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Abstract: Data from HLA typing studies have made significant contributions to genetic theories about the Austronesian diaspora and the health of descendant populations. To help further unravel pattern and process elements, we have typed HLA and MICA loci at high resolution in DNA samples from well defined groups of Maori and Polynesian individuals. Our results show a restricted set of HLA class I alleles compared with other well characterised populations. In contrast, the class II HLA-DRB1 locus seems to be diverse in Maori and Polynesians and both groups show high frequencies of HLA-DRB1 ∗ 04:03, -DRB1 ∗ 08:03, -DRB1 ∗ 09:01 and -DRB1 ∗ 12:01. Our survey also provides the first ever MICA datasets for Polynesians and reveal unusual distributions and associations with the HLA-B locus. Overall, our data provide further support for a hybrid origin for Maori and Polynesians. One novel feature of our study is the finding that the gene sequence of the HLA-B ∗ 40:10 allele in Polynesians is a recombinant of HLA-B ∗ 55:02 and -B ∗ 40:01. HLA-B ∗ 40:10 is in close association with HLA-C ∗ 04:03, an allele identified as a hybrid of HLA-C ∗ 04 and -C ∗ 02. In this respect, our data resemble those reports on Amerindian tribes where inter-allele recombination has been a common means of generating diversity. However, we emphasize that Amerindian gene content per se is only a very minor element of the overall Polynesian genepool. The wider significance of HLA and MICA allele frequencies across the Pacific for modern day health is also discussed in terms of the frequency relative to reference populations of disease known to be associated with specific HLA and MICA markers. Thus, Polynesians and Maori are largely unaffected by “European autoimmune diseases” such as ankylosing spondylitis, uveitis and coeliacs disease, yet there are several Maori- and Polynesian-specific autoimmune diseases where the HLA and MICA associations are still to be determined. [Copyright &y& Elsevier]

Highlights from the article: The New Zealand (NZ) population is made up of many ethnic groups, with 88 different ethnicities identified in the national census of 2013, this contributes to human leucocyte antigen (HLA) diversity in New Zealand. HLA alleles of 2832 unrelated individuals typed by next generation sequencing (NGS) were analysed to examine HLA polymorphism in the modern New Zealand population. Twelve alleles not listed as C/WD in 2013 were found to be common (allele frequency >0.001), (DRB3*02:24, DRB3*03:01:03, DQA1*01:04:02, DQB1*05:01:24, DQB1*06:01:05, DPA1*02:01:02, DPA1*02:02:02, DPA1*02:06, DPA1*02:07, DPA1*02:01:04, DPB1*135:01, DPB1*296:01); and 14 alleles were found to be common while only listed as well documented in 2013 (A*02:12, B*15:06, B*40:10:01, B*56:02:01, C*03:02:02, C*04:82, C*07:01:02, C*15:05:02, DRB1*14:08, DRB4*01:03:02, DQA1*01:02:02, DQA1*05:09, DQA1*06:01:01, DPB1*104:01).