The diagnosis of clonality by molecular techniques generally depends on the detection of unique molecular events such as specific gene rearrangements in a small percentage of malignant cells in the total cell population [1, 2]. Gene rearrangement analyses by PCR for immunoglobulin, T-cell receptor, and bcl-2 genes are valuable diagnostic tools now offered by many molecular pathology laboratories to aid in the diagnosis of leukemia and lymphoma [3, 4]. The need to assess the overall performance and quality of the assay requires the control samples be analyzed in parallel with the patient samples [5, 6]. The most commonly used control samples are previously tested and validated patient specimens. However, such material is limited, and new control samples often need to be characterized when old ones are used up. Therefore, a readily available and renewable source of cells would greatly facilitate the use of controls and standardization of the assays. We have previously characterized 15 leukemia and lymphoma cell lines with the aim to use them as controls in molecular gene rearrangement assays [7]. We have studied their gene rearrangement patterns by Southern blot analysis and PCR, using primers distributed by InVivoScribe Technologies (IVS) that are based on the work by Miller et al.[5]. Since 2003, when the new and standardized BIOMED-2 primers were developed [8, 9], a number of studies have been carried out to validate these primers for the detection of immunoglobulin and T-cell receptor gene rearrangements [10–15]. To date, however, a comprehensive comparison of the original IVS primers with the BIOMED-2 primers has not been reported. In the present study, therefore, we compared the BIOMED-2 primers with the original IVS primers, using 13 of the same 15 cell lines previously characterized. In addition, we also compared those two primer sets for a limited number of clinical samples.

Six B-and seven T-cell lines were cultured as recommended by the ATCC. DNA was isolated using the Puregene DNA Kit. Anonymized DNAs from 50 clinical patient specimens were obtained from a reference laboratory. The original IVS and BIOMED-2 primer kits, both of which are commercially distributed by IVS, were used as recommended in the instructions for the respective kits. Each kit contains 1–5 separate primer mixes. All samples were analyzed with the complete set of primer mixes provided in each kit, with the exception of BIOMED-2 for IgH, where primer mixes D and E were not used. Electrophoresis of the heteroduplex-treated PCR products was performed in a 10% polyacrylamide gel.