Droplet digital PCR based analysis of chimerism using a panel of Indel markers

Abstract

Cell identity, a fundamental concept in biology, emerges from the interplay of gene expressions, cellular functions, and genomic fingerprints. Chimerism refers to the presence of two genetically distinct types of cells within an individual. Monitoring of chimerism is an important tool to evaluate the evolution of engraftment after transplant and to detect the relapse of the underlying hematological neoplasm or the occurrence of graft rejection. Also, continuous monitoring is an essential tool that can provide guidance for early therapeutic intervention. Digital droplet PCR (ddPCR) is a promising alternative to the standard quantitative PCR to assess the chimerism below 1% due to an excellent performance in the assessment of small amounts of specific targets in a complex biological sample. Here, we describe the development of a panel of ddPCR based assays for chimeric analysis. We found a group of 25 indels showing a good discrimination power when tested with artificial mixtures of DNA samples.