A Multiplex PCR for Detection of Genetic Aberrations in Non-Hodkin’s Lymphoma.
Authors: Nyvold Charlotte Guldborg , Bendix Knud , Hamilton-Dutoit Stephen J. , Melsvik Dorte , Tønder Hanne , Hokland Peter 
Published: April 2020

Abstract
Aim: To develop a multiplex PCR method applicable in a clinical setting for the simultaneous detection of the chromosomal lesions t(11;14)(q13q32), t(14;18)(q32;q21), t(2;5)(p23;q35), t(11;18)(q21;q21), t(3q27;var), and t(8;14)(q24;q32) frequently found in non-Hodgkin lymphoma (NHL).
Methods: DNA and RNA were prepared from 50μm lymph node (LN) sections by homogenization on a FastPrep instrument (Qbiogene, Cedex, France) followed by automated nucleic acid purification on a MagNa-Pure LC robot (Roche Diagnostics, Basel, Switzerland). The multiplex PCR was condensed in four PCR tubes. The first covered the MTC and mTCp94 region of BCL1/IGH fusion DNA, the MBR and MCR breakpoint regions of BCL2/IGH fusion DNA together with the control gene TCF20. The second included the API2/MLT and ALK/NPM breakpoints on cDNA along with β-ACTIN as a control gene. The third contained primers amplifying eight different fusions partners of BCL6 (IGH (14q32), IGL (22q11), HSP89α (14q32), HSP90β (6p12), PIM1 (6p21), TFR (3q26), TTF (4p13), and H4 (6p21)) on cDNA together with β-ACTIN as the control gene. The fourth tube harbored a long range PCR with primers detecting the CMYC/IGH breakpoints on genomic DNA (Cμ, Cγ, Cα, and joining region of the IGH (Basso et al., 1999, Am J Pathology)) together with ABL as a control gene.
Patient samples and cell lines: One-hundred-and-twelve LN biopsies frozen in Tissue-Tek OCT Compound (Sakura, Vaerloese, Denmark) were randomly selected from consecutive patients referred with suspected hematological malignancy. The following cell lines were used as positive controls: B-CLL line JVM-2 (t(11;14)+), NHL lines DOHH-2 (t(14;18)+, t(8;14)+) and WSU-NHL (t(14;18)+), Burkitt’s lymphoma lines BL-41, BL-70 (t(8;14)+), and MD901 (t(3;22)+), T-NHL line Karpas 299 (t(2;5)+), and ALL line MD903 (t(3;14)+). Results: In pilot experiments employing cell lines and fresh LN material, this optimized multiplex PCR reaction proved to be simple and fast with a short turnover time, considering the large number of genetic aberrations detected. In a retrospective LN material encompassing 112 blinded samples, BCL1/IGH fusion DNA with breakpoint in the MTC region was detected once while BCL2/IGH was found in 20 samples (19 in MBR and one in MCR). BCL6/IGH fusion cDNA was found in three samples while the TTF gene was utilized twice as translocation partner to BCL6. Finally, CMYC/IGH fusion DNA was detected three times (1 IGHCα, 2 IGHCγ). All PCR products apart from CMYC/IGH were sequenced and verified the specific chromosomal lesions. Nineteen were excluded due to weak control bands in the first three PCR tubes, while 38 were excluded in the long range PCR detecting CMYC/IGH.
Conclusion: We conclude that the NHL multiplex PCR described is an easy and timesaving method for identifying heterogeneous molecular disease markers in NHL. The standardized DNA- and RNA preparation together with the condensation into four PCR tubes, moreover, makes it convenient to the clinical setting. Application of this assay and identification of positive cases has the added advantage that quantitative real-time PCR monitoring residual disease can be applied.