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Related Experiment Video

Updated: Jan 5, 2026

Author Spotlight: A Computational Pipeline for Analyzing Chimeric Noncoding RNA-Target RNA Interactions in High-Throughput Sequencing Data
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Rchimerism: An R Package for Automated Chimerism Data Analysis.

Zohair Siddiqui1, Juan Maldonado1, Jeremy Grojean2

  • 1Department of Computer Science, Saint Louis University, St. Louis, Missouri.

The Journal of Molecular Diagnostics : JMD
|October 13, 2019
PubMed
Summary

A new R package, Rchimerism, automates chimerism testing for hematopoietic stem cell transplantation patients. This free software significantly reduces analysis time and human error, ensuring accurate monitoring of donor cell engraftment or disease relapse.

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Area of Science:

  • Hematology
  • Bioinformatics
  • Molecular Biology

Background:

  • Quantitative chimerism testing is crucial for monitoring hematopoietic stem cell transplantation (HSCT) outcomes, including donor cell engraftment and disease relapse.
  • Current methods rely on PCR amplification of short tandem repeat loci and capillary electrophoresis, followed by manual data analysis.
  • Manual analysis is time-consuming, prone to errors, and lacks automated solutions for selecting informative loci and calculating chimerism percentages.

Purpose of the Study:

  • To develop and validate a free, user-friendly software package for automated chimerism data analysis.
  • To significantly reduce the time and potential for human error associated with manual chimerism testing.
  • To provide a reliable tool for noncommercial laboratories involved in HSCT patient monitoring.

Main Methods:

  • Development of Rchimerism, an R shiny package designed for automated chimerism analysis.
  • Implementation of algorithms for automatic selection of informative short tandem repeat loci.
  • Calculation of chimerism percentages and presentation of results via an intuitive graphical user interface.

Main Results:

  • Rchimerism demonstrated 100% concordance with manual calculations across 60 patient samples.
  • The software drastically reduced analysis time from 20-80 minutes (manual) to over 1 minute.
  • Automated selection of informative loci and calculation of chimerism percentages were successfully achieved.

Conclusions:

  • Rchimerism offers a fully automated, accurate, and efficient solution for chimerism testing in HSCT.
  • The free availability of Rchimerism makes advanced chimerism analysis accessible to noncommercial research and clinical laboratories.
  • This tool has the potential to improve patient care by enabling faster and more reliable monitoring of transplantation success.