Comparison of single nucleotide polymorphisms and short tandem repeats as markers for differentiating between donors...

To analyze transplant rejection and to distinguish between donor and recipient, it is necessary to select a marker from single nucleotide polymorphism (SNP), short tandem repeat (STR), and human leukocyte antigen (HLA) testing. SNPs are bi-allelic and the polymerase chain reaction method used for SNP testing has the advantage of lower cost than sequencing methods. In this study, we aimed to distinguish donors from recipients using a combination of existing commercialized STRs and the SNPs identified.

All selected SNPs complied with the following criterion known and validated minor allele frequency (MAF) ≥43% in Korean and reported ethnicities from global populations (HapMap, 1000 Genomes, and the Korean Reference Genome project). The STR assays were performed for 16 tetranucleotide repeat loci.

DNA from the 52 donor/recipient pairs were tested for informative markers. The median age of the recipients was 47 years. MAF in the 52 pairs was 1.0%-76.0%. The probability of informative genotypes (I) was 0.001-0.124. The summation of I was 0.680. In the 52 donor recipient pairs, the selected SNPs showed a 0.031 average probability of being informative. The probability of identity in our study was 0.122-0.348. SNP panel configuration distinguished 100% of 52 donors/recipient pairs.

Donors and recipients were distinguished by STR and 22 SNPs with MAF identified from SNP databases. Seventeen SNPs were able to distinguish between donors and recipients (I value=0.039).