Next generation sequencing characterizes the extent of HLA diversity in an Argentinian registry population

Abstract

Next generation DNA sequencing is used to determine the HLA-A, -B, -C, -DRB1, and -DQB1 assignments of 1472 unrelated volunteers for the unrelated donor registry in Argentina. The analysis characterized all HLA exons and introns for class I alleles; at least exons 2, 3 for HLA-DRB1; and exons 2 to 6 for HLA-DQB1. Of the distinct alleles present, there are 330 class I and 98 class II. The majority (~98%) of the cumulative allele frequency at each locus is contributed by alleles that appear at a frequency of at least 1 in 1000. Fourteen (18.2%) of the 77 novel class I and II alleles carry nonsynonymous variation within their exons; 52 (75.4%) class I novel alleles carry only single, apparently random, nucleotide variation within their introns/untranslated regions. Alleles encoding protein variation not usually detected by typing focused only on the exons encoding the antigen recognition domain are 1.0% of the class I assignments and 7.3% of the class II assignments (predominantly DQB1*02:02:01, DQB1*03:19:01, and DRB1*14:54:01). Updates to the common and well documented list of alleles include 10 alleles previously thought to be uncommon but that are found at least 30 times. Five locus haplotypes estimated using the expectation-maximization algorithm as present 3 or more times total 187. While the known HLA diversity continues to increase, the conservation of known allele sequences is remarkable. Overall, the HLA diversity observed in the Argentinian population reflects its European and Native American ancestry.

High‐resolution HLA allele and haplotype frequencies in majority and minority populations of Costa Rica and Nicaragua: Differential admixture proportions in neighboring countries

“…The absence of statistically significant LD among allele blocks forming some of these extended haplotypes despite involving well‐known, frequent haplotypes (e.g. A*02:01:01∼C*07:02:01∼B*07:02:01∼DRB1*15:01:01G ), previously reported to lack full LD in a sample of Argentinians) or well‐known, ethnic‐specific B~C linkages (eg, B*45:01 ~ C*16:01:01 common in populations of African descent) could be reflecting a lack of statistical power to allow for this detection due to the small sample sizes in our study, especially in cases involving LD between two high‐frequency alleles (eg, A*02:01:01~C*07:02:01 ). In several cases, homozygosity, as well as excluded family data for some individuals also confirm the existence of the estimated extended haplotypes in their diplotypes despite the lack of full LD across the allele pairs forming them.…”

Next generation sequencing characterizes HLA diversity in a registry population from the Netherlands

“…The increased utilization of DNA sequencing for typing registry populations has provided higher resolution HLA assignments, speeding donor selection. The application of next generation DNA sequencing to compile full length sequences of HLA genes has improved the ability to interpret sequencing results . Overall, the HLA‐related activities of the registries have provided an ever expanding view of HLA diversity .…”

“…Table S3 lists CWD alleles with names extended since the 2013 report and the number of occurrences of the alleles that share the truncated names in this dataset. Only alleles not listed in our previous report or that have a difference from that report in which allele is more frequent are included. The most frequent alleles are usually those extended with “01” (eg, A*02:05:01:01 appears 15 times while A*02:05:01:02 did not appear).…”

“…One difference from the distribution of alleles observed in an Argentinian registry is A*68:01:02:01 vs A*68:01:02:02 . Matchis has A*68:01:02:02 as more frequent (43 observations compared to 10) while the Argentinian registry has A*68:01:02:01 as more frequent (73 to 25) …”

“…The intron variation observed, like that observed in an Argentinian registry, appears to be primarily single nucleotide variation. Table S5 shows the variation in the alleles with the three field designation C*04:01:01 .…”