title: Evaluation of 16 SNPs allele-specific to quantify post hSCT chimerism by SYBR green-based qRT-PCR.
abstract: 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.
authors.affiliation: Department of Clinical and Experimental Oncology, Universidade Federal de São Paulo (UNIFESP), São Paulo/SP, Brazil. c_arthur_almeida@msn.com
authors.forename: Carlos Arthur Cardoso
authors.initials: CA
authors.lastname: Almeida
authors.forename: Juliana Luporini
authors.initials: JL
authors.lastname: Dreyfuss
authors.forename: Marily Maria
authors.initials: MM
authors.lastname: Azevedo-Shimmoto
authors.forename: Maria Stela
authors.initials: MS
authors.lastname: Figueiredo
authors.forename: José Salvador Rodrigues
authors.initials: JS
authors.lastname: de Oliveira
mesh_terms: D000328:Adult; D052160:Benzothiazoles; D004247:DNA / Q000737:chemistry; D003959:Diamines; D005260:Female; D005456:Fluorescent Dyes; D005819:Genetic Markers / Q000235:genetics*; D005838:Genotype; D006410:Hematopoiesis / Q000235:genetics; D018380:Hematopoietic Stem Cell Transplantation; D006801:Humans; D019520:Living Donors; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D009930:Organic Chemicals / Q000737:chemistry; D020641:Polymorphism, Single Nucleotide; D011804:Quinolines; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods*; D018183:Transplantation Chimera / Q000235:genetics*; D014184:Transplantation, Homologous; D061349:Unrelated Donors
chemical_list: D052160:Benzothiazoles; D003959:Diamines; D005456:Fluorescent Dyes; D005819:Genetic Markers; D009930:Organic Chemicals; D011804:Quinolines; C098022:SYBR Green I; D004247:DNA