PMID- 28687858
OWN - NLM
STAT- MEDLINE
DCOM- 20180803
LR  - 20231112
IS  - 1432-1211 (Electronic)
IS  - 0093-7711 (Print)
IS  - 0093-7711 (Linking)
VI  - 70
IP  - 1
DP  - 2018 Jan
TI  - A genomic perspective on HLA evolution.
PG  - 5-27
LID - 10.1007/s00251-017-1017-3 [doi]
AB  - Several decades of research have convincingly shown that classical human 
      leukocyte antigen (HLA) loci bear signatures of natural selection. Despite this 
      conclusion, many questions remain regarding the type of selective regime acting 
      on these loci, the time frame at which selection acts, and the functional 
      connections between genetic variability and natural selection. In this review, we 
      argue that genomic datasets, in particular those generated by next-generation 
      sequencing (NGS) at the population scale, are transforming our understanding of 
      HLA evolution. We show that genomewide data can be used to perform robust and 
      powerful tests for selection, capable of identifying both positive and balancing 
      selection at HLA genes. Importantly, these tests have shown that natural 
      selection can be identified at both recent and ancient timescales. We discuss how 
      findings from genomewide association studies impact the evolutionary study of HLA 
      genes, and how genomic data can be used to survey adaptive change involving 
      interaction at multiple loci. We discuss the methodological developments which 
      are necessary to correctly interpret genomic analyses involving the HLA region. 
      These developments include adapting the NGS analysis framework so as to deal with 
      the highly polymorphic HLA data, as well as developing tools and theory to search 
      for signatures of selection, quantify differentiation, and measure admixture 
      within the HLA region. Finally, we show that high throughput analysis of 
      molecular phenotypes for HLA genes-namely transcription levels-is now a feasible 
      approach and can add another dimension to the study of genetic variation.
FAU - Meyer, Diogo
AU  - Meyer D
AD  - Department of Genetics and Evolutionary Biology, University of Sao Paulo, 
      05508-090, Sao Paulo, SP, Brazil. diogo@ib.usp.br.
FAU - C Aguiar, Vitor R
AU  - C Aguiar VR
AD  - Department of Genetics and Evolutionary Biology, University of Sao Paulo, 
      05508-090, Sao Paulo, SP, Brazil.
FAU - Bitarello, Barbara D
AU  - Bitarello BD
AD  - Department of Genetics and Evolutionary Biology, University of Sao Paulo, 
      05508-090, Sao Paulo, SP, Brazil.
AD  - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary 
      Anthropology, Leipzig, Germany.
FAU - C Brandt, Debora Y
AU  - C Brandt DY
AD  - Department of Genetics and Evolutionary Biology, University of Sao Paulo, 
      05508-090, Sao Paulo, SP, Brazil.
AD  - Department of Integrative Biology, University of California, Berkeley, CA, USA.
FAU - Nunes, Kelly
AU  - Nunes K
AD  - Department of Genetics and Evolutionary Biology, University of Sao Paulo, 
      05508-090, Sao Paulo, SP, Brazil.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PT  - Review
DEP - 20170707
PL  - United States
TA  - Immunogenetics
JT  - Immunogenetics
JID - 0420404
RN  - 0 (HLA Antigens)
RN  - 0 (Histocompatibility Antigens Class I)
RN  - 0 (Histocompatibility Antigens Class II)
SB  - IM
MH  - Alleles
MH  - Evolution, Molecular
MH  - Genetic Variation/genetics
MH  - Genome-Wide Association Study
MH  - Genomics
MH  - HLA Antigens/*genetics
MH  - High-Throughput Nucleotide Sequencing/methods
MH  - Histocompatibility Antigens Class I/genetics
MH  - Histocompatibility Antigens Class II/genetics
MH  - Histocompatibility Testing/methods
MH  - Humans
MH  - Major Histocompatibility Complex/*genetics
MH  - Polymorphism, Genetic/genetics
MH  - Selection, Genetic/genetics
PMC - PMC5748415
OTO - NOTNLM
OT  - Balancing selection
OT  - Evolution
OT  - Genomics
OT  - HLA (human leukocyte antigen)
OT  - MHC (major histocompatibility complex)
EDAT- 2017/07/09 06:00
MHDA- 2018/08/04 06:00
PMCR- 2017/07/07
CRDT- 2017/07/09 06:00
PHST- 2016/10/25 00:00 [received]
PHST- 2017/06/16 00:00 [accepted]
PHST- 2017/07/09 06:00 [pubmed]
PHST- 2018/08/04 06:00 [medline]
PHST- 2017/07/09 06:00 [entrez]
PHST- 2017/07/07 00:00 [pmc-release]
AID - 10.1007/s00251-017-1017-3 [pii]
AID - 1017 [pii]
AID - 10.1007/s00251-017-1017-3 [doi]
PST - ppublish
SO  - Immunogenetics. 2018 Jan;70(1):5-27. doi: 10.1007/s00251-017-1017-3. Epub 2017 
      Jul 7.