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Baxter-Lowe LA. The changing landscape of HLA typing: Understanding how and when HLA typing data can be used with confidence from bench to bedside. Hum Immunol 2021; 82:466-477. [PMID: 34030895 DOI: 10.1016/j.humimm.2021.04.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/26/2021] [Accepted: 04/29/2021] [Indexed: 12/11/2022]
Abstract
Human leukocyte antigen (HLA) genes are extraordinary for their extreme diversity and widespread impact on human health and disease. More than 30,000 HLA alleles have been officially named and more alleles continue to be discovered at a rapid pace. HLA typing systems which have been developed to detect HLA diversity have advanced rapidly and are revolutionizing our understanding of HLA's clinical importance. However, continuous improvements in knowledge and technology have created challenges for clinicians and scientists. This review explains how differences in HLA typing systems can impact the HLA types that are assigned. The consequences of differences in laboratory testing methods and reference databases are described. The challenges of using HLA types that are not equivalent are illustrated. A fundamental understanding of the continual expansion of our understanding of HLA diversity and limitations in some of the typing data is essential for using typing data appropriately in clinical and research settings.
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Affiliation(s)
- Lee Ann Baxter-Lowe
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, USA; Department of Pathology, University of Southern California, USA.
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Horton R, Gibson R, Coggill P, Miretti M, Allcock RJ, Almeida J, Forbes S, Gilbert JGR, Halls K, Harrow JL, Hart E, Howe K, Jackson DK, Palmer S, Roberts AN, Sims S, Stewart CA, Traherne JA, Trevanion S, Wilming L, Rogers J, de Jong PJ, Elliott JF, Sawcer S, Todd JA, Trowsdale J, Beck S. Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project. Immunogenetics 2008; 60:1-18. [PMID: 18193213 PMCID: PMC2206249 DOI: 10.1007/s00251-007-0262-2] [Citation(s) in RCA: 235] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2007] [Accepted: 10/29/2007] [Indexed: 02/05/2023]
Abstract
The human major histocompatibility complex (MHC) is contained within about 4 Mb on the short arm of chromosome 6 and is recognised as the most variable region in the human genome. The primary aim of the MHC Haplotype Project was to provide a comprehensively annotated reference sequence of a single, human leukocyte antigen-homozygous MHC haplotype and to use it as a basis against which variations could be assessed from seven other similarly homozygous cell lines, representative of the most common MHC haplotypes in the European population. Comparison of the haplotype sequences, including four haplotypes not previously analysed, resulted in the identification of >44,000 variations, both substitutions and indels (insertions and deletions), which have been submitted to the dbSNP database. The gene annotation uncovered haplotype-specific differences and confirmed the presence of more than 300 loci, including over 160 protein-coding genes. Combined analysis of the variation and annotation datasets revealed 122 gene loci with coding substitutions of which 97 were non-synonymous. The haplotype (A3-B7-DR15; PGF cell line) designated as the new MHC reference sequence, has been incorporated into the human genome assembly (NCBI35 and subsequent builds), and constitutes the largest single-haplotype sequence of the human genome to date. The extensive variation and annotation data derived from the analysis of seven further haplotypes have been made publicly available and provide a framework and resource for future association studies of all MHC-associated diseases and transplant medicine.
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Affiliation(s)
- Roger Horton
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Richard Gibson
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Penny Coggill
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Marcos Miretti
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Richard J. Allcock
- School of Surgery and Pathology, University of Western Australia, Nedlands, 6009 WA Australia
| | - Jeff Almeida
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Simon Forbes
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - James G. R. Gilbert
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Karen Halls
- The Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry Wellcome Building of Cancer and Developmental Biology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN UK
| | - Jennifer L. Harrow
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Elizabeth Hart
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Kevin Howe
- CRUK Cambridge Research Institute, Robinson Way, Cambridge, CB2 0RE UK
| | - David K. Jackson
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Sophie Palmer
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Anne N. Roberts
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Addenbrooke’s Hospital, Cambridge, CB2 0XY UK
| | - Sarah Sims
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - C. Andrew Stewart
- National Cancer Institute, P.O. Box B., 567/206, Frederick, MD 21702 USA
| | - James A. Traherne
- Department of Pathology, Immunology Division, University of Cambridge, Cambridge, CB2 1QP UK
| | - Steve Trevanion
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Laurens Wilming
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Jane Rogers
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Pieter J. de Jong
- Children’s Hospital Oakland Research Institute, Oakland, CA 94609-1673 USA
| | - John F. Elliott
- Alberta Diabetes Institute (ADI), Department of Medical Microbiology and Immunology, Division of Dermatology and Cutaneous Sciences, University of Alberta, Edmonton, AB T6G 2H7 Canada
| | - Stephen Sawcer
- Department of Clinical Neurosciences, University of Cambridge, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 2QQ UK
| | - John A. Todd
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Addenbrooke’s Hospital, Cambridge, CB2 0XY UK
| | - John Trowsdale
- Department of Pathology, Immunology Division, University of Cambridge, Cambridge, CB2 1QP UK
| | - Stephan Beck
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
- UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BD UK
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Královicová J, Vorechovsky I. Position-dependent repression and promotion of DQB1 intron 3 splicing by GGGG motifs. THE JOURNAL OF IMMUNOLOGY 2006; 176:2381-8. [PMID: 16455996 DOI: 10.4049/jimmunol.176.4.2381] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Alternative splicing of HLA-DQB1 exon 4 is allele-dependent and results in variable expression of soluble DQbeta. We have recently shown that differential inclusion of this exon in mature transcripts is largely due to intron 3 variants in the branch point sequence (BPS) and polypyrimidine tract. To identify additional regulatory cis-elements that contribute to haplotype-specific splicing of DQB1, we systematically examined the effect of guanosine (G) repeats on intron 3 removal. We found that the GGG or GGGG repeats generally improved splicing of DQB1 intron 3, except for those that were adjacent to the 5' splice site where they had the opposite effect. The most prominent splicing enhancement was conferred by GGGG motifs arranged in tandem upstream of the BPS. Replacement of a G-rich segment just 5' of the BPS with a series of random sequences markedly repressed splicing, whereas substitutions of a segment further upstream that lacked the G-rich elements and had the same size did not result in comparable splicing inhibition. Systematic mutagenesis of both suprabranch guanosine quadruplets (G(4)) revealed a key role of central G residues in splicing enhancement, whereas cytosines in these positions had the most prominent repressive effects. Together, these results show a significant role of tandem G(4)NG(4) structures in splicing of both complete and truncated DQB1 intron 3, support position dependency of G repeats in splicing promotion and inhibition, and identify positively and negatively acting sequences that contribute to the haplotype-specific DQB1 expression.
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Affiliation(s)
- Jana Královicová
- Division of Human Genetics, University of Southampton, School of Medicine, UK
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