DEBATE ROUND TABLE Interactive ChimerTrack software facilitates computation, visual displays and long-term tracking of chimeric status based on STRs

Chimerism testing has become an important service provided by the post-transplantation monitoring laboratory. This is because chimeric status serves as a useful indication of the cellular dynamics involved in engraftment, or relapse of a malignant recipient cell population, particularly following stem cell transplantation. Previous reports in this Debate Round-Table on chimerism testing reflect the current interest in quantitatively estimating chimeric status based on an analysis of microsatellite markers, or short tandem repeats (STRs). The principal advantage of this approach is its high sensitivity coupled with the potential quantitative character of the results. The latter affords a most useful capability to follow a patient’s chimeric status over time, that is, long-term trends. Despite sophisticated technological approaches for analyzing DNA, the final phase of the process – when % chimerism is calculated – usually relies on manual transcription of the sequencer results followed by manual computation. Moreover, although STR data are well suited for long-term profiling of chimeric status in a patient, a manual retrospective graphic analysis comparing the present to previous samples is not a feasible undertaking for every patient sample. Fortunately, such computational and data analytic tasks are typical of the capabilities of current computer technology. Platforms are available that can interactively facilitate computation while providing the capabilities for immediate data analysis within the current sample, and across different samples. For this reason it has been possible to develop an application within the Microsoft Excel platform, called ChimerTrack. The software operates in Excel and can be used in many of the laboratories whose papers have appeared in this Debate-Roundtable. The purpose of this communication is to describe the features and functionality options of the algorithm. At the outset it should be emphasized that the software was created in response to our particular laboratory’s needs. Most of our patients are HLA matched and receive allogeneic hematopoetic stem cell transplants. We do not routinely enrich or fractionate our cell samples prior to DNA extraction from peripheral blood. Chimeric status evaluation is based on 10 STR markers (plus amelogenin) amplified using a multiplex PCR kit, with fluorescence detection, optimized for forensic DNA analysis, viz, ABI AmpliflSTR SGMþ. PCR products are sequenced with an ABI 3100 Genetic Analyzer, and these data are analyzed with the ABI Genescan program, which produces an estimate of the quantity of DNA at the STR alleles. The ChimerTrack utility, which normally is used for Genescan data, runs on Excel 2000 and Excel 97 and will accommodate STR analysis results obtained from any software utilizing the Microsoft platform. Other laboratories have developed their own macros for import and computation of sequencer data, and a commercial product is also available by SystemLink as part of a larger laboratory management software package.