Skip to main content
SpringerLink
Log in

Human Leukocyte Antigen (HLA) Region in Human Population Studies

  • Chapter
  • First Online:
Evolution of the Human Genome I

Part of the book series: Evolutionary Studies ((EVOLUS))

Abstract

Human leukocyte antigen (HLA) genes function to present processed antigenic peptides to immune cells, hence their major importance in eliciting immune responses. HLA genes have been extensively studied for their disease associations and pre-/posttransplantation applications. Due to their highly polymorphic nature, HLA genes are also used for population genetic studies. This chapter summarizes the structure, functions, nomenclature, genotyping methods, and population genetic applications of the HLA system.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Institutional subscriptions

References

  • Alfonso C, Karlsson L (2000) Nonclassical MHC class II molecules. Annu Rev Immunol 18:113–142

    Article  CAS  PubMed  Google Scholar 

  • Ando H, Mizuki N, Ando R, Miyata Y, Miyata S, Wakisaka K, Inoko H (1996) HLA-C genotyping in the Japanese population using the PCR-SSP method. Tissue Antigens 48:55–58

    Article  CAS  PubMed  Google Scholar 

  • Bentley G, Higuchi R, Hoglund B, Goodridge D, Sayer D, Trachtenberg EA, Erlich HA (2009) Highresolution, high-throughput HLA genotyping by next-generation sequencing. Tissue Antigens. 74:393–403

    Google Scholar 

  • Browning SR, Browning BL (2007) Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet 81:1084–1097

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • EMBL-EBI (2017) IMGT/HLA statistics. Retrieved from http://www.ebi.ac.uk/ipd/imgt/hla/stats.html

  • Felsenstein J (1981) Maximum likelihood estimation of evolutionary trees from continuous characters. Am J Hum Genet 25:471–492

    Google Scholar 

  • Hanihara K (1991) Dual structure model for the population history of the Japanese. Jpn Rev 2:1–33

    Google Scholar 

  • Hill AV, Allsopp CE, Kwiatkowski D, Anstey NM, Twumasi P, Rowe PA, Bennett S, Brewster D, McMichael AJ, Greenwood BM (1991) Common west African HLA antigens are associated with protection from severe malaria. Nature 352:595–600

    Article  CAS  PubMed  Google Scholar 

  • Hosomichi K, Jinam TA, Mitsunaga S, Nakaoka H, Inoue I (2013) Phase-defined complete sequencing of the HLA genes by next-generation sequencing. BMC Genomics 14:355

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kulski JK, Shiina T, Anzai T, Kohara S, Inoko H (2002) Comparative genomic analysis of the MHC: the evolution of class I duplication blocks, diversity and complexity from shark to man. Immunol Rev 190:95–122

    Article  CAS  PubMed  Google Scholar 

  • Levine JE, Yang SY (1994) SSOP typing of the tenth international histocompatibility workshop reference cell lines for HLA-C alleles. Tissue Antigens 44:174–183

    Article  CAS  PubMed  Google Scholar 

  • Mack SJ, Bugawan TL, Moonsamy PV, Erlich JA, Trachtenberg EA, Paik YK, Begovich AB, Saha N, Beck HP, Stoneking M, Erlich HA (2000) Evolution of Pacific/Asian populations inferred from HLA class II allele frequency distributions. Tissue Antigens 55:383–400

    Article  CAS  PubMed  Google Scholar 

  • Meyer D, Single RM, Mack SJ, Erlich HA, Thomson G (2006) Signatures of demographic history and natural selection in the human major histocompatibility complex loci. Genetics 173:2121–2142

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Milner CM, Campbell RD (2001) Genetic organization of the human MHC class III region. Front Biosci 6:D914–D926

    Article  CAS  PubMed  Google Scholar 

  • Nakaoka H, Mitsunaga S, Hosomichi K, Shyh-yuh L, Sawamoto T, Fujiwara T, Tsutsui N, Suematsu K, Shinagawa A, Inoko H, Inoue I (2013) Detection of ancestry informative HLA alleles confirms the admixed origins of Japanese population. PLoS One 8:e60793

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nei M (1972) Genetic distance between populations. Am Nat 106:283–291

    Article  Google Scholar 

  • Nei M, Tajima F, Tateno Y (1983) Accuracy of estimated phylogenetic trees from molecular data. II. Gene frequency data. J Mol Evol 19:153–170

    Article  CAS  PubMed  Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  • Sanchez-Mazas A (2007) An apportionment of human HLA diversity. Tissue Antigens. 1:198–202

    Google Scholar 

  • Scheet P, Stephens M (2006) A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet 78:629–644

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shiina T, Hosomichi K, Inoko H, Kulski JK (2009) The HLA genomic loci map: expression, interaction, diversity and disease. J Hum Genet 54:15–39

    Article  CAS  PubMed  Google Scholar 

  • Stephens HA (2001) MICA and MICB genes: can the enigma of their polymorphism be resolved? Trends Immunol 22:378–385

    Article  CAS  PubMed  Google Scholar 

  • Terasaki PI, McClelland JD (1964) Microdroplet assay of human serum cytotoxins. Nature 204:998–1000

    Article  CAS  PubMed  Google Scholar 

  • Wang C, Krishnakumar S, Wilhelmy J, Babrzadeh F, Stepanyan L, Su LF, Levinson D, Fernandez-Vina MA, Davis RW, Davis MM, Mindrinos M (2012) High-throughput, high-fidelity HLA genotyping with deep sequencing. Proc Natl Acad Sci USA 109:8676–8681

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Williams TM (2001) Human leukocyte antigen gene polymorphism and the histocompatibility laboratory. J Mol Diagn 3:98–104

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wright S (1949) The genetical structure of populations. Ann Eugenics 15:323–354

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Division of Population Genetics, National Institute of Genetics, Mishima, Japan

    Timothy A. Jinam

Authors
  1. Timothy A. Jinam
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Timothy A. Jinam .

Editor information

Editors and Affiliations

  1. Division of Population Genetics, National Institute of Genetics, Mishima, Japan

    Naruya Saitou

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Japan KK

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Jinam, T.A. (2017). Human Leukocyte Antigen (HLA) Region in Human Population Studies. In: Saitou, N. (eds) Evolution of the Human Genome I. Evolutionary Studies. Springer, Tokyo. https://doi.org/10.1007/978-4-431-56603-8_9

Download citation

Publish with us

Policies and ethics

Search

Navigation