High-Throughput Copy Number Profiling by Digital Multiplex Ligation-Dependent Probe Amplification in Multiple Myeloma

Szabolcs Kosztolányi, Richárd Kiss, Lilit Atanesyan, Ambrus Gángó, Karel de Groot, Maryvonne Steenkamer, Pál Jáksó, András Matolcsy, Béla Kajtár, László Pajor, Károly Szuhai, Suvi Savola, Csaba Bödör, Donát Alpár

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Abstract

Multiple myeloma (MM) is a genetically heterogeneous disease with a diverse clinical outcome. Copy number alterations (CNAs), including whole chromosome and subchromosomal gains and losses, are common contributors of the pathogenesis and have demonstrated prognostic impact in MM. We tested the performance of digital multiplex ligation-dependent probe amplification (digitalMLPA), a novel technique combining MLPA and next-generation sequencing, to detect disease-related CNAs. Copy number status at 371 genomic loci was simultaneously analyzed in 56 diagnostic bone marrow samples, which were also examined by conventional MLPA and interphase fluorescence in situ hybridization (iFISH). On average, digitalMLPA identified 4.4 subchromosomal CNAs per patient. The increased number of probes compared with conventional MLPA allowed a detailed mapping of CNAs, especially on chromosome 1, where 24 different patterns were observed in 38 patients harboring loss(1p) and/or gain(1q). iFISH, MLPA, and digitalMLPA results at loci investigated by multiple methods showed a congruency of 95%. Besides precise characterization of hyperdiploid karyotypes not efficiently achievable by iFISH or MLPA, digitalMLPA unraveled 156 CNAs not detected by the other two methods in 45 patients (80%). In addition, we provide proof of principle that digitalMLPA can detect known point mutations, in this case the BRAFV600E. Our study demonstrates the robustness of digitalMLPA to profile CNAs and to screen point mutations in MM, which could efficiently be used in myeloma diagnostics.

Original languageEnglish
Pages (from-to)777-788
Number of pages12
JournalJournal of Molecular Diagnostics
Volume20
Issue number6
DOIs
Publication statusPublished - Nov 2018

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ASJC Scopus subject areas

  • Pathology and Forensic Medicine
  • Molecular Medicine

Cite this

Kosztolányi, S., Kiss, R., Atanesyan, L., Gángó, A., de Groot, K., Steenkamer, M., Jáksó, P., Matolcsy, A., Kajtár, B., Pajor, L., Szuhai, K., Savola, S., Bödör, C., & Alpár, D. (2018). High-Throughput Copy Number Profiling by Digital Multiplex Ligation-Dependent Probe Amplification in Multiple Myeloma. Journal of Molecular Diagnostics, 20(6), 777-788. https://doi.org/10.1016/j.jmoldx.2018.06.004