Interim results from a multicenter trial assessing the clinical relevance of copy number aberrations detected by a shallow whole-genome sequencing analysis (LeukoPrint) in multiple myeloma. Free

Multiple myeloma (MM) is a malignancy of clonal plasma cells, accounting for 10% of hematologic malignancies. Both primary (occurring early, including IgH translocation and hyperdiploidy) and secondary (acquired during disease progression, including del 17p/TP53, del 13q, amp 1q) cytogenetic abnormalities play a critical role in disease pathogenesis, prognosis, and therapeutic decisions. While conventional karyotyping is hindered by the low proliferative activity of plasma cells in MM, fluorescence in situ hybridization (FISH), as the gold standard for this purpose, provides only targeted detection being less cost-effective. LeukoPrint is a novel technology based on a shallow (1x) whole-genome sequencing (sWGS) to profile copy number aberrations (CNAs) in MM. Our previous works have demonstrated LeukoPrint's superior performance over FISH and karyotyping in cytogenetic characterization and risk stratification in MM and other malignancies, prompting a prospective multicenter clinical trial (ChiCTR2300077768) to assess the clinical relevance of LeukoPrint-detected CNAs in MM. The interim results of the first 102 participants were reported here.

In this multicenter clinical trial, we aim to enroll a total of 396 patients who were newly diagnosed as active multiple myeloma (aMM) according to the International Myeloma Working Group (IWMG 2014) criteria for the diagnosis of MM. By June 12, 2025, 102 patients have been enrolled from 7 participating hospitals in China. The study was approved by all institutional Ethics Committees, with informed consent obtained from all participants. For each patient, LeukoPrint was used to assess CNAs in paired bone marrow (gDNA from CD138-purified plasma cells) and peripheral blood (circulating cell-free DNA, cfDNA), collected at diagnosis, post-induction, and relapse phases. CNAs only those greater than 5 Mbp were analyzed. For most patients, Karyotyping and FISH were also performed in parallel, and their results were compared with LeukoPrint data. Risk stratification was performed following the Mayo Stratification of Myeloma and Risk-adapted Therapy (mSMART) criteria.

LeukoPrint detected CNAs in 91 out of 102 patients (89.2%), with a total of 868 CNAs identified. The most frequent alterations were 1q+ and -13, each present in 51% of the cohort. Odd numbered trisomies, including +9, +15, +19, and +5, represent another type of common CNAs, which are detected in 46.1% of the cohort and commonly cluster together in individual patients. Among patients with IGH translocations, subdiploidies were prevalent (54%), while hyperdiploidies were rare (13%), suggesting mutual exclusivity between these primary genetic events. In contrast, hyperdiploidies were detected in 40% of patients lacking IGH translocations. FISH (1q21+, 13q14-, and 17p13-) was examined in parallel with LeukoPrint in 94 cases, and the overall consistency was 88.0% (Kappa test: 0.73, strong consistency), while the sensitivity and specificity were 85.7% and 89.1%, respectively. Among 40% of patients who were FISH-negative, LeukoPrint detected CNAs in 80% of cases, showing its superior detection capacity over FISH. Although follow-up data are unavailable for this cohort, our prior findings demonstrated that LeukoPrint-detected additional CNAs, including trisomy, hyperdiploidy, and subdiploidy, redefined risk stratification according to mSMART criteria in 17.2% of patients. Moreover, LeukoPrint demonstrated significantly higher CNA detection rates than karyotyping (90.1% vs. 8.8%) in a direct comparison of 91 cases. This substantial disparity likely reflects the known limitation of karyotyping in MM due to the low proliferative activity of plasma cells. Finally, LeukoPrint was successfully performed on blood-derived ctDNA in all but one patient (excluded due to hemolysis). CNAs were detected in 89.1% of bone marrow samples compared to 61.4% of blood samples, demonstrating the clinical feasibility of ctDNA-based liquid biopsy.

LeukoPrint outperforms both FISH and karyotyping, representing a convenient, efficient, and cost-effective platform for comprehensive genome-wide CNA profiling in MM. Our data also demonstrates its clinical utility for liquid biopsy using ctDNA. Collectively, these findings position LeukoPrint as both a complementary tool and potential replacement for traditional cytogenetic approaches in MM diagnostics.