL）的微创、基于血液的检测已成为辅助癌症早期检测的筛查工具。虽然cfDNA对CRC的检测已展现出高灵敏度和特异性，但对APL的检测则不那么成功。为了理解这些局限性，我们评估了血浆样本中APL cfDNA生物标志物的流行情况。通过生物样本库获取了61例（FFPE n=27，FF n=34）个体的福尔马林固定石蜡包埋（FFPE）或新鲜冷冻（FF）APL组织及配对的正常血液样本。使用全基因组测序（WGS）数据设计定制的、仅供研究使用的、个体化的、基于mPCR-NGS的循环肿瘤DNA（ctDNA）检测。对与组织和全血采集同时收集的配对血浆样本进行评估，以检测血浆中循环APL生物标志物的存在。分别在FFPE和FF中计算整体队列、按APL亚型和病变大小的灵敏度。由于亚型分布与筛查试验中的预期流行率不同（pmids 38477985、40455622），构建了一个代表最终关键研究的分布，以便计算出具有代表性的灵敏度估计值。总体而言，在90%特异性下，经亚型发病率校正的APL血浆灵敏度在配对FFPE和FF组织样本中分别为25%和37%。FFPE样本中较低的血浆检出率可能是由于FFPE组织保存方法导致的组织gDNA完整性受损以及个体化mPCR检测设计能力受限。检出样本的血浆样本变异等位基因频率（VAF）中位数在FFPE和FF中分别为3.6x10-5和1.4x10-5。计算了每种APL亚型的APL血浆灵敏度，包括高级别异型增生（FFPE：40%，N=10；FF：38%，N=10）、绒毛状生长>25%（FFPE：25%，N=8；FF：38%，N=13）、管状腺瘤>10 mm（FFPE：25%，N=4；FF：33%，N=3）和锯齿状病变>10 mm（FFPE：20%，N=5；FF：50%，N=8）。总体而言，灵敏度随病变大小增加而升高（FFPE：4-10 mm 20%，11-20 mm 30%，21-30 mm 50%，≥31 mm 50%；FF：4-10 mm 22%，11-20 mm 47%，21-30 mm 67%，≥31 mm：33%）。在本研究中，我们使用组织指导的ctDNA检测建立了APL ctDNA释放的基线，可用于优化旨在以预期水平检测游离DNA中APL的检测方法。
查看英文原文 English abstract
Minimally invasive, blood-based tests for the detection of colorectal cancer (CRC) and advanced precancerous lesions (APLs) have emerged as a screening tool to aid in the early detection of cancer. While cell-free (cf)DNA detection of CRC has demonstrated high sensitivity and specificity, APL detection has been less successful. In an effort to understand these limitations, we evaluated the prevalence of APL cfDNA biomarkers from plasma samples. Formalin-fixed, paraffin-embedded (FFPE) or fresh frozen (FF) APL tissue and matched normal blood samples from 61 (FFPE n=27, FF n=34) individuals were obtained through biobanks. Whole-genome sequencing (WGS) data was used to design custom, research-use only, personalized, mPCR-NGS-based circulating tumor (ct)DNA assays. Matched plasma samples collected at the same time as tissue and whole blood collection were evaluated for the presence of circulating APL biomarkers in plasma. Sensitivity was calculated in FFPE and FF for the overall cohorts, by APL subtype, and lesion size. Because the subtype distribution differed from expected prevalence in screening trials (pmids 38477985, 40455622), a distribution was constructed to be representative of the final pivotal study so that a reflective sensitivity estimate could be calculated. Overall at a 90% specificity, APL plasma sensitivity adjusted for subtype incidence was 25% and 37% in matched FFPE and FF tissue samples, respectively. The lower plasma detection rate in FFPE samples could be due to the compromised tissue gDNA integrity and personalized mPCR assay design-ability with FFPE tissue preservation methodology. Median plasma sample variant allele frequencies (VAF) of detected samples was 3.6x10-5 and 1.4x10-5 for FFPE and FF, respectively. APL plasma sensitivity for was calculated for each APL subtype, including high-grade dysplasia (FFPE: 40%, N=10; FF: 38%, N=10), villous growth >25% (FFPE: 25%, N=8; FF: 38%, N=13), tubular adenomas >10 mm (FFPE: 25%, N=4; FF: 33%, N=3), and serrated lesions >10 mm (FFPE: 20%, N=5; FF: 50%, N=8). In general, sensitivity increased as lesion size increased (FFPE: 4-10 mm 20%, 11-20 mm 30%, 21-30 mm 50%, ≥31 mm 50%; FF: 4-10 mm 22%, 11-20 mm 47%, 21-30 mm 67%, ≥31 mm: 33%). In this study, we established a baseline of APL ctDNA shedding using a tissue-informed ctDNA assay that can be used for optimizing assays designed to detect APLs at expected levels in cell-free DNA.
利益披露 Disclosure
F. Lu,
Natera, Inc. Employment, Stock, Stock Option.
L. Cerna,
Natera, Inc. Employment, Stock, Stock Option.
S. Alexander,
Natera, Inc. Employment, Stock, Stock Option.
N. Tbeileh,
Natera, Inc. Employment, Stock, Stock Option.
E. Atolia,
Natera, Inc. Employment, Stock, Stock Option.
D. Hafez,
Natera, Inc. Employment, Stock, Stock Option.
E. Kirkizlar,
Natera, Inc. Employment, Stock, Stock Option.
M. Rabinowitz,
Natera, Inc. Employment, g., Board of Directors, non-salaried role), Stock, Stock Option, ), Travel, Patent, Consulting/Advisory Role.
MyOme Employment, g., Board of Directors, non-salaried role), Stock, Stock Option, ), Travel, Patent, Consulting/Advisory Role.
Marble Therapeutics Employment, g., Board of Directors, non-salaried role), Stock, Stock Option, Consulting/Advisory Role.
A. Aleshin,
Natera, Inc. Employment, g., Board of Directors, non-salaried role), Stock, Stock Option.
T. Kawli,
Natera, Inc. Employment, Stock, Stock Option.