Table 1.
Comparison of chimerism/microchimerism laboratory detection techniques.
| Technique | Fragment Analysis# | qPCR | dPCR | NGS |
|---|---|---|---|---|
| Targeted Genetic Variant | limited number of multiallelic markers (STR) | limited number of biallelic markers (SNP, DIP) | limited number of biallelic markers (SNP, DIP) | unlimited number of biallelic markers (SNP) |
| Limit of Detection | >1% | 1–0.01% | 1–0.01% | 1–0.01% |
| TAT | short | shortest | short | longer |
| Equipment Cost | considerable | relatively lower | considerable | considerable |
| Allo-HSCT Marker number* | 3 | 2 | 2 | not relevant |
| Advantages | gold standard #; widespread application; large experience |
high sensitivity; short TAT |
high sensitivity; high precision |
high number. of SNPs; simultaneous chimerism & MRD |
| Technical Limitations | stutter peak; preferential amplification; semi-quantitative | labor-intensive optimization; calibration curve; PCR inhibitors; duplicate low no. of variants |
dependent on DNA concentration; low number of variants |
infrastructure costs; longer TAT; bioinformatics; lack of standardization |
# Fragment analysis has been used for the longest time albeit due to its low sensitivity it is not suitable for microchimerism detection. * Minimum number of markers for allo-HSCT follow-up. Abbreviations: dPCR: digital PCR; DIP: deletion insertion polymorphism; HSCT: hematopoietic stem cell transplantation; MRD: measurable residual disease; NGS: next generation sequencing; qPCR: real time quantitative PCR; SNP: single nucleotide polymorphism; STR: short tandem repeat; TAT: turnaround time.