Comparative analysis of interphase FISH and RT-PCR to detect bcr-abl translocation in chronic myelogenous leukemia and related disorders.

The t(9;22)(q34;q1 1) between the abl and bcr genes plays a pivotal role in the diagnosis and pathogenesis of chronic myelogenous leukemia (CML). Its detection is routinely accomplished by Southern blot analysis and karyotyping. Interphase fluorescence in situ hybridization (FISH) and reverse transcriptase-polymerase chain reaction (RT-PCR) are emerging molecular techniques that offer viable alternatives. We analyzed 40 samples of peripheral blood and bone marrow (CML, 16; acute myelogenous leukemia, 6; acute lymphoblastic leukemia [ALL], 1; chronic lymphoblastic leukemia, 2; myelodysplasias, 4; myeloproliferative disorders, unclassified, 3; nonleukemic hematologic malignancies, 3; hypercellular bone marrow, 1; normal control samples, 2; and K562 cell line samples, 2) for the presence of bcr-abl fusion gene and its messenger RNA (mRNA) transcript by FISH and RT-PCR, respectively. We compared the results with results of Southern blot analysis and karyotyping when available. Cost analysis was performed. Thirty-three samples were evaluable by FISH; 14 of 14 evaluable CML samples and one ALL sample were positive for bcr-abl by FISH (100%). The other 15 evaluable samples were negative; 16 of 16 (100%) and 13 of 16 (81%) of CML cases were positive for bcr-abl mRNA by RT-PCR (chemiluminescent blot method) and RT-PCR (colorimetric method), respectively. The ALL sample was positive by both RT-PCR methods. All other samples were negative by RT-PCR (chemiluminescent blot method), and all but 1 case of myeloproliferative disorder tested negative by RT-PCR (colorimetric method). We conclude the utility of FISH and RT-PCR is associated with certain limitations, such as insufficient RNA for RT-PCR and the occasional absence of internal positive FISH control signals. However, each procedure offers (with a high concordance rate) a specific and cost-effective alternative to Southern blot analysis and karyotyping and improved turnaround time for the detection of bcr-abl fusion gene or its mRNA transcript.

The use of amplified variable number of tandem repeats (VNTR) in the detection of chimerism following bone marrow transplantation. A comparison with restriction fragment length polymorphism (RFLP) by Southern blotting.

Chimerism analysis after allogeneic bone marrow transplantation (alloBMT) allows detection of early marrow engraftment, disease relapse, and graft rejection. Our objective was to do retrospective and prospective studies of chimerism analysis by restriction fragment length polymorphism (RFLP) by Southern blotting and variable number of tandem repeats (VNTR) by polymerase chain reaction (PCR) to compare and contrast the methods. The retrospective group comprised 46 samples from 26 patients previously analyzed by RFLP, while the prospective group contained 34 samples from 25 patients. Using four different VNTR primers (D1S80, D17S30, D1S111, and APO-B), the recipient and donor samples amplified by the PCR were screened for unique banding patterns. The VNTR primer with the unique banding pattern was used to detect chimerism in each sample. A total of 635 VNTR analyses were performed. Interpretation was blinded for previous RFLP results. A comparison between the VNTR and RFLP results and a cost analysis of the two procedures were done. A unique VNTR banding pattern was present in 49 of 51 patients (identical twins in one case). The VNTR analysis showed complete chimerism in 68 samples, mixed chimerism in 9, and recurrences in 2. This agreed with the RFLP results in 64 (80%) of 80 samples. Failure to detect 1% to 10% of recipient DNA accounted for 15 (VNTR, 8; RFLP, 7) discordances. Follow-up revealed all donor DNA in five cases, decreasing quantities of recipient DNA in two cases (six samples), and no additional studies available in four cases. In one case, VNTR detected a complete chimerism when the DNA was insufficient for RFLP analysis. The cost analysis revealed an approximately 50% savings with the use of VNTR; VNTR is a viable alternative to RFLP in the detection of chimerism after bone marrow transplantation and offers substantial cost savings, faster turnaround time, easier preparation of the DNA, smaller DNA requirements, and the elimination of radioisotopes and cumbersome restriction enzymes.

Inexpensive handheld device for the construction of high-density nucleic acid arrays.

We report an easy-to-use, 384-pin handheld arraying and replicating device (ARD) for constructing high-density replicas of nucleic acids and E. coli transformants. We have modified an existing 384-pin tool to include a novel guide system to ensure vertical pin movement and enhance reproducibility. An asymmetric rectangular multiplexing frame is designed to increase the array density to 1536 dots on a standard microplate-size nylon membrane and to reduce the time and effort involved in producing array replicas. Our initial studies used the ARD to construct 1536-dot arrays of ovarian cDNA clones. We have hybridized these arrays with 32P-labeled probes, which resulted in distinctive signals for either visual interpretation or semiautomatic spot detection and signal integration.

The usefulness of a rapid PCR methodology to detect rearranged Ig heavy chain genes in lymphoproliferative disease in a diagnostic setting.

Polymerase chain reaction (PCR) was used to amplify the DNA fragments of the framework 3 region (FR3) of the immunoglobulin heavy (IgH) chain genes, from the tissue of 66 patients with B-lymphoproliferative diseases and 74 patients with other malignant diseases, reactive or normal tissue. The assay performed with 77% sensitivity, 100% specificity and 89% efficacy. In addition, the PCR assay cost less than 25% of the cost performing Southern blot analysis of tumor DNA, which has been the test performed to date, and had a turn around time of 24 hrs rather than the 7-14 days required to obtain a result from Southern blot analysis. These results suggest that PCR analysis of B-cell lymphoproliferative disease is superior to Southern blot analysis, in the setting of a diagnostic laboratory.