J Clin Pathol doi:10.1136/jclinpath-2012-201224
  • Original article

Evaluation of 16 SNPs allele-specific to quantify post hSCT chimerism by SYBR green-based qRT-PCR

  1. José Salvador Rodrigues de Oliveira1,3
  1. 1Department of Clinical and Experimental Oncology, Universidade Federal de São Paulo (UNIFESP), São Paulo/SP, Brazil
  2. 2School of Pharmaceutical Sciences. Universidade Federal de Alagoas (UFAL), Maceió/AL, Brazil
  3. 3BMT Unit. Santa Marcelina Hospital, São Paulo/SP, Brazil
  1. Correspondence to Professor Carlos Arthur Cardoso Almeida, Escola de Enfermagem e Farmácia, Universidade Federal de Alagoas, Campus AC Simões, Av. Lourival Melo Mota, s/n, Tabuleiro do Martins, Maceió, AL 57072-970, Brazil; c_arthur_almeida{at}
  • Received 20 September 2012
  • Revised 6 November 2012
  • Accepted 6 November 2012
  • Published Online First 2 January 2013


The importance of monitoring post haematopoietic stem cell transplantation (hSCT) chimerism has been defined in numerous publications. Single-nucleotide polymorphisms (SNPs) are molecular markers that vary significantly among different populations. Allied to a very sensible technique, SNP assays seem to be very sensitive (0.001%) when post hSCT chimerism is measured. However, well known SNP frequencies are limited to certain populations, mainly in countries where there is a high level of diversity in its population, therefore restricting their use worldwide. Amplification by SYBR green based quantitative real time PCR of eight pairs of allele-specific SNPs (MLH-1, PECAM-1, ICAM-1, SUR-1, HA-1, rs715405, rs713503, rs2296600) was conducted in 88 patient/donor pairs, who underwent allogeneic myeloablative or non-myeloablative hSCT. One informative allele was detected in at least 42% (n=37) of the samples; 20% (n=18) had at least two informative alleles; 10% (n=9) had at least three informative alleles; 9% (n=8) had more than three informative alleles and 18% (n=16) showed no informative allele at all. Overall, the frequency of informative alleles for these SNPs in the Brazilian population was very low. Consequently, the amount of information attained reached 9% of those expected, being able to discriminate only eight pairs of donor/recipient samples with more than three informative alleles, making them useless for the quantification of chimerism in our routine.

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