Comparison of Sequence Specific Primers in the Next Generation Sequencing in Human Leukocyte Antigen Typing for Transplant Recipients

Abstract

Objective: To compare two human leukocyte antigen (HLA) typing methods, namely sequence specific primers (SSP) and next generation sequencing (NGS) for alleles concordance Study Design: Descriptive study. Place and Duration of Study: Immunology department, Armed Forces Institute of Pathology, Rawalpindi, Pakistan, from December 2019 to May 2020. Methodology: A total of 48 subjects, including 30 males and 18 females, were typed by NGS at 7 loci, making a total of 672 types loci. SSP typing was done for 276 loci among these. Comparison was made at SSP level of low resolution. NGS typing was done with Illumina’s MiSeq instrument using Omixon HLA holotype 7 loci kit and analysis done with HLA twin software. SSP typing was done with micro SSP kit from onelambda. Statistical analysis was done using statistical package for social sciences (SPSS) version 24.0. Results: Among the 672 NGS types loci and 276 SSP types loci, there were mismatches at one B locus and one C locus, whereby NGS computed HLA-B*58:01 and HLA-C*12:02 while SSP detected HLA-B*57 and HLA-C*05, respectively. At remaining 274 loci, HLA typing fully matched at low resolution, making concordance rate 99.3%. Commonest alleles detected by NGS were HLA-A*02:01, B*51:01, C*07:02, DPB1*04:01, DQA1*01:03, DQB1*02:01 and DRB1*13:01. Conclusion: Batch testing, high throughput, improved accuracy, more loci coverage, maximum gene coverage including all exons and introns and high-resolution typing confer significant advantages to next generation sequencing over old methods of HLA typing. This technique is suitable for high throughput laboratories. High running cost hampers its routine implementation in 3rd world countries.