PO.BCS01.11 · 生物信息与计算
利用6碱基基因组通过联合甲基化与片段组学分析对cfDNA进行完整多组学分析，以增强临床癌症cfDNA样本的分类
Using the 6-base genome for full multiomic analysis of cfDNA through combined methylation and fragmentomic analysis to enhance classification of clinical cancer cfDNA samples
作者与单位 Authors & Affiliations
摘要 Abstract
中文摘要
在总的游离DNA（cfDNA）池中灵敏地检测循环肿瘤DNA（ctDNA），对于通过液体活检进行癌症的早期诊断，以及在治疗和缓解期间监测ctDNA水平至关重要。这可实现对治疗反应的更早监测、微小残留病灶的识别以及癌症的早期检测。然而，ctDNA通常仅占总cfDNA的一小部分，给传统的基于生物标志物的检测方法带来了重大挑战。近来，基于片段组学的方法在液体活检样本中的ctDNA检测方面显示出令人鼓舞的结果，多项研究表明，分析跨基因组区域的片段大小分布、5'末端基序的频率以及功能性基因组位点附近的核小体定位模式，可显著提高灵敏度和特异性。诸如使用 duet evoC 进行6碱基测序（可区分5-甲基胞嘧啶（5mC）与5-羟甲基胞嘧啶（5hmC））等先进甲基化组分析方法的出现，进一步拓展了分析格局。将5mC和5hmC分析与ctDNA检测策略相结合，扩展了可辨别的片段末端基序的谱系，并为片段大小和核小体定位分析提供了正交的数据层。这些多维度表观遗传学特征有望显著提高ctDNA检测的分辨率和准确性。在此，我们评估了这些额外的表观遗传学层对来自健康志愿者和不同分期结直肠癌患者队列的液体活检样本中ctDNA检测的影响。我们发现，除了健康人群与早期或晚期CRC之间存在不同的5mC和5hmC谱之外，在跨这些组别比较时片段组学指标也存在明显差异。我们识别出在来自健康个体和CRC患者的cfDNA中核小体定位存在差异的调控区域。最后，我们比较了片段组学和表观遗传学模态（单独及联合）对CRC患者进行分类的能力。这些分类器证明了完整多组学数据集在cfDNA应用中的实用价值。
查看英文原文 English abstract
Sensitive detection of circulating tumour DNA (ctDNA) within the total pool of cell-free DNA (cfDNA) is crucial for the early diagnosis of cancer via liquid biopsy, and for monitoring ctDNA levels during treatment and remission. This enables earlier monitoring of treatment response, identification of minimal residual disease, and early detection of cancer. However, ctDNA typically represents only a minor fraction of overall cfDNA, posing significant challenges for conventional biomarker-based detection methods. Recently, fragmentomics-based approaches have shown promising results for ctDNA detection in liquid biopsy samples, with studies demonstrating that analysis of fragment size distributions across genomic regions, the frequency of 5' end motifs, and nucleosome positioning patterns near functional genomic sites can substantially enhance sensitivity and specificity. The advent of advanced methylomic profiling methods, such as 6-base sequencing with duet evoC, which distinguishes 5-methylcytosine (5mC) from 5-hydroxymethylcytosine (5hmC), has further expanded the analytical landscape. Integrating 5mC and 5hmC profiling with ctDNA detection strategies extends the spectrum of discernible fragment end motifs and provides orthogonal data layers to fragment size and nucleosome positioning analysis. These multidimensional epigenetic signatures hold the potential to markedly improve the resolution and accuracy of ctDNA detection. Here, we evaluate the impact of these additional epigenetic layers on ctDNA detection in liquid biopsy samples from a cohort of healthy volunteers and patients with different stages of colorectal cancer. We show that as well as different 5mC and 5hmC profiles between healthy, and early or late stage CRC, there are distinct differences in fragmentomics metrics when comparing across these groups. We identify regulatory regions displaying differences in nucleosome positioning in cfDNA derived from healthy individuals and CRC patients. Finally, we compare the ability of fragmentomics and epigenetic modalities (individually and in combination) to classify CRC patients. These classifiers evidence the utility of full multiomic datasets in cfDNA applications.
利益披露 Disclosure
T. Charlesworth, None..
S. Ciaramaglia, None.