Abstract
Aim The aim of this study was to complete full gene sequences for previously reported HLA class I sequences for the IPD-IMGT/HLA database. Methods We identified 569 class I alleles in ∼ 99,000 individuals typed for a U.S. donor registry that had incomplete sequences in the IPD-IMGTHLA database. The alleles had been typed by a combined Sanger SBT-SSOP workflow focused on exons 2 + 3. Single locus alleles were amplified with primers annealing in the 5’ and 3’ UTR and the sequences of exons and introns determined with an Illumina Miseq using an in-house protocol. Results Most (423, 74%) of the 569 alleles were found in a single cell. The majority of the class I full length sequences were identical to the most similar HLA allele (e.g., C*01:70 differed by only a single exon 2 nucleotide when compared to C*01:02:01:01). Two novel HLA-A alleles with exon 2/3 variation were not detected by SBT/SSO due to inability to phase key polymorphic nucleotides [A*03:150, *26:01:01G vs. A*03:01:01:01 + A*26:149 (new); A*02:01:55 + *33:03:01G vs. A*02:01:01:01 + *33:03:33 (new)]. Overall, new alleles were found in 18 (3.2%) samples; most in the targeted incomplete allele. Most (14, 78%) showed variation in intron and UTR regions. Some of the incomplete alleles (49/569) could not be characterized because the allele combination did not allow phasing of the sequences (e.g., C*07:01:01:01 + *07:27:01 had no polymorphic nucleotides within a span of 2298 bp (introns 2–7)). Conclusions Class I gene sequences outside exons 2 + 3 are conserved. Genotypes with novel alleles can be missed by typing assays that do not provide comprehensive phasing. Increasing the knowledge of full sequences for all alleles will improve the accuracy of HLA typing. Download : Download high-res image (153KB) Download : Download full-size image J.S. Ng: 4. Scientific/Medical Advisor; Company/Organization; Georgetown University. C.K. Hurley: 4. Scientific/Medical Advisor; Company/Organization; Georgetown University.
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