Whole-genome informed circulating tumor DNA analysis by multiplex digital PCR for disease monitoring in B-cell lymphomas: a proof-of-concept study

Frontiers in Oncology

Oncology

Anna Gellerbring¹  Moa Hägglund¹  Ashwini Jeggari¹  Anna Lyander¹  Hero Nikdin Awier²  Birgitta Sander³  Linn Deleskog Spångberg⁴  Karin E. Smedby⁵  Kristina Sonnevi⁵  Tove Wästerlid⁵  Birna Thorvaldsdottir⁶  Leily Rabbani⁶  Zahra Haider⁶  Aron Skaftason⁶  Cecilia Jylhä⁷  Emma Tham⁷  Aleksandra Krstic⁷  Richard Rosenquist⁸  Georgios Rassidakis⁹ 

[1] Clinical Genomics Stockholm, Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology, Stockholm, Sweden;Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden;Department of Laboratory Medicine, Division of Pathology and Cancer Diagnostics, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden;Department of Medicine, Division of Clinical Epidemiology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden;Department of Medicine, Division of Clinical Epidemiology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden;Department of Hematology, Karolinska University Hospital, Stockholm, Sweden;Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden;Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden;Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden;Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden;Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden;Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden;Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden;Department of Clinical Pathology and Cancer Diagnostics, Karolinska University Laboratory, Stockholm, Sweden;

关键词: cell-free DNA (cfDNA);    whole genome sequence (WGS);    liquid biopsy;    lymphoma;    measurable (minimal) residual disease (MRD);    droplet digital (ddPCR);    CtDNA;    IGH-BCL2 translocation;   

DOI  :  10.3389/fonc.2023.1176698

 received in 2023-02-28, accepted in 2023-05-02,  发布年份 2023

来源: Frontiers

【 摘 要 】

IntroductionAnalyzing liquid biopsies for tumor-specific aberrations can facilitate detection of measurable residual disease (MRD) during treatment and at follow-up. In this study, we assessed the clinical potential of using whole-genome sequencing (WGS) of lymphomas at diagnosis to identify patient-specific structural (SVs) and single nucleotide variants (SNVs) to enable longitudinal, multi-targeted droplet digital PCR analysis (ddPCR) of cell-free DNA (cfDNA).MethodsIn 9 patients with B-cell lymphoma (diffuse large B-cell lymphoma and follicular lymphoma), comprehensive genomic profiling at diagnosis was performed by 30X WGS of paired tumor and normal specimens. Patient-specific multiplex ddPCR (m-ddPCR) assays were designed for simultaneous detection of multiple SNVs, indels and/or SVs, with a detection sensitivity of 0.0025% for SV assays and 0.02% for SNVs/indel assays. M-ddPCR was applied to analyze cfDNA isolated from serially collected plasma at clinically critical timepoints during primary and/or relapse treatment and at follow-up.ResultsA total of 164 SNVs/indels were identified by WGS including 30 variants known to be functionally relevant in lymphoma pathogenesis. The most frequently mutated genes included KMT2D, PIM1, SOCS1 and BCL2. WGS analysis further identified recurrent SVs including t(14;18)(q32;q21) (IGH::BCL2), and t(6;14)(p25;q32) (IGH::IRF4). Plasma analysis at diagnosis showed positive circulating tumor DNA (ctDNA) levels in 88% of patients and the ctDNA burden correlated with baseline clinical parameters (LDH and sedimentation rate, p-value <0.01). While clearance of ctDNA levels after primary treatment cycle 1 was observed in 3/6 patients, all patients analyzed at final evaluation of primary treatment showed negative ctDNA, hence correlating with PET-CT imaging. One patient with positive ctDNA at interim also displayed detectable ctDNA (average variant allele frequency (VAF) 6.9%) in the follow-up plasma sample collected 2 years after final evaluation of primary treatment and 25 weeks before clinical manifestation of relapse.ConclusionIn summary, we demonstrate that multi-targeted cfDNA analysis, using a combination of SNVs/indels and SVs candidates identified by WGS analysis, provides a sensitive tool for MRD monitoring and can detect lymphoma relapse earlier than clinical manifestation.

【 授权许可】

Unknown   
Copyright © 2023 Haider, Wästerlid, Spångberg, Rabbani, Jylhä, Thorvaldsdottir, Skaftason, Awier, Krstic, Gellerbring, Lyander, Hägglund, Jeggari, Rassidakis, Sonnevi, Sander, Rosenquist, Tham and Smedby