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Single molecule real-time DNA sequencing of the full HLA-E gene for 212 reference cell lines

Jonathan A M Lucas¹, James D Hayhurst¹, Thomas R Turner^1,2

¹Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom.

|April 1, 2020

Abstract:

We have developed a genotyping assay that produces fully phased, unambiguous HLA-E genotyping using Pacific Biosciences' single molecule real-time DNA sequencing. In total 212 cell lines were genotyped, including the panel of 107 established at the 10th International Histocompatibility Workshop. Our results matched the previously known HLA-E genotype in 94 (44.3%) cell lines, in all cases either improving or equalling previous genotyping resolution. Three (1.4%) cells had discrepant HLA-E genotyping data and 115 (54.2%) had no previous HLA-E data. The HLA-E genotypes for four (1.9%) cell lines resulted in a change of zygosity by identifying two distinct haplotypes. We discovered eight novel HLA-E alleles, extended the known reference sequence of seven and confirmed the existence of a further 10.

Keywords:

HLA HLA-E International HLA and Immunogenetics Workshop SMRT sequencing cell lines genetic polymorphism

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