转移性癌症患者细胞外囊泡相关 DNA 的低覆盖度全基因组测序。

Low-coverage whole-genome sequencing of extracellular vesicle-associated DNA in patients with metastatic cancer.

机构信息

Department of Medical Oncology, Sir Charles Gairdner Hospital, Perth, WA, Australia.

School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia.

出版信息

Sci Rep. 2021 Feb 17;11(1):4016. doi: 10.1038/s41598-021-83436-1.

DOI:10.1038/s41598-021-83436-1

PMID:33597619

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7889887/

Abstract

Low-coverage whole-genome sequencing (LC-WGS) can provide insight into oncogenic molecular changes. Serum extracellular vesicles (EV) represent a novel liquid biopsy source of tumoral DNA. This study compared copy number alteration (CNA) profiles generated from LC-WGS of formalin-fixed paraffin-embedded (FFPE) tumoral DNA and EV-DNA obtained from cancer patients. Patients with squamous cell carcinoma of the base of tongue (n = 3) and cutaneous squamous cell carcinoma (n = 2) were included. LC-WGS (0.5-1X coverage) was performed on FFPE-DNA and serum EV-DNA. Similarity between CNA profiles was analysed using QDNAseq. FFPE samples had a mean CNA of 31 (range 17-50) over 1.9 × 10 (range 1.0-2.6 × 10) bp in length, and EV samples had a mean CNA value of 17 (range 7-19) over 7.6 × 10 (range 2.9-15 × 10) bp in length. A mean of 8 (range 0-21) CNA over 5.9 × 10 (range 1.6-14 × 10) bp in length was found to overlap between EV and FFPE-derived samples per patient. Although the mean correlation efficient between samples was r = 0.34 (range - .08 to 0.99), this was not statistically significant (p > 0.05). Regions of highest deletion and duplication in FFPE samples were not well reflected in the EV-DNA. Selected CNA regions in EV-associated DNA were reflective of the primary tumor, however appreciation of global CNA and areas of most significant change was lost. The utility of LC-WGS of EV-derived DNA is likely limited to molecular alterations of known interest.

摘要

低覆盖度全基因组测序（LC-WGS）可以提供致癌分子变化的见解。血清细胞外囊泡（EV）代表肿瘤 DNA 的新型液体活检来源。本研究比较了来自福尔马林固定石蜡包埋（FFPE）肿瘤 DNA 的 LC-WGS 和从癌症患者获得的 EV-DNA 生成的拷贝数改变（CNA）图谱。纳入了基底舌鳞状细胞癌（n=3）和皮肤鳞状细胞癌（n=2）患者。对 FFPE-DNA 和血清 EV-DNA 进行 LC-WGS（0.5-1X 覆盖度）。使用 QDNAseq 分析 CNA 图谱的相似性。FFPE 样本的平均 CNA 为 31（范围 17-50），长度为 1.9×10（范围 1.0-2.6×10）bp，EV 样本的平均 CNA 值为 17（范围 7-19），长度为 7.6×10（范围 2.9-15×10）bp。每位患者的 EV 和 FFPE 衍生样本之间平均有 8（范围 0-21）个 CNA，长度为 5.9×10（范围 1.6-14×10）bp。尽管样本之间的平均相关系数为 r=0.34（范围-0.08 至 0.99），但这并不具有统计学意义（p>0.05）。FFPE 样本中最高缺失和重复区域在 EV-DNA 中未得到很好反映。EV 相关 DNA 中的选定 CNA 区域反映了原发性肿瘤，但失去了对全局 CNA 和最显著变化区域的认识。LC-WGS 对 EV 衍生 DNA 的应用可能仅限于已知感兴趣的分子改变。