Challenges in Determining Genotypes for Pharmacogenetics in Allogeneic Hematopoietic Cell Transplant Recipients

J Mol Diagn. 2016 Sep;18(5):638-642. doi: 10.1016/j.jmoldx.2016.03.007. Epub 2016 Jun 29.


As part of a pharmacogenetic study, paired blood and oral fluid samples were tested for the IL28B polymorphism (rs12979860) before and after hematopoietic cell transplantation (HCT) to evaluate changes in the genotype and investigate the utility of genotyping in oral fluid in HCT recipients. In 54 patients with leukemia >18 years of age, samples were collected approximately 7 days before HCT and 60 days after HCT. IL28B polymorphism testing was performed using real-time PCR with allele-specific probes. Twenty-four patients had the same genotype as their donors. In 30 patients, the genotype was different from that of the donor. In the oral fluid samples, 4 retained the recipient's genotype, and 18 had a genotype that matched that of the donor. In the remaining 8 patients, the results could not be characterized and appeared to be a combination of both, suggesting mixed proportions of donor and recipient cells. The assumption was that the sloughed epithelial cells of the mouth are of recipient origin. However, oral fluid is a mixture that contains varying numbers of cells of the recipient and immunomodulatory cells from the donor. Therefore, the use of oral fluid after HCT for clinical pharmacogenetics purposes needs further investigation.

MeSH terms

  • Adult
  • Aged
  • Alleles
  • Female
  • Genetic Testing
  • Genetic Variation
  • Genotype*
  • Hematopoietic Stem Cell Transplantation* / methods
  • Humans
  • Interferons
  • Interleukins / genetics
  • Male
  • Middle Aged
  • Neoplasms / diagnosis
  • Neoplasms / genetics
  • Neoplasms / therapy
  • Pharmacogenetics*
  • Tissue Donors
  • Transplant Recipients*
  • Transplantation Conditioning / methods
  • Transplantation, Homologous
  • Young Adult


  • IFNL3 protein, human
  • Interleukins
  • Interferons