Genotyping of the ABCG2 gene using Matrix-Associated Laser Desorption/Ionisation, Time-of-Flight Mass Spectrometry

Abstract

Objectives: The aim of this study was to evaluate the applicability of genotyping of the ABCG2 gene using MALDI-TOF MS and to estimate the allele frequency in the Japanese population.

Background: Jr (a-) phenotype has a prevalence of approximately 0·05% among Japanese blood donors; DNA-based genotyping was conducted to investigate the molecular basis of the Jr (a-) phenotype along with serological typing. To detect all SNPs of the ABCG2 gene, a high-throughput SNP genotyping platform is needed.

Methods: Overall, 1004 Jr (a-) blood samples were collected from blood donors in Japan and pre-genotyped. To detect the SNPs of the ABCG2 gene using MALDI-TOF MS, polymerase chain reaction and unextend primer were designed. In total, 205 Jr (a-) samples were genotyped using MALDI-TOF MS analysis.

Results: The SNPs of 1004 Jr (a-) samples were identified using the HRM analysis and DNA sequencing, and 799 of 1004 (80%) Jr (a-) samples had the homozygous for c.376 T. The designed primers for MALDI-TOF MS perfectly detected the SNPs of the ABCG2 gene. A total of 205 Jr (a-) samples were genotyped using MALDI-TOF MS. Calling failures occurred in only two samples with the mutations c.736CT to c.376C and c.421C to c.421CA. The concordance rate between the pre-genotyped and MALDI-TOF MS-based genotyping results was very high (99·02%) for all ABCG2 alleles.

Conclusions: Jr (a-) Japanese donors had almost the homozygous for c.376 T. However, detections of more than 20 SNPs of the ABCG2 gene for the JR blood group genotyping are needed. MALDI-TOF MS-based genotyping was highly concordant with the pre-genotyped results for all ABCG2 alleles.

Keywords: ABCG2 gene; DNA-based genotyping; Jr (a−) phenotype; MALDI -TOF.