Performance of a multiplexed ampliconbased next-generation sequencing assay for HLA typing

Chang Liu, Brian F. Duffy, Eric T. Weimer, Maureen C. Montgomery, Jo Ellen Jennemann, Rachel Hill, Donna Phelan, Lindsay Lay, Bijal A. Parikh

Research output: Contribution to journalArticle

Abstract

Background Next-generation sequencing (NGS) has enabled efficient high-resolution typing of human leukocyte antigen (HLA) genes with minimal ambiguity. Most commercially available assays amplify individual or subgroup of HLA genes by long-range PCR followed by library preparation and sequencing. The AllType assay simplifies the workflow by amplifying 11 transplantrelevant HLA genes in one PCR reaction. Here, we report the performance of this unique workflow evaluated using 218 genetically diverse samples. Methods Five whole genes (HLA-A/B/C/DQA1/DPA1) and six near-whole genes (HLA-DRB1/ DRB345/DQB1/DPB1; excluding exon 1 and part of intron 1) were amplified in a multiplexed, long-range PCR. Manual library preparation was performed per manufacturer's protocol, followed by template preparation and chip loading on the Ion Chef, and sequencing on the Ion S5 sequencer. Pre-specified rules for quality control and repeat testing were followed; technologists were blinded to the reference results. The concordance between AllType and reference results was determined at 2-field resolution. We also describe the ranges of input DNA and library concentrations, read number per sample and per locus, and key health metrics in relation to typing results. Results The concordance rates were 98.6%, 99.8% and 99.9% at the sample (n = 218), genotype (n = 1688), and allele (n = 3376) levels, respectively. Three genotypes were discordant, all of which shared the same G group typing results with the reference. Most ambiguous genotypes (116 out of 144, 80.6%) were due to the lack of exon 1 and intron 1 coverage for HLADRB1/ DRB345/DQB1/DPB1 genes. A broad range of input DNA concentrations and library concentrations were tolerated. Per sample read numbers were adequate for accurate genotyping. Per locus read numbers showed some inter-lot variations, and a trend toward improved inter-locus balance was observed with later lots of reagents. Conclusion The AllType assay on the Ion Chef/Ion S5 platform offers a robust and efficient workflow for clinical HLA typing at the 2-field resolution. The multiplex PCR strategy simplifies the laboratory procedure without compromising the typing accuracy.

Original languageEnglish
Article numbere0232050
JournalPloS one
Volume15
Issue number4
DOIs
StatePublished - Apr 2020
Externally publishedYes

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    Liu, C., Duffy, B. F., Weimer, E. T., Montgomery, M. C., Jennemann, J. E., Hill, R., Phelan, D., Lay, L., & Parikh, B. A. (2020). Performance of a multiplexed ampliconbased next-generation sequencing assay for HLA typing. PloS one, 15(4), [e0232050]. https://doi.org/10.1371/journal.pone.0232050