美国斯坦福大学Ash A. Alizadeh、Maximilian Diehn等研究人员合作实现对循环肿瘤DNA的灵敏检测。这一研究成果于2021年7月22日在线发表在国际学术期刊《自然—生物技术》上。

研究人员报道了分阶段变异富集和检测的测序（PhasED-seq），这种方法利用单个DNA片段中的多个体细胞突变来提高循环肿瘤来源的DNA（ctDNA）检测的灵敏度。利用2,538个肿瘤的全基因组序列，研究人员确定了阶段性变异及其与突变特征的关联。结果表明，即使没有分子条形码，PhasED-seq的检测极限也超过了先前的方法，包括双重条形码，使参与者样本的ctDNA检测在ppm范围内。

研究人员对213名B细胞淋巴瘤患者的678份标本进行了分析，包括弥漫性大B细胞淋巴瘤治疗前和治疗期间的系列无细胞DNA样本。在使用基于下一代测序的方法（称为深层测序的癌症个性化剖析）治疗两个周期后检测不到ctDNA的参与者中，有25%的人可以通过PhasED-seq检测到ctDNA，并且其预后结果更差。最后，研究人员还展示了PhasED-seq在实体瘤中的应用。

据介绍，ctDNA是许多癌症的一种新兴生物标志物，但目前检测方法的灵敏度有限，降低了其对诊断最小残留疾病的效用。

附：英文原文

Title: Enhanced detection of minimal residual disease by targeted sequencing of phased variants in circulating tumor DNA

Author: David M. Kurtz, Joanne Soo, Lyron Co Ting Keh, Stefan Alig, Jacob J. Chabon, Brian J. Sworder, Andre Schultz, Michael C. Jin, Florian Scherer, Andrea Garofalo, Charles W. Macaulay, Emily G. Hamilton, Binbin Chen, Mari Olsen, Joseph G. Schroers-Martin, Alexander F. M. Craig, Everett J. Moding, Mohammad S. Esfahani, Chih Long Liu, Ulrich Dhrsen, Andreas Httmann, Ren-Olivier Casasnovas, Jason R. Westin, Mark Roschewski, Wyndham H. Wilson, Gianluca Gaidano, Davide Rossi, Maximilian Diehn, Ash A. Alizadeh

Issue&Volume: 2021-07-22

Abstract: Circulating tumor-derived DNA (ctDNA) is an emerging biomarker for many cancers, but the limited sensitivity of current detection methods reduces its utility for diagnosing minimal residual disease. Here we describe phased variant enrichment and detection sequencing (PhasED-seq), a method that uses multiple somatic mutations in individual DNA fragments to improve the sensitivity of ctDNA detection. Leveraging whole-genome sequences from 2,538 tumors, we identify phased variants and their associations with mutational signatures. We show that even without molecular barcodes, the limits of detection of PhasED-seq outperform prior methods, including duplex barcoding, allowing ctDNA detection in the ppm range in participant samples. We profiled 678 specimens from 213 participants with B cell lymphomas, including serial cell-free DNA samples before and during therapy for diffuse large B cell lymphoma. In participants with undetectable ctDNA after two cycles of therapy using a next-generation sequencing-based approach termed cancer personalized profiling by deep sequencing, an additional 25% have ctDNA detectable by PhasED-seq and have worse outcomes. Finally, we demonstrate the application of PhasED-seq to solid tumors. The sensitivity of circulating tumor DNA detection is improved by identifying sequences with two or more mutations.

DOI: 10.1038/s41587-021-00981-w

Source: https://www.nature.com/articles/s41587-021-00981-w