Ultra-low coverage whole genome sequencing of ccfDNA in multiple myeloma: A tool for laboratory routine?

• Published in: Cancer treatment and research communications 2021, Vol.28, p.100380-100380, Article 100380
• Main Authors: Rengifo, Laura Yissel, Smits, Sanne, Buedts, Lieselot, Delforge, Michel, Dehaspe, Luc, Tousseyn, Thomas, Boeckx, Nancy, Lehnert, Stefan, Michaux, Lucienne, Vermeesch, Joris Robert, Vandenberghe, Peter, Dewaele, Barbara
• Format: Article
• Language: English
• Subjects: Bone Marrow; Cell-Free Nucleic Acids; Chromothripsis; DNA Copy Number Variations; Humans; In Situ Hybridization, Fluorescence; Molecular cytogenetics; Multiple myeloma; Multiple Myeloma - genetics; Plasma Cells; Tumor fraction; Ultra‐low coverage sequencing; Whole Genome Sequencing
• ISSN: 2468-2942; 2468-2942
• DOI: 10.1016/j.ctarc.2021.100380

•For patients with Multiple Myeloma cytogenetic profiling with FISH on plasma cells from bone marrow samples (BM-PCs) is the current gold standard, but variable infiltration of plasma cells or failed aspiration can hamper this process.•We identified CNAs in circulating ccfDNA of 18 patients and comparison with paired samples from BM-PCs provided reliable information from the genome and CNA genetic markers of high risk disease.•Our study suggests the feasibility of using ULCS in ccfDNA to reveal CNAs in MM in a routine setting specially in cases where BM analysis is inconvenient. Multiple myeloma (MM), is a heterogeneous disease in which chromosomal abnormalities are important for prognostic risk stratification. Cytogenetic profiling with FISH on plasma cells from bone marrow samples (BM-PCs) is the current gold standard, but variable infiltration of plasma cells or failed aspiration can hamper this process. Ultra-low coverage sequencing (ULCS) of circulating cell-free DNA (ccfDNA) may offer a minimally invasive alternative for the work-up of these cases. We compared ULCS, aCGH and FISH on selected BM-PCs in a routine setting with ULCS of ccfDNA for the detection of somatic copy number aberrations (CNAs) in MM. Purified CD138+ BM-PCs of 23 MM patients at initiation of their treatment were subjected to aCGH, FISH and ULCS. Paired samples of peripheral blood-ccfDNA obtained at diagnosis were analyzed by ULCS and compared to the results found in BM-PCs. Using ULCS of ccfDNA, cytogenetic markers were identified in 18 out of 23 patients; five cases could not be analyzed due to low (≤3%) tumor fraction (TF). High similarity between CNA profiles of BM-PCs and ccfDNA was found. Moreover, 78% of the ccfDNA profiles resulted in the same risk classification as the routine FISH and/or BM-PCs ULCS and aCGH. Chromothripsis was detected in five patients; these had the highest TF values (range 7.1% to 42%) in our series and their profiles showed other high-risk anomalies. This proof-of-principle study indicates that ULCS of ccfDNA can reveal CNAs in MM and should be explored further as a cost-efficient alternative, especially in cases where BM-PC purification fails.