In an effort to overcome the sensitivity and analysis shortcomings of STR-based transplant monitoring methods, and to improve upon the current state of the art in qPCR-based chimerism analysis and laboratory workflow, we have created a new assay and software suite. Our chemistries were chosen to be compatible with all major qPCR platforms and our software can integrate with any of those machines.We utilize a panel of multiplexed qPCR research assays and software to comparatively genotype and quantify multiple samples on a single plate. The assays are designed and validated to detect INDEL variants between individuals. These differences are used to track individuals’ genomic material in chimeric mixtures. The software analyzes output from qPCR machines and presents unique marker choices in their genomic context, allowing for knowledgeable informative assay decision making and use in post-transplant monitoring. The software enables any number of combinations of samples to be genotyped, facilitating rapid multiple donor analyses. The results from the genotyping are stored by the software for recall during subsequent monitoring. Reports from a monitoring test may be generated from a single time point or using the longitudinal data collected from the individual over time - providing a temporal view for better understanding rejection or relapse kinetics. Our software allows for customized test set up, it performs all calculations necessary to execute the test, it generates a printable protocol to assist laboratory work and it generates sample set up files to import into qPCR machines. The software accepts standard qPCR data output for generating results.This assay system provides the highest probability of finding informative markers, as compared to other commercially-available qPCR systems. The tests and software are compatible with a variety of qPCR platforms. Our software solution reduces manual calculations, increases flexibility in experimental execution, generates complete protocols for use in the lab and stores and plots data.J. Adema: Employee; Company/Organization; GenDx. D. Roovers: Employee; Company/Organization; GenDx. N. Westerink: Employee; Company/Organization; GenDx. E. Rozemuller: Employee; Company/Organization; GenDx, KimerDx BV. Stock Shareholder; Company/Organization; GenDx, KimerDx BV. D. Bost: Employee; Company/Organization; KimerDx BV. Stock Shareholder; Company/Organization; KimerDx BV.