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Sartoris S, Del Pozzo G. Exploring the HLA complex in autoimmunity: From the risk haplotypes to the modulation of expression. Clin Immunol 2024; 265:110266. [PMID: 38851519 DOI: 10.1016/j.clim.2024.110266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/29/2024] [Accepted: 05/30/2024] [Indexed: 06/10/2024]
Abstract
The genes mapping at the HLA region show high density, strong linkage disequilibrium and high polymorphism, which affect the association of HLA class I and class II genes with autoimmunity. We focused on the HLA haplotypes, genomic structures consisting of an array of specific alleles showing some degrees of genetic association with different autoimmune disorders. GWASs in many pathologies have identified variants in either the coding loci or the flanking regulatory regions, both in linkage disequilibrium in haplotypes, that are frequently associated with increased risk and may influence gene expression. We discuss the relevance of the HLA gene expression because the level of surface heterodimers determines the number of complexes presenting self-antigen and, thus, the strength of pathogenic autoreactive T cells immune response.
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Affiliation(s)
- Silvia Sartoris
- Dept. of Medicine, Section of Immunology University of Verona School of Medicine, Verona, Italy
| | - Giovanna Del Pozzo
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso" National Research Council (CNR), Naples, Italy.
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2
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Sverchkova A, Burkholz S, Rubsamen R, Stratford R, Clancy T. Integrative HLA typing of tumor and adjacent normal tissue can reveal insights into the tumor immune response. BMC Med Genomics 2024; 17:37. [PMID: 38281021 PMCID: PMC10821267 DOI: 10.1186/s12920-024-01808-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 01/12/2024] [Indexed: 01/29/2024] Open
Abstract
BACKGROUND The HLA complex is the most polymorphic region of the human genome, and its improved characterization can help us understand the genetics of human disease as well as the interplay between cancer and the immune system. The main function of HLA genes is to recognize "non-self" antigens and to present them on the cell surface to T cells, which instigate an immune response toward infected or transformed cells. While sequence variation in the antigen-binding groove of HLA may modulate the repertoire of immunogenic antigens presented to T cells, alterations in HLA expression can significantly influence the immune response to pathogens and cancer. METHODS RNA sequencing was used here to accurately genotype the HLA region and quantify and compare the level of allele-specific HLA expression in tumors and patient-matched adjacent normal tissue. The computational approach utilized in the study types classical and non-classical Class I and Class II HLA alleles from RNA-seq while simultaneously quantifying allele-specific or personalized HLA expression. The strategy also uses RNA-seq data to infer immune cell infiltration into tumors and the corresponding immune cell composition of matched normal tissue, to reveal potential insights related to T cell and NK cell interactions with tumor HLA alleles. RESULTS The genotyping method outperforms existing RNA-seq-based HLA typing tools for Class II HLA genotyping. Further, we demonstrate its potential for studying tumor-immune interactions by applying the method to tumor samples from two different subtypes of breast cancer and their matched normal breast tissue controls. CONCLUSIONS The integrative RNA-seq-based HLA typing approach described in the study, coupled with HLA expression analysis, neoantigen prediction and immune cell infiltration, may help increase our understanding of the interplay between a patient's tumor and immune system; and provide further insights into the immune mechanisms that determine a positive or negative outcome following treatment with immunotherapy such as checkpoint blockade.
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Affiliation(s)
- Angelina Sverchkova
- NEC OncoImmunity, Oslo Cancer Cluster, Innovation Park, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Scott Burkholz
- Flow Pharma, Inc, Warrensville Heights, Galaxy Parkway, OH, 4829, USA
| | - Reid Rubsamen
- Flow Pharma, Inc, Warrensville Heights, Galaxy Parkway, OH, 4829, USA
- University Hospitals, Cleveland Medical Center, Cleveland, OH, USA
- Case Western Reserve School of Medicine, Cleveland, OH, USA
| | - Richard Stratford
- NEC OncoImmunity, Oslo Cancer Cluster, Innovation Park, Oslo, Norway
| | - Trevor Clancy
- NEC OncoImmunity, Oslo Cancer Cluster, Innovation Park, Oslo, Norway.
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3
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Shiina T, Kulski JK. HLA Genetics for the Human Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1444:237-258. [PMID: 38467984 DOI: 10.1007/978-981-99-9781-7_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Highly polymorphic human leukocyte antigen (HLA) molecules (alleles) expressed by different classical HLA class I and class II genes have crucial roles in the regulation of innate and adaptive immune responses, transplant rejection and in the pathogenesis of numerous infectious and autoimmune diseases. To date, over 35,000 HLA alleles have been published from the IPD-IMGT/HLA database, and specific HLA alleles and HLA haplotypes have been reported to be associated with more than 100 different diseases and phenotypes. Next generation sequencing (NGS) technology developed in recent years has provided breakthroughs in various HLA genomic/gene studies and transplant medicine. In this chapter, we review the current information on the HLA genomic structure and polymorphisms, as well as the genetic context in which numerous disease associations have been identified in this region.
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Affiliation(s)
| | - Jerzy K Kulski
- Tokai University School of Medicine, Isehara, Japan
- School of Biomedical Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
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4
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Alper CA, Dawkins RL, Kulski JK, Larsen CE, Lloyd SS. Editorial: Population genomic architecture: Conserved polymorphic sequences (CPSs), not linkage disequilibrium. Front Genet 2023; 14:1140350. [PMID: 36777737 PMCID: PMC9911302 DOI: 10.3389/fgene.2023.1140350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 01/17/2023] [Indexed: 01/28/2023] Open
Affiliation(s)
- Chester A. Alper
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA, United States,Department of Pediatrics, Harvard Medical School, Boston, MA, United States,*Correspondence: Chester A. Alper, ; Roger L. Dawkins, ; Jerzy K. Kulski, ; Charles E. Larsen, ; Sally S. Lloyd,
| | - Roger L. Dawkins
- CY O’Connor ERADE Village Foundation, North Dandalup, WA, Australia,*Correspondence: Chester A. Alper, ; Roger L. Dawkins, ; Jerzy K. Kulski, ; Charles E. Larsen, ; Sally S. Lloyd,
| | - Jerzy K. Kulski
- Department of Molecular Life Sciences, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Japan,*Correspondence: Chester A. Alper, ; Roger L. Dawkins, ; Jerzy K. Kulski, ; Charles E. Larsen, ; Sally S. Lloyd,
| | - Charles E. Larsen
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA, United States,Department of Pediatrics, Harvard Medical School, Boston, MA, United States,*Correspondence: Chester A. Alper, ; Roger L. Dawkins, ; Jerzy K. Kulski, ; Charles E. Larsen, ; Sally S. Lloyd,
| | - Sally S. Lloyd
- CY O’Connor ERADE Village Foundation, North Dandalup, WA, Australia,*Correspondence: Chester A. Alper, ; Roger L. Dawkins, ; Jerzy K. Kulski, ; Charles E. Larsen, ; Sally S. Lloyd,
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5
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Alper CA. The Path to Conserved Extended Haplotypes: Megabase-Length Haplotypes at High Population Frequency. Front Genet 2021; 12:716603. [PMID: 34422017 PMCID: PMC8378214 DOI: 10.3389/fgene.2021.716603] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 07/13/2021] [Indexed: 11/13/2022] Open
Abstract
This minireview describes the history of the conceptual development of conserved extended haplotypes (CEHs): megabase-length haplotypes that exist at high (≥0.5%) population frequency. My career began in internal medicine, shifted to pediatrics, and clinical practice changed to research. My research interest was initially in hematology: on plasma proteins, their metabolism, synthesis, and function. This narrowed to a focus on proteins of the human complement system, their role in immunity and their genetics, beginning with polymorphism and deficiency of C3. My group identified genetic polymorphisms and/or inherited deficiencies of C2, C4, C6, and C8. After defining glycine-rich beta glycoprotein as factor B (Bf) in the properdin system, we found that the genes for Bf (CFB), C2, C4A, and C4B were inherited as a single haplotypic unit which we named the "complotype." Complotypes are located within the major histocompatibility complex (MHC) between HLA-B and HLA-DRB1 and are designated (in arbitrary order) by their CFB, C2, C4A, and C4B types. Pedigree analysis revealed long stretches (several megabases) of apparently fixed DNA within the MHC that we referred to as "extended haplotypes" (later as "CEHs"). About 10 to 12 common CEHs constitute at least 25 - 30% of MHC haplotypes among European Caucasian populations. These CEHs contain virtually all the most common markers of MHC-associated diseases. In the case of type 1 diabetes, we have proposed a purely genetic and epigenetic model (with a small number of Mendelian recessive disease genes) that explains all the puzzling features of the disease, including its rising incidence.
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Affiliation(s)
- Chester A Alper
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, United States.,Department of Pediatrics, Harvard Medical School, Boston, MA, United States
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6
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Cun Y, Shi L, Kulski JK, Liu S, Yang J, Tao Y, Zhang X, Shi L, Yao Y. Haplotypic Associations and Differentiation of MHC Class II Polymorphic Alu Insertions at Five Loci With HLA-DRB1 Alleles in 12 Minority Ethnic Populations in China. Front Genet 2021; 12:636236. [PMID: 34305999 PMCID: PMC8292818 DOI: 10.3389/fgene.2021.636236] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 06/08/2021] [Indexed: 01/11/2023] Open
Abstract
The analysis of polymorphic variations in the human major histocompatibility complex (MHC) class II genomic region on the short-arm of chromosome 6 is a scientific enquiry to better understand the diversity in population structure and the effects of evolutionary processes such as recombination, mutation, genetic drift, demographic history, and natural selection. In order to investigate associations between the polymorphisms of HLA-DRB1 gene and recent Alu insertions (POALINs) in the HLA class II region, we genotyped HLA-DRB1 and five Alu loci (AluDPB2, AluDQA2, AluDQA1, AluDRB1, AluORF10), and determined their allele frequencies and haplotypic associations in 12 minority ethnic populations in China. There were 42 different HLA-DRB1 alleles for ethnic Chinese ranging from 12 alleles in the Jinuo to 28 in the Yugur with only DRB1∗08:03, DRB1∗09:01, DRB1∗12:02, DRB1∗14:01, DRB1∗15:01, and DRB1∗15:02 present in all ethnic groups. The POALINs varied in frequency between 0.279 and 0.514 for AluDPB2, 0 and 0.127 for AluDQA2, 0.777 and 0.995 for AluDQA1, 0.1 and 0.455 for AluDRB1 and 0.084 and 0.368 for AluORF10. By comparing the data of the five-loci POALIN in 13 Chinese ethnic populations (including Han-Yunnan published data) against Japanese and Caucasian published data, marked differences were observed between the populations at the allelic or haplotypic levels. Five POALIN loci were in significant linkage disequilibrium with HLA-DRB1 in different populations and AluDQA1 had the highest percentage association with most of the HLA-DRB1 alleles, whereas the nearby AluDRB1 indel was strongly haplotypic for only DRB1∗01, DRB1∗10, DRB1∗15 and DRB1∗16. There were 30 five-locus POALIN haplotypes inferred in all populations with H5 (no Alu insertions except for AluDQA1) and H21 (only AluDPB2 and AluDQA1 insertions) as the two predominant haplotypes. Neighbor joining trees and principal component analyses of the Alu and HLA-DRB1 polymorphisms showed that genetic diversity of these genomic markers is associated strongly with the population characteristics of language family, migration and sociality. This comparative study of HLA-DRB1 alleles and multilocus, lineage POALIN frequencies of Chinese ethnic populations confirmed that POALINs whether investigated alone or together with the HLA class II alleles are informative genetic and evolutionary markers for the identification of allele and haplotype lineages and genetic variations within the same and/or different populations.
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Affiliation(s)
- Yina Cun
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Lei Shi
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Jerzy K Kulski
- Faculty of Health and Medical Sciences, University of Western Australia Medical School, Crawley, WA, Australia
| | - Shuyuan Liu
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Jia Yang
- Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Disease, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Yufen Tao
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Xinwen Zhang
- Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Disease, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Li Shi
- Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Disease, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Yufeng Yao
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
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7
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Kulski JK, Suzuki S, Shiina T. Haplotype Shuffling and Dimorphic Transposable Elements in the Human Extended Major Histocompatibility Complex Class II Region. Front Genet 2021; 12:665899. [PMID: 34122517 PMCID: PMC8193847 DOI: 10.3389/fgene.2021.665899] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/12/2021] [Indexed: 12/26/2022] Open
Abstract
The major histocompatibility complex (MHC) on chromosome 6p21 is one of the most single-nucleotide polymorphism (SNP)-dense regions of the human genome and a prime model for the study and understanding of conserved sequence polymorphisms and structural diversity of ancestral haplotypes/conserved extended haplotypes. This study aimed to follow up on a previous analysis of the MHC class I region by using the same set of 95 MHC haplotype sequences downloaded from a publicly available BioProject database at the National Center for Biotechnology Information to identify and characterize the polymorphic human leukocyte antigen (HLA)-class II genes, the MTCO3P1 pseudogene alleles, the indels of transposable elements as haplotypic lineage markers, and SNP-density crossover (XO) loci at haplotype junctions in DNA sequence alignments of different haplotypes across the extended class II region (∼1 Mb) from the telomeric PRRT1 gene in class III to the COL11A2 gene at the centromeric end of class II. We identified 42 haplotypic indels (20 Alu, 7 SVA, 13 LTR or MERs, and 2 indels composed of a mosaic of different transposable elements) linked to particular HLA-class II alleles. Comparative sequence analyses of 136 haplotype pairs revealed 98 unique XO sites between SNP-poor and SNP-rich genomic segments with considerable haplotype shuffling located in the proximity of putative recombination hotspots. The majority of XO sites occurred across various regions including in the vicinity of MTCO3P1 between HLA-DQB1 and HLA-DQB3, between HLA-DQB2 and HLA-DOB, between DOB and TAP2, and between HLA-DOA and HLA-DPA1, where most XOs were within a HERVK22 sequence. We also determined the genomic positions of the PRDM9-recombination suppression sequence motif ATCCATG/CATGGAT and the PRDM9 recombination activation partial binding motif CCTCCCCT/AGGGGAG in the class II region of the human reference genome (NC_ 000006) relative to published meiotic recombination positions. Both the recombination and anti-recombination PRDM9 binding motifs were widely distributed throughout the class II genomic regions with 50% or more found within repeat elements; the anti-recombination motifs were found mostly in L1 fragmented repeats. This study shows substantial haplotype shuffling between different polymorphic blocks and confirms the presence of numerous putative ancestral recombination sites across the class II region between various HLA class II genes.
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Affiliation(s)
- Jerzy K Kulski
- Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, WA, Australia.,Department of Molecular Life Sciences, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Shingo Suzuki
- Department of Molecular Life Sciences, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Takashi Shiina
- Department of Molecular Life Sciences, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Japan
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8
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Kulski JK, Suzuki S, Shiina T. SNP-Density Crossover Maps of Polymorphic Transposable Elements and HLA Genes Within MHC Class I Haplotype Blocks and Junction. Front Genet 2021; 11:594318. [PMID: 33537058 PMCID: PMC7848197 DOI: 10.3389/fgene.2020.594318] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 11/24/2020] [Indexed: 12/12/2022] Open
Abstract
The genomic region (~4 Mb) of the human major histocompatibility complex (MHC) on chromosome 6p21 is a prime model for the study and understanding of conserved polymorphic sequences (CPSs) and structural diversity of ancestral haplotypes (AHs)/conserved extended haplotypes (CEHs). The aim of this study was to use a set of 95 MHC genomic sequences downloaded from a publicly available BioProject database at NCBI to identify and characterise polymorphic human leukocyte antigen (HLA) class I genes and pseudogenes, MICA and MICB, and retroelement indels as haplotypic lineage markers, and single-nucleotide polymorphism (SNP) crossover loci in DNA sequence alignments of different haplotypes across the Olfactory Receptor (OR) gene region (~1.2 Mb) and the MHC class I region (~1.8 Mb) from the GPX5 to the MICB gene. Our comparative sequence analyses confirmed the identity of 12 haplotypic retroelement markers and revealed that they partitioned the HLA-A/B/C haplotypes into distinct evolutionary lineages. Crossovers between SNP-poor and SNP-rich regions defined the sequence range of haplotype blocks, and many of these crossover junctions occurred within particular transposable elements, lncRNA, OR12D2, MUC21, MUC22, PSORS1A3, HLA-C, HLA-B, and MICA. In a comparison of more than 250 paired sequence alignments, at least 38 SNP-density crossover sites were mapped across various regions from GPX5 to MICB. In a homology comparison of 16 different haplotypes, seven CEH/AH (7.1, 8.1, 18.2, 51.x, 57.1, 62.x, and 62.1) had no detectable SNP-density crossover junctions and were SNP poor across the entire ~2.8 Mb of sequence alignments. Of the analyses between different recombinant haplotypes, more than half of them had SNP crossovers within 10 kb of LTR16B/ERV3-16A3_I, MLT1, Charlie, and/or THE1 sequences and were in close vicinity to structurally polymorphic Alu and SVA insertion sites. These studies demonstrate that (1) SNP-density crossovers are associated with putative ancestral recombination sites that are widely spread across the MHC class I genomic region from at least the telomeric OR12D2 gene to the centromeric MICB gene and (2) the genomic sequences of MHC homozygous cell lines are useful for analysing haplotype blocks, ancestral haplotypic landscapes and markers, CPSs, and SNP-density crossover junctions.
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Affiliation(s)
- Jerzy K. Kulski
- Faculty of Health and Medical Sciences, Medical School, The University of Western Australia, Crawley, WA, Australia
- Division of Basic Medical Science and Molecular Medicine, Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Shingo Suzuki
- Division of Basic Medical Science and Molecular Medicine, Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Takashi Shiina
- Division of Basic Medical Science and Molecular Medicine, Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
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9
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Do MD, Le LGH, Nguyen VT, Dang TN, Nguyen NH, Vu HA, Mai TP. High-Resolution HLA Typing of HLA-A, -B, -C, -DRB1, and -DQB1 in Kinh Vietnamese by Using Next-Generation Sequencing. Front Genet 2020; 11:383. [PMID: 32425978 PMCID: PMC7204072 DOI: 10.3389/fgene.2020.00383] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 03/27/2020] [Indexed: 12/19/2022] Open
Abstract
Human leukocyte antigen (HLA) genotyping displays the particular characteristics of HLA alleles and haplotype frequencies in each population. Although it is considered the current gold standard for HLA typing, high-resolution sequence-based HLA typing is currently unavailable in Kinh Vietnamese populations. In this study, high-resolution sequence-based HLA typing (3-field) was performed using an amplicon-based next-generation sequencing platform to identify the HLA-A, -B, -C, -DRB1, and -DQB1 alleles of 101 unrelated healthy Kinh Vietnamese individuals from southern Vietnam. A total of 28 HLA-A, 41 HLA-B, 21 HLA-C, 26 HLA-DRB1, and 25 HLA-DQB1 alleles were identified. The most frequently occurring HLA alleles were A∗11:01:01, B∗15:02:01, C∗07:02:01, DRB1∗12:02:01, and DQB1∗03:01:01. Haplotype calculation showed that A∗29:01:01∼B∗07:05:01, DRB1∗12:02:01∼DQB1∗3:01:01, A∗29:01:01∼C∗15:05:02∼B∗07:05:01, A∗33:03:01∼B∗58:01:01∼DRB1∗03:01:01, and A∗29:01:01∼C∗15:05:02∼B∗07:05:01∼DRB1∗10:01:01∼DQB1∗05:01:01 were the most common haplotypes in the southern Kinh Vietnamese population. Allele distribution and haplotype analyses demonstrated that the Vietnamese population shares HLA features with South-East Asians but retains unique characteristics. Data from this study will be potentially applicable in medicine and anthropology.
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Affiliation(s)
- Minh Duc Do
- Center for Molecular Biomedicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Linh Gia Hoang Le
- Center for Molecular Biomedicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Vinh The Nguyen
- Center for Molecular Biomedicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Tran Ngoc Dang
- Faculty of Public Health, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Nghia Hoai Nguyen
- Center for Molecular Biomedicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Hoang Anh Vu
- Center for Molecular Biomedicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Thao Phuong Mai
- Department of Physiology, Pathophysiology and Immunology, Faculty of Medicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
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10
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Dawkins RL, Lloyd SS. MHC Genomics and Disease: Looking Back to Go Forward. Cells 2019; 8:cells8090944. [PMID: 31438577 PMCID: PMC6769595 DOI: 10.3390/cells8090944] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/15/2019] [Accepted: 08/16/2019] [Indexed: 02/07/2023] Open
Abstract
Ancestral haplotypes are conserved but extremely polymorphic kilobase sequences, which have been faithfully inherited over at least hundreds of generations in spite of migration and admixture. They carry susceptibility and resistance to diverse diseases, including deficiencies of CYP21 hydroxylase (47.1) and complement components (18.1), as well as numerous autoimmune diseases (8.1). The haplotypes are detected by segregation within ethnic groups rather than by SNPs and GWAS. Susceptibility to some other diseases is carried by specific alleles shared by multiple ancestral haplotypes, e.g., ankylosing spondylitis and narcolepsy. The difference between these two types of association may explain the disappointment with many GWAS. Here we propose a pathway for combining the two different approaches. SNP typing is most useful after the conserved ancestral haplotypes have been defined by other methods.
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Affiliation(s)
- Roger L Dawkins
- Centre for Innovation in Agriculture, Murdoch University and C Y O'Connor ERADE Village Foundation, North Dandalup 6207, Western Australia, Australia.
| | - Sally S Lloyd
- Centre for Innovation in Agriculture, Murdoch University and C Y O'Connor ERADE Village Foundation, North Dandalup 6207, Western Australia, Australia
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11
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Vadva Z, Larsen CE, Propp BE, Trautwein MR, Alford DR, Alper CA. A New Pedigree-Based SNP Haplotype Method for Genomic Polymorphism and Genetic Studies. Cells 2019; 8:E835. [PMID: 31387299 PMCID: PMC6721696 DOI: 10.3390/cells8080835] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 12/25/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) are usually the most frequent genomic variants. Directly pedigree-phased multi-SNP haplotypes provide a more accurate view of polymorphic population genomic structure than individual SNPs. The former are, therefore, more useful in genetic correlation with subject phenotype. We describe a new pedigree-based methodology for generating non-ambiguous SNP haplotypes for genetic study. SNP data for haplotype analysis were extracted from a larger Type 1 Diabetes Genetics Consortium SNP dataset based on minor allele frequency variation and redundancy, coverage rate (the frequency of phased haplotypes in which each SNP is defined) and genomic location. Redundant SNPs were eliminated, overall haplotype polymorphism was optimized and the number of undefined haplotypes was minimized. These edited SNP haplotypes from a region containing HLA-DRB1 (DR) and HLA-DQB1 (DQ) both correlated well with HLA-typed DR,DQ haplotypes and differentiated HLA-DR,DQ fragments shared by three pairs of previously identified megabase-length conserved extended haplotypes. In a pedigree-based genetic association assay for type 1 diabetes, edited SNP haplotypes and HLA-typed HLA-DR,DQ haplotypes from the same families generated essentially identical qualitative and quantitative results. Therefore, this edited SNP haplotype method is useful for both genomic polymorphic architecture and genetic association evaluation using SNP markers with diverse minor allele frequencies.
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Affiliation(s)
- Zareen Vadva
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Charles E Larsen
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
| | - Bennett E Propp
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Michael R Trautwein
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Dennis R Alford
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Chester A Alper
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
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12
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Eberhard HP, Schmidt AH, Mytilineos J, Fleischhauer K, Müller CR. Common and well-documented HLA alleles of German stem cell donors by haplotype frequency estimation. HLA 2019; 92:206-214. [PMID: 30117303 PMCID: PMC6175154 DOI: 10.1111/tan.13378] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 06/14/2018] [Accepted: 08/13/2018] [Indexed: 01/11/2023]
Abstract
We present a catalog of common and well-documented (CWD) alleles of the German population for the six HLA loci A, B, C, DRB1, DQB1, and DPB1. This study is based on a sample of over 5 million volunteer adult hematopoietic stem cell donors from the 26 German donor centers. To establish the catalog, allele and haplotype frequencies were estimated with a validated implementation of the expectation-maximization algorithm. CWD criteria similar to existing CWD catalogs were applied in order to be able to put our findings into the context of relevant existing references. Overall, 2155 HLA-A, -B, -C, -DRB1, -DQB1, and -DPB1 alleles were identified as CWD in the German donor population representing about 20% of the HLA alleles at two-field resolution in the IPD-IMGT/HLA Database release v3.25.0 from July 2016 for these six loci. We found a substantial concordance of CWD alleles between the three catalogs and showed the contribution of the German donor population to the CWD alleles domain. In conclusion, the definition of CWD criteria that allow interoperability, scalability, and flexibility will be crucial for the development of a worldwide CWD catalog.
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Affiliation(s)
- Hans-Peter Eberhard
- ZKRD Zentrales Knochenmarkspender-Register für die Bundesrepublik Deutschland, Ulm, Germany
| | | | - Joannis Mytilineos
- SKD Stiftung Knochenmark- und Stammzellspende Deutschland, Birkenfeld, Germany.,Institute of Clinical Transfusion Medicine and Immunogenetics, German Red Cross Blood Transfusion Service Baden Wuerttemberg-Hessen and University Hospital Ulm, Ulm, Germany.,DGI Deutsche Gesellschaft für Immungenetik e.V., Essen, Germany
| | | | - Carlheinz R Müller
- ZKRD Zentrales Knochenmarkspender-Register für die Bundesrepublik Deutschland, Ulm, Germany.,DGI Deutsche Gesellschaft für Immungenetik e.V., Essen, Germany
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13
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Increased MHC Matching by C4 Gene Compatibility in Unrelated Donor Hematopoietic Stem Cell Transplantation. Biol Blood Marrow Transplant 2019; 25:891-898. [DOI: 10.1016/j.bbmt.2018.12.759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/19/2018] [Indexed: 12/22/2022]
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14
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Petersdorf EW, O'hUigin C. The MHC in the era of next-generation sequencing: Implications for bridging structure with function. Hum Immunol 2019; 80:67-78. [PMID: 30321633 PMCID: PMC6542361 DOI: 10.1016/j.humimm.2018.10.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 09/24/2018] [Accepted: 10/01/2018] [Indexed: 12/19/2022]
Abstract
The MHC continues to have the most disease-associations compared to other regions of the human genome, even in the genome-wide association study (GWAS) and single nucleotide polymorphism (SNP) era. Analysis of non-coding variation and their impact on the level of expression of HLA allotypes has shed new light on the potential mechanisms underlying HLA disease associations and alloreactivity in transplantation. Next-generation sequencing (NGS) technology has the capability of delineating the phase of variants in the HLA antigen-recognition site (ARS) with non-coding regulatory polymorphisms. These relationships are critical for understanding the qualitative and quantitative implications of HLA gene diversity. This article summarizes current understanding of non-coding region variation of HLA loci, the consequences of regulatory variation on HLA expression, the role for evolution in shaping lineage-specific expression, and the impact of HLA expression on disease susceptibility and transplantation outcomes. A role for phased sequencing methods for the MHC, and perspectives for future directions in basic and applied immunogenetic studies of the MHC are presented.
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Affiliation(s)
- Effie W Petersdorf
- University of Washington, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, D4-115, Seattle, WA 98109, United States.
| | - Colm O'hUigin
- Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Microbiome and Genetics Core, Building 37, Room 4140B, Bethesda, MD 20852, United States.
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15
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Alper CA, Larsen CE, Trautwein MR, Alford DR. A stochastic epigenetic Mendelian oligogenic disease model for type 1 diabetes. J Autoimmun 2018; 96:123-133. [PMID: 30309752 DOI: 10.1016/j.jaut.2018.09.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/12/2018] [Indexed: 01/14/2023]
Abstract
The incidence of type 1 diabetes (T1D) and some other complex diseases is increasing. The cause has been attributed to an undefined changing environment. We examine the role of the environment (or any changing non-genetic mechanism) in causing the rising incidence, and find much evidence against it: 1) Dizygotic twin T1D concordance is the same as siblings of patients in general; 2) If the environment is responsible for both the discordance among identical twins of patients with T1D and its rising incidence, the twin concordance rate should be rising, but it is not; 3) Migrants from high-to low-incidence countries continue to have high-incidence children; 4) TID incidence among the offspring of two T1D parents is identical to the monozygotic twin rate. On the other hand, genetic association studies of T1D have revealed strong susceptibility in the major histocompatibility complex and many optional additive genes of small effect throughout the human genome increasing T1D risk. We have, from an analysis of previously published family studies, developed a stochastic epigenetic Mendelian oligogenic (SEMO) model consistent with published observations. The model posits a few required recessive causal genes with incomplete penetrance explaining virtually all of the puzzling features of T1D, including its rising incidence and the specific low T1D incidence rates among first-degree relatives of patients. Since historic selection against any causal gene could prevent T1D, we postulate that the rising incidence is because of increasing population mixing of parents from some previously isolated populations that had selected against different causal genes.
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Affiliation(s)
- Chester A Alper
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA; Department of Pediatrics, Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA.
| | - Charles E Larsen
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA; Department of Pediatrics, Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA
| | - Michael R Trautwein
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Dennis R Alford
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
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16
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Lloyd SS, Steele EJ, Valenzuela JL, Dawkins RL. Haplotypes for Type, Degree, and Rate of Marbling in Cattle Are Syntenic with Human Muscular Dystrophy. Int J Genomics 2017; 2017:6532837. [PMID: 28913347 PMCID: PMC5585636 DOI: 10.1155/2017/6532837] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/28/2017] [Indexed: 01/04/2023] Open
Abstract
Traditional analyses of a QTL on Bota 19 implicate a surfeit of candidates, but each is of marginal significance in explaining the deposition of healthy, low melting temperature fat within marbled muscle of Wagyu cattle. As an alternative approach, we have used genomic, multigenerational segregation to identify 14 conserved, ancestral 20 Mb haplotypes. These determine the degree and rate of marbling in Wagyu and other breeds of cattle. The melting temperature of intramuscular fat is highly heritable and traceable by haplotyping. Fortunately, for the production of healthy beef, some of these haplotypes are sufficiently penetrant to be expressed in heterozygous crossbreds, thereby allowing selection of sires which will improve the healthiness of beef produced under even harsh climatic conditions. The region of Bota 19 is syntenic to a region of Hosa 17 known to be important in muscle metabolism and in determining susceptibility to a form of human muscular dystrophy.
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Affiliation(s)
- Sally S. Lloyd
- CY O'Connor ERADE Village Foundation, P.O. Box 5100, Canning Vale South, WA 6155, Australia
- Melaleuka Stud, 24 Genomics Rise, Piara Waters, WA 6112, Australia
- Centre for Innovation in Agriculture, Murdoch University, Murdoch, WA 6150, Australia
| | - Edward J. Steele
- CY O'Connor ERADE Village Foundation, P.O. Box 5100, Canning Vale South, WA 6155, Australia
| | - Jose L. Valenzuela
- CY O'Connor ERADE Village Foundation, P.O. Box 5100, Canning Vale South, WA 6155, Australia
- Melaleuka Stud, 24 Genomics Rise, Piara Waters, WA 6112, Australia
| | - Roger L. Dawkins
- CY O'Connor ERADE Village Foundation, P.O. Box 5100, Canning Vale South, WA 6155, Australia
- Melaleuka Stud, 24 Genomics Rise, Piara Waters, WA 6112, Australia
- Centre for Innovation in Agriculture, Murdoch University, Murdoch, WA 6150, Australia
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17
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Abstract
A haplotype is a string of nucleotides or alleles at nearby loci on one chromosome, usually inherited as a unit. Within the major histocompatibility complex (MHC) region on human chromosome 6p, independent population studies of multiple families have identified conserved extended haplotypes (CEHs) that segregate as long stretches (≥1 megabase) of essentially identical DNA sequence at relatively high (≥0.5 %) population frequency ("genetic fixity"). CEHs were first identified through segregation analysis in the early 1980s. In European Caucasian populations, the most frequent 30 CEHs account for at least one-third of all MHC haplotypes. These CEHs provide all of the known individual MHC susceptibility and protective genetic markers within those populations for several complex genetic diseases. Haplotypes are rigorously determined directly by sequencing single chromosomes or by Mendelian segregation analysis using families with informative genotypes. Four parental haplotypes are assigned unambiguously using genotypes from the two parents and from two of their haploidentical (to each other) children. However, the most common current technique to phase haplotypes is probabilistic statistical imputation, using unrelated subjects. Such probabilistic techniques have failed to detect CEHs and are thus of questionable value in identifying long-range haplotype structure and, consequently, genetic structure-function relationships. Finally, with haplotypes rigorously defined, association studies can determine frequencies of alleles among unrelated patient haplotypes vs. those among only unaffected family members (i.e., control alleles/haplotypes). Such studies reduce, as much as possible, the confounding effects of population stratification common to all genetic studies.
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Affiliation(s)
- Chester A Alper
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, CLS_03, 3 Blackfan Circle, Boston, MA, 02115, USA.
- Department of Pediatrics, Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA.
| | - Charles E Larsen
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, CLS_03, 3 Blackfan Circle, Boston, MA, 02115, USA
- Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA
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18
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Ruffier M, Kähäri A, Komorowska M, Keenan S, Laird M, Longden I, Proctor G, Searle S, Staines D, Taylor K, Vullo A, Yates A, Zerbino D, Flicek P. Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation. Database (Oxford) 2017; 2017:3074789. [PMID: 28365736 PMCID: PMC5467575 DOI: 10.1093/database/bax020] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 02/07/2017] [Accepted: 02/20/2017] [Indexed: 01/09/2023]
Abstract
The Ensembl software resources are a stable infrastructure to store, access and manipulate genome assemblies and their functional annotations. The Ensembl 'Core' database and Application Programming Interface (API) was our first major piece of software infrastructure and remains at the centre of all of our genome resources. Since its initial design more than fifteen years ago, the number of publicly available genomic, transcriptomic and proteomic datasets has grown enormously, accelerated by continuous advances in DNA-sequencing technology. Initially intended to provide annotation for the reference human genome, we have extended our framework to support the genomes of all species as well as richer assembly models. Cross-referenced links to other informatics resources facilitate searching our database with a variety of popular identifiers such as UniProt and RefSeq. Our comprehensive and robust framework storing a large diversity of genome annotations in one location serves as a platform for other groups to generate and maintain their own tailored annotation. We welcome reuse and contributions: our databases and APIs are publicly available, all of our source code is released with a permissive Apache v2.0 licence at http://github.com/Ensembl and we have an active developer mailing list ( http://www.ensembl.org/info/about/contact/index.html ). Database URL http://www.ensembl.org.
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Affiliation(s)
- Magali Ruffier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andreas Kähäri
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Monika Komorowska
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stephen Keenan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthew Laird
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ian Longden
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Glenn Proctor
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Steve Searle
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Daniel Staines
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kieron Taylor
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alessandro Vullo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrew Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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19
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Howrigan DP, Simonson MA, Davies G, Harris SE, Tenesa A, Starr JM, Liewald DC, Deary IJ, McRae A, Wright MJ, Montgomery GW, Hansell N, Martin NG, Payton A, Horan M, Ollier WE, Abdellaoui A, Boomsma DI, DeRosse P, Knowles EEM, Glahn DC, Djurovic S, Melle I, Andreassen OA, Christoforou A, Steen VM, Hellard SL, Sundet K, Reinvang I, Espeseth T, Lundervold AJ, Giegling I, Konte B, Hartmann AM, Rujescu D, Roussos P, Giakoumaki S, Burdick KE, Bitsios P, Donohoe G, Corley RP, Visscher PM, Pendleton N, Malhotra AK, Neale BM, Lencz T, Keller MC. Genome-wide autozygosity is associated with lower general cognitive ability. Mol Psychiatry 2016; 21:837-43. [PMID: 26390830 PMCID: PMC4803638 DOI: 10.1038/mp.2015.120] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/23/2015] [Accepted: 07/13/2015] [Indexed: 01/12/2023]
Abstract
Inbreeding depression refers to lower fitness among offspring of genetic relatives. This reduced fitness is caused by the inheritance of two identical chromosomal segments (autozygosity) across the genome, which may expose the effects of (partially) recessive deleterious mutations. Even among outbred populations, autozygosity can occur to varying degrees due to cryptic relatedness between parents. Using dense genome-wide single-nucleotide polymorphism (SNP) data, we examined the degree to which autozygosity associated with measured cognitive ability in an unselected sample of 4854 participants of European ancestry. We used runs of homozygosity-multiple homozygous SNPs in a row-to estimate autozygous tracts across the genome. We found that increased levels of autozygosity predicted lower general cognitive ability, and estimate a drop of 0.6 s.d. among the offspring of first cousins (P=0.003-0.02 depending on the model). This effect came predominantly from long and rare autozygous tracts, which theory predicts as more likely to be deleterious than short and common tracts. Association mapping of autozygous tracts did not reveal any specific regions that were predictive beyond chance after correcting for multiple testing genome wide. The observed effect size is consistent with studies of cognitive decline among offspring of known consanguineous relationships. These findings suggest a role for multiple recessive or partially recessive alleles in general cognitive ability, and that alleles decreasing general cognitive ability have been selected against over evolutionary time.
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Affiliation(s)
- D P Howrigan
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Genetics, Broad Institute of Harvard and MIT, Cambridge Center, Cambridge, MA, USA
| | - M A Simonson
- Division of Data Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - G Davies
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - S E Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Medical Genetics Section, University of Edinburgh Centre for Genomic and Experimental Medicine and MRC Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK
| | - A Tenesa
- Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit, Western General Hospital, University of Edinburgh, Edinburgh, UK
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, UK
| | - J M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, UK
| | - D C Liewald
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - I J Deary
- Department of Psychology, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - A McRae
- Queensland Institute of Medical Research Berghofer, Brisbane, QLD, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - M J Wright
- Queensland Institute of Medical Research Berghofer, Brisbane, QLD, Australia
| | - G W Montgomery
- Queensland Institute of Medical Research Berghofer, Brisbane, QLD, Australia
| | - N Hansell
- Queensland Institute of Medical Research Berghofer, Brisbane, QLD, Australia
| | - N G Martin
- Queensland Institute of Medical Research Berghofer, Brisbane, QLD, Australia
| | - A Payton
- Centre for Integrated Genomic Medical Research, Institute of Population Health, University of Manchester, Manchester, UK
| | - M Horan
- Centre for Clinical and Cognitive Neurosciences, Institute of Brain Behaviour and Mental Health, University of Manchester, Salford Royal NHS Foundation Trust, Salford, UK
| | - W E Ollier
- Centre for Integrated Genomic Medical Research, Institute of Population Health, University of Manchester, Manchester, UK
| | - A Abdellaoui
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
- Neuroscience Campus Amsterdam, Amsterdam, The Netherlands
| | - D I Boomsma
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
- Neuroscience Campus Amsterdam, Amsterdam, The Netherlands
- EMGO+ Institute for Health and Care Research, Amsterdam, The Netherlands
| | - P DeRosse
- Division of Psychiatry Research, Zucker Hillside Hospital, Glen Oaks, NY, USA
- Center for Psychiatric Neuroscience, Feinstein Institute for Medical Research, Manhasset, NY, USA
- Hofstra North Shore - LIJ School of Medicine, Departments of Psychiatry and Molecular Medicine, Hempstead, NY, USA
| | - E E M Knowles
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - D C Glahn
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - S Djurovic
- NORMENT, KG Jebsen Centre, Oslo, Norway
- Oslo University Hospital, Oslo, Norway
| | - I Melle
- NORMENT, KG Jebsen Centre, Oslo, Norway
- Oslo University Hospital, Oslo, Norway
- University of Oslo, Oslo, Norway
| | - O A Andreassen
- NORMENT, KG Jebsen Centre, Oslo, Norway
- Oslo University Hospital, Oslo, Norway
- University of Oslo, Oslo, Norway
| | - A Christoforou
- K.G. Jebsen Centre for Psychosis Research, Dr. Einar Martens Research Group for Biological Psychiatry, Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - V M Steen
- K.G. Jebsen Centre for Psychosis Research, Dr. Einar Martens Research Group for Biological Psychiatry, Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - S L Hellard
- K.G. Jebsen Centre for Psychosis Research, Dr. Einar Martens Research Group for Biological Psychiatry, Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - K Sundet
- NORMENT, KG Jebsen Centre, Oslo, Norway
- Department of Psychology, University of Oslo, Oslo, Norway
| | - I Reinvang
- Department of Psychology, University of Oslo, Oslo, Norway
| | - T Espeseth
- Department of Psychology, University of Oslo, Oslo, Norway
- Norwegian Center for Mental Disorders Research, KG Jebsen Centre for Psychosis Research, Oslo University Hospital, Oslo, Norway
| | - A J Lundervold
- K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, University of Bergen, Bergen, Norway
- Department of Biological and Medical Psychology, University of Bergen, Bergen, Norway
- Kavli Research Centre for Aging and Dementia, Haraldsplass Deaconess Hospital, Bergen, Norway
| | - I Giegling
- Department of Psychiatry, University of Halle, Halle, Germany
| | - B Konte
- Department of Psychiatry, University of Halle, Halle, Germany
| | - A M Hartmann
- Department of Psychiatry, University of Halle, Halle, Germany
| | - D Rujescu
- Department of Psychiatry, University of Halle, Halle, Germany
| | - P Roussos
- Department of Psychiatry, Friedman Brain Institute, Department of Genetics and Genomic Sciences, and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- James J. Peters VA Medical Center, Mental Illness Research Education and Clinical Center (MIRECC), Bronx, NY, USA
| | - S Giakoumaki
- Department of Psychology, University of Crete, Rethymno, Crete, Greece
| | - K E Burdick
- Department of Psychiatry, Friedman Brain Institute, Department of Genetics and Genomic Sciences, and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - P Bitsios
- Department of Psychiatry, Faculty of Medicine, University of Crete, Heraklion, Crete, Greece
- Computational Medicine Laboratory, Institute of Computer Science at FORTH, Heraklion, Greece
| | - G Donohoe
- School of Psychology, National University of Ireland Galway, Galway, Ireland
| | - R P Corley
- Institute for Behavioral Genetics, University of Colorado at Boulder, Boulder, CO, USA
| | - P M Visscher
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Queensland Institute of Medical Research Berghofer, Brisbane, QLD, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
- University of Queensland Diamantina Institute, The University of Queensland, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - N Pendleton
- Centre for Integrated Genomic Medical Research, Institute of Population Health, University of Manchester, Manchester, UK
| | - A K Malhotra
- Division of Psychiatry Research, Zucker Hillside Hospital, Glen Oaks, NY, USA
- Center for Psychiatric Neuroscience, Feinstein Institute for Medical Research, Manhasset, NY, USA
- Hofstra North Shore - LIJ School of Medicine, Departments of Psychiatry and Molecular Medicine, Hempstead, NY, USA
| | - B M Neale
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Genetics, Broad Institute of Harvard and MIT, Cambridge Center, Cambridge, MA, USA
| | - T Lencz
- Division of Psychiatry Research, Zucker Hillside Hospital, Glen Oaks, NY, USA
- Center for Psychiatric Neuroscience, Feinstein Institute for Medical Research, Manhasset, NY, USA
- Hofstra North Shore - LIJ School of Medicine, Departments of Psychiatry and Molecular Medicine, Hempstead, NY, USA
| | - M C Keller
- Institute for Behavioral Genetics, University of Colorado at Boulder, Boulder, CO, USA
- Department of Psychology, University of Colorado at Boulder, Boulder, CO, USA
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20
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Zhang J, Zhao L, Wang B, Gao J, Wang L, Li L, Cui B, Hu M, Hong J, Gu W, Wang W, Ning G. HLA-A*33-DR3 and A*33-DR9 haplotypes enhance the risk of type 1 diabetes in Han Chinese. J Diabetes Investig 2016; 7:514-21. [PMID: 27181214 PMCID: PMC4931201 DOI: 10.1111/jdi.12462] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 12/13/2015] [Accepted: 12/16/2015] [Indexed: 01/13/2023] Open
Abstract
Aims/Introduction To investigate the typing for human leukocyte antigen (HLA) class I in Chinese patients with type 1 diabetes as a complement screening for HLA class II. Materials and Methods A total of 212 type 1 diabetic patients and 200 healthy controls were enrolled. The genetic polymorphisms of HLA class I and II were examined with a high‐resolution polymerase chain reaction sequence‐based typing method. Results The haplotype, A*33:03‐B*58:01‐C*03:02(A33), was associated with type 1 diabetes (P = 1.0 × 10−4, odds ratio 3.2 [1.738–5.843]). The A33‐DR3 and A33‐DR9 haplotypes significantly enhanced the risk of type 1 diabetes (A33‐DR3, odds ratio 5.1 [2.40–10.78], P = 4.0 × 10−6; A33‐DR9, odds ratio 13.0 [1.69–100.32], P = 0.004). In type 1 diabetic patients, compared with A33‐DR3‐negative carriers, A33‐DR3‐positive carriers had significantly lower percentages of CD3+CD4+ T cells (42.5 ± 7.72 vs 37.0 ± 8.35%, P = 0.023), higher percentages of CD3+CD8+ T cells (27.4 ± 7.09 vs 32.8 ± 5.98%, P = 0.005) and T‐cell receptor α/β T cells (70.0 ± 7.00 vs 73.6 ± 6.25%, P = 0.031), and lower CD4/CD8 ratios (1.71 ± 0.75 vs 1.16 ± 0.35, P = 0.003). Conclusions It is the first time that the haplotypes A33‐DR3 and A33‐DR9 were found with an enhanced predisposition to type 1 diabetes in Han Chinese. A33‐DR3 was associated with a reduction in the helper‐to‐cytotoxic cell ratio and preferential increase of T‐cell receptor α/β T cell. The typing for HLA class I and its immunogenetic effects are important for more accurate HLA class II haplotype risk prediction and etiology research in type 1 diabetic patients.
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Affiliation(s)
- Juanjuan Zhang
- Department of Endocrine and Metabolic diseases, Ruijin Hospital, Shanghai Jiao-Tong University, School of Medicine, Shanghai Key Laboratory for Endocrine Tumors, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases and Shanghai E-institute for Endocrinology, Shanghai, China
| | - Liebin Zhao
- Department of Endocrine and Metabolic diseases, Ruijin Hospital, Shanghai Jiao-Tong University, School of Medicine, Shanghai Key Laboratory for Endocrine Tumors, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases and Shanghai E-institute for Endocrinology, Shanghai, China
| | - Bokai Wang
- Department of Endocrine and Metabolic diseases, Ruijin Hospital, Shanghai Jiao-Tong University, School of Medicine, Shanghai Key Laboratory for Endocrine Tumors, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases and Shanghai E-institute for Endocrinology, Shanghai, China
| | - Jie Gao
- Department of Endocrine and Metabolic diseases, Ruijin Hospital, Shanghai Jiao-Tong University, School of Medicine, Shanghai Key Laboratory for Endocrine Tumors, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases and Shanghai E-institute for Endocrinology, Shanghai, China
| | - Li Wang
- Department of Endocrine and Metabolic diseases, Ruijin Hospital, Shanghai Jiao-Tong University, School of Medicine, Shanghai Key Laboratory for Endocrine Tumors, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases and Shanghai E-institute for Endocrinology, Shanghai, China
| | - Li Li
- Department of Endocrine and Metabolic diseases, Ruijin Hospital, Shanghai Jiao-Tong University, School of Medicine, Shanghai Key Laboratory for Endocrine Tumors, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases and Shanghai E-institute for Endocrinology, Shanghai, China
| | - Bin Cui
- Department of Endocrine and Metabolic diseases, Ruijin Hospital, Shanghai Jiao-Tong University, School of Medicine, Shanghai Key Laboratory for Endocrine Tumors, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases and Shanghai E-institute for Endocrinology, Shanghai, China
| | - Min Hu
- Center for Transplant and Renal Research, Westmead Millennium Institute, University of Sydney, Sydney, New South Wales, Australia
| | - Jie Hong
- Department of Endocrine and Metabolic diseases, Ruijin Hospital, Shanghai Jiao-Tong University, School of Medicine, Shanghai Key Laboratory for Endocrine Tumors, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases and Shanghai E-institute for Endocrinology, Shanghai, China
| | - Weiqiong Gu
- Department of Endocrine and Metabolic diseases, Ruijin Hospital, Shanghai Jiao-Tong University, School of Medicine, Shanghai Key Laboratory for Endocrine Tumors, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases and Shanghai E-institute for Endocrinology, Shanghai, China
| | - Weiqing Wang
- Department of Endocrine and Metabolic diseases, Ruijin Hospital, Shanghai Jiao-Tong University, School of Medicine, Shanghai Key Laboratory for Endocrine Tumors, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases and Shanghai E-institute for Endocrinology, Shanghai, China
| | - Guang Ning
- Department of Endocrine and Metabolic diseases, Ruijin Hospital, Shanghai Jiao-Tong University, School of Medicine, Shanghai Key Laboratory for Endocrine Tumors, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases and Shanghai E-institute for Endocrinology, Shanghai, China.,Laboratory for Endocrine & Metabolic Diseases, Institute of Health Science, Shanghai JiaoTong University, School of Medicine and Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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21
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Saw WY, Liu X, Khor CC, Takeuchi F, Katsuya T, Kimura R, Nabika T, Ohkubo T, Tabara Y, Yamamoto K, Yokota M, Teo YY, Kato N. Mapping the genetic diversity of HLA haplotypes in the Japanese populations. Sci Rep 2015; 5:17855. [PMID: 26648100 PMCID: PMC4673465 DOI: 10.1038/srep17855] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 11/06/2015] [Indexed: 11/09/2022] Open
Abstract
Japan has often been viewed as an Asian country that possesses a genetically homogenous community. The basis for partitioning the country into prefectures has largely been geographical, although cultural and linguistic differences still exist between some of the districts/prefectures, especially between Okinawa and the mainland prefectures. The Major Histocompatibility Complex (MHC) region has consistently emerged as the most polymorphic region in the human genome, harbouring numerous biologically important variants; nevertheless the presence of population-specific long haplotypes hinders the imputation of SNPs and classical HLA alleles. Here, we examined the extent of genetic variation at the MHC between eight Japanese populations sampled from Okinawa, and six other prefectures located in or close to the mainland of Japan, specifically focusing at the haplotypes observed within each population, and what the impact of any variation has on imputation. Our results indicated that Okinawa was genetically farther to the mainland Japanese than were Gujarati Indians from Tamil Indians, while the mainland Japanese from six prefectures were more homogeneous than between northern and southern Han Chinese. The distribution of haplotypes across Japan was similar, although imputation was most accurate for Okinawa and several mainland prefectures when population-specific panels were used as reference.
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Affiliation(s)
- Woei-Yuh Saw
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117549.,Life Sciences Institute, National University of Singapore, Singapore 117456
| | - Xuanyao Liu
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117549.,NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore 117456
| | - Chiea-Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672
| | - Fumihiko Takeuchi
- Department of Gene Diagnostics and Therapeutics, National Center for Global Health and Medicine, Tokyo, Japan 162-8655
| | - Tomohiro Katsuya
- Department of Clinical Gene Therapy, Osaka University Graduate School of Medicine, Suita, Japan 565-0871
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Japan 903-0215
| | - Toru Nabika
- Department of Functional Pathology, Shimane University School of Medicine, Izumo, Japan 693-8501
| | - Takayoshi Ohkubo
- Department of Hygiene and Public Health, Teikyo University School of Medicine, Tokyo, Japan 162-8655
| | - Yasuharu Tabara
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan 606-8501
| | - Ken Yamamoto
- Department of Medical Chemistry, Kurume University School of Medicine, Kurume, Japan 830-0011
| | - Mitsuhiro Yokota
- Department of Genome Science, School of Dentistry, Aichi Gakuin University, Nagoya, Japan 464-8651
| | | | - Yik-Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117549.,Life Sciences Institute, National University of Singapore, Singapore 117456.,NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore 117456.,Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672.,Department of Gene Diagnostics and Therapeutics, National Center for Global Health and Medicine, Tokyo, Japan 162-8655.,Department of Statistics and Applied Probability, National University of Singapore, Singapore
| | - Norihiro Kato
- Department of Gene Diagnostics and Therapeutics, National Center for Global Health and Medicine, Tokyo, Japan 162-8655
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22
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Intrahaplotypic Variants Differentiate Complex Linkage Disequilibrium within Human MHC Haplotypes. Sci Rep 2015; 5:16972. [PMID: 26593880 PMCID: PMC4655331 DOI: 10.1038/srep16972] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 10/22/2015] [Indexed: 12/21/2022] Open
Abstract
Distinct regions of long-range genetic fixation in the human MHC region, known as conserved extended haplotypes (CEHs), possess unique genomic characteristics and are strongly associated with numerous diseases. While CEHs appear to be homogeneous by SNP analysis, the nature of fine variations within their genomic structure is unknown. Using multiple, MHC-homozygous cell lines, we demonstrate extensive sequence conservation in two common Asian MHC haplotypes: A33-B58-DR3 and A2-B46-DR9. However, characterization of phase-resolved MHC haplotypes revealed unique intra-CEH patterns of variation and uncovered 127 single nucleotide variants (SNVs) which are missing from public databases. We further show that the strong linkage disequilibrium structure within the human MHC that typically confounds precise identification of genetic features can be resolved using intra-CEH variants, as evidenced by rs3129063 and rs448489, which affect expression of ZFP57, a gene important in methylation and epigenetic regulation. This study demonstrates an improved strategy that can be used towards genetic dissection of diseases.
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23
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Steele EJ, Lloyd SS. Soma-to-germline feedback is implied by the extreme polymorphism at IGHV relative to MHC: The manifest polymorphism of the MHC appears greatly exceeded at Immunoglobulin loci, suggesting antigen-selected somatic V mutants penetrate Weismann's Barrier. Bioessays 2015; 37:557-69. [PMID: 25810320 DOI: 10.1002/bies.201400213] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 02/15/2015] [Accepted: 02/24/2015] [Indexed: 01/22/2023]
Abstract
Soma-to-germline feedback is forbidden under the neo-Darwinian paradigm. Nevertheless, there is a growing realization it occurs frequently in immunoglobulin (Ig) variable (V) region genes. This is a surprising development. It arises from a most unlikely source in light of the exposure of co-author EJS to the haplotype data of RL Dawkins and others on the polymorphism of the Major Histocompatibility Complex, which is generally assumed to be the most polymorphic region in the genome (spanning ∼4 Mb). The comparison between the magnitude of MHC polymorphism with estimates for the human heavy chain immunoglobulin V locus (spanning ∼1 Mb), suggests IGHV could be many orders of magnitude more polymorphic than the MHC. This conclusion needs airing in the literature as it implies generational churn and soma-to-germline gene feedback. Pedigree-based experimental strategies to resolve the IGHV issue are outlined.
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Affiliation(s)
- Edward J Steele
- C.Y. O'Connor ERADE Village Foundation, Piara Waters, WA, Australia
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24
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Erdem G, Seifried SE. No Evidence of Human Leukocyte Antigen Gene Association With Rheumatic Fever Among Children in Samoa. J Pediatric Infect Dis Soc 2015; 4:71-3. [PMID: 26407361 PMCID: PMC5965876 DOI: 10.1093/jpids/pit064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 07/25/2013] [Indexed: 11/14/2022]
Abstract
Human leukocyte antigens (HLAs) have been implicated in rheumatic fever pathogenesis. This pilot whole genome association study compares genotypes of Samoan children with rheumatic fever to unaffected siblings and unrelated healthy controls. No risk-related genotypes were associated with HLA genes. Thirteen Regions of Interest were identified as candidates for further study.
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Affiliation(s)
| | - Steven E. Seifried
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu
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25
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Puangpetch A, Koomdee N, Chamnanphol M, Jantararoungtong T, Santon S, Prommas S, Hongkaew Y, Sukasem C. HLA-B allele and haplotype diversity among Thai patients identified by PCR-SSOP: evidence for high risk of drug-induced hypersensitivity. Front Genet 2015; 5:478. [PMID: 25657656 PMCID: PMC4302987 DOI: 10.3389/fgene.2014.00478] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 12/30/2014] [Indexed: 01/11/2023] Open
Abstract
Background: There are 3 classes of HLA molecules; HLA class I, II and III, of which different classes have different functions. HLA-B gene which belongs to HLA class I play an important role predicting drug hypersensitivity. Materials and Methods: Nine hundred and eighty-six Thai subjects who registered at a pharmacogenomics laboratory were determined for HLA-B genotype using a two-stage sequence-specific oligonucleotide probe system (PCR-SSOP). Results: In this study, HLA-B alleles did not deviate from Hardy-Weinberg equilibrium (P > 0.05). The most common HLA-B alleles observed in this population were HLA-B*46:01 (11.51%), HLA-B*58:01 (8.62%), HLA-B*40:01 (8.22%), HLA-B*15:02 (8.16%) and HLA-B*13:01 (6.95%). This finding revealed that HLA-B allele frequency in the Thai population was consistent with the Chinese population (p > 0.05), however, differed from the Malaysian population (p < 0.05). The top five HLA-B genotypes were HLA-B*40:01/46:01 (2.13%), HLA-B*46:01/46:01 (2.03%), HLA-B*40:01/58:01 (2.03%), HLA-B*46:01/58:01 (1.93%) and HLA-B*15:02/46:01 (1.83%). This study found that 15.92% of Thai subjects carry HLA-B*15:02, which has been associated with carbamazepine-induced severe cutaneous adverse drug reactions (SCARs). Moreover, 16.33% of Thai subjects carry the HLA-B*58:01 allele, which has been associated with allopurinol-induced SCARs. Conclusion: This study demonstrates a high diversity of HLA-B polymorphisms in this Thai population. The high frequency of HLA-B pharmacogenomic markers in the population emphasizes the importance of such screening to predict/avoid drug hypersensitivity.
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Affiliation(s)
- Apichaya Puangpetch
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University Bangkok, Thailand ; Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center, Ramathibodi Hospital, Mahidol University Bangkok, Thailand
| | - Napatrupron Koomdee
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University Bangkok, Thailand ; Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center, Ramathibodi Hospital, Mahidol University Bangkok, Thailand
| | - Montri Chamnanphol
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University Bangkok, Thailand ; Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center, Ramathibodi Hospital, Mahidol University Bangkok, Thailand
| | - Thawinee Jantararoungtong
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University Bangkok, Thailand ; Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center, Ramathibodi Hospital, Mahidol University Bangkok, Thailand
| | - Siwalee Santon
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University Bangkok, Thailand ; Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center, Ramathibodi Hospital, Mahidol University Bangkok, Thailand
| | - Santirhat Prommas
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University Bangkok, Thailand ; Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center, Ramathibodi Hospital, Mahidol University Bangkok, Thailand
| | - Yaowaluck Hongkaew
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University Bangkok, Thailand ; Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center, Ramathibodi Hospital, Mahidol University Bangkok, Thailand
| | - Chonlaphat Sukasem
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University Bangkok, Thailand ; Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center, Ramathibodi Hospital, Mahidol University Bangkok, Thailand
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26
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Iampietro M, Morissette G, Gravel A, Dubuc I, Rousseau M, Hasan A, O'Reilly RJ, Flamand L. Human herpesvirus 6B immediate-early I protein contains functional HLA-A*02, HLA-A*03, and HLA-B*07 class I restricted CD8(+) T-cell epitopes. Eur J Immunol 2014; 44:3573-84. [PMID: 25243920 DOI: 10.1002/eji.201444931] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 08/11/2014] [Accepted: 09/18/2014] [Indexed: 11/07/2022]
Abstract
Human herpesvirus 6B (HHV-6B) is a ubiquitous pathogen with frequent reactivation observed in immunocompromised patients such as BM transplant (BMT) recipients. Adoptive immunotherapy is a promising therapeutic avenue for the treatment of opportunistic infections, including herpesviruses. While T-cell immunotherapy can successfully control CMV and EBV reactivations in BMT recipients, such therapy is not available for HHV-6 infections, in part due to a lack of identified protective CD8(+) T-cell epitopes. Our goal was to identify CD8(+) T-cell viral epitopes derived from the HHV-6B immediate-early protein I and presented by common human leukocyte Ag (HLA) class I alleles including HLA-A*02, HLA-A*03, and HLA-B*07. These epitopes were functionally tested for their ability to induce CD8(+) T-cell expansion and kill HHV-6-infected autologous cells. Cross-reactivity of specific HHV-6B-expanded T cells against HHV-6A-infected cells was also confirmed for a conserved epitope presented by HLA-A*02 molecule. Our findings will help push forward the field of adoptive immunotherapy for the treatment and/or the prevention of HHV-6 reactivation in BMT recipients.
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Affiliation(s)
- Mathieu Iampietro
- Division of Infectious Disease and Immunity, CHU de Quebec Research Center, Quebec City, Canada
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27
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Dominant sequences of human major histocompatibility complex conserved extended haplotypes from HLA-DQA2 to DAXX. PLoS Genet 2014; 10:e1004637. [PMID: 25299700 PMCID: PMC4191933 DOI: 10.1371/journal.pgen.1004637] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 07/30/2014] [Indexed: 11/19/2022] Open
Abstract
We resequenced and phased 27 kb of DNA within 580 kb of the MHC class II region in 158 population chromosomes, most of which were conserved extended haplotypes (CEHs) of European descent or contained their centromeric fragments. We determined the single nucleotide polymorphism and deletion-insertion polymorphism alleles of the dominant sequences from HLA-DQA2 to DAXX for these CEHs. Nine of 13 CEHs remained sufficiently intact to possess a dominant sequence extending at least to DAXX, 230 kb centromeric to HLA-DPB1. We identified the regions centromeric to HLA-DQB1 within which single instances of eight “common” European MHC haplotypes previously sequenced by the MHC Haplotype Project (MHP) were representative of those dominant CEH sequences. Only two MHP haplotypes had a dominant CEH sequence throughout the centromeric and extended class II region and one MHP haplotype did not represent a known European CEH anywhere in the region. We identified the centromeric recombination transition points of other MHP sequences from CEH representation to non-representation. Several CEH pairs or groups shared sequence identity in small blocks but had significantly different (although still conserved for each separate CEH) sequences in surrounding regions. These patterns partly explain strong calculated linkage disequilibrium over only short (tens to hundreds of kilobases) distances in the context of a finite number of observed megabase-length CEHs comprising half a population's haplotypes. Our results provide a clearer picture of European CEH class II allelic structure and population haplotype architecture, improved regional CEH markers, and raise questions concerning regional recombination hotspots. The human major histocompatibility complex (MHC) is a gene-dense region highly enriched in immune response genes. MHC genetic variation is among the highest in the human genome and is associated with both tissue transplant compatibility and many genetic disorders. Long-range (1–3 Mb) MHC haplotypes of essentially identical DNA sequence at relatively high (≥0.5%) population frequency (“genetic fixity”), called conserved extended haplotypes (CEHs), comprise roughly half of all European population haplotypes. We sequenced an aggregate of 27 kb over 580 kb in the MHC class II region from HLA-DQA2 to DAXX in 158 European haplotypes to quantify the breakdown of this genetic fixity in the centromeric portion of the MHC and to determine the representative nature within that region of eight previously fully or nearly fully sequenced “common” European haplotypes. We identified the dominant sequences of 13 European CEHs and determined where the “common” sequences did (or did not) represent related CEHs. We found patterns of shared sequence identity among different CEHs surrounded by fixed (for each CEH) but differing sequence. Our direct observational results for population haplotypes explain the mutual occurrence of CEHs and short (5–200 kb) blocks of fixed sequence detected by the statistical measure of linkage disequilibrium.
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28
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Ross IL, Babu S, Armstrong T, Zhang L, Schatz D, Pugliese A, Eisenbarth G, Baker II P. HLA similarities indicate shared genetic risk in 21-hydroxylase autoantibody positive South African and United States Addison's disease. ACTA ACUST UNITED AC 2014; 84:361-9. [DOI: 10.1111/tan.12407] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 06/02/2014] [Accepted: 06/12/2014] [Indexed: 10/25/2022]
Affiliation(s)
- I. L. Ross
- University of Cape Town; Cape Town South Africa
| | - S. Babu
- Barbara Davis Center for Childhood Diabetes; University of Colorado; Aurora CL, USA
| | - T. Armstrong
- Barbara Davis Center for Childhood Diabetes; University of Colorado; Aurora CL, USA
| | - L. Zhang
- Barbara Davis Center for Childhood Diabetes; University of Colorado; Aurora CL, USA
| | - D. Schatz
- Diabetes Center; University of Florida College of Medicine; Gainesville FL, USA
| | - A. Pugliese
- Diabetes Research Institute; University of Miami; Miami FL, USA
| | - G. Eisenbarth
- Barbara Davis Center for Childhood Diabetes; University of Colorado; Aurora CL, USA
| | - P. Baker II
- Barbara Davis Center for Childhood Diabetes; University of Colorado; Aurora CL, USA
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29
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Johanneson B, Chen D, Enroth S, Cui T, Gyllensten U. Systematic validation of hypothesis-driven candidate genes for cervical cancer in a genome-wide association study. Carcinogenesis 2014; 35:2084-8. [DOI: 10.1093/carcin/bgu125] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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30
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Sundqvist E, Buck D, Warnke C, Albrecht E, Gieger C, Khademi M, Lima Bomfim I, Fogdell-Hahn A, Link J, Alfredsson L, Søndergaard HB, Hillert J, Oturai AB, Hemme B, Kockum I, Olsson T. JC polyomavirus infection is strongly controlled by human leucocyte antigen class II variants. PLoS Pathog 2014; 10:e1004084. [PMID: 24763718 PMCID: PMC3999271 DOI: 10.1371/journal.ppat.1004084] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 03/03/2014] [Indexed: 01/27/2023] Open
Abstract
JC polyomavirus (JCV) carriers with a compromised immune system, such as in HIV, or subjects on immune-modulating therapies, such as anti VLA-4 therapy may develop progressive multifocal leukoencephalopathy (PML) which is a lytic infection of oligodendrocytes in the brain. Serum antibodies to JCV mark infection occur only in 50–60% of infected individuals, and high JCV-antibody titers seem to increase the risk of developing PML. We here investigated the role of human leukocyte antigen (HLA), instrumental in immune defense in JCV antibody response. Anti-JCV antibody status, as a surrogate for JCV infection, were compared to HLA class I and II alleles in 1621 Scandinavian persons with MS and 1064 population-based Swedish controls and associations were replicated in 718 German persons with MS. HLA-alleles were determined by SNP imputation, sequence specific (SSP) kits and a reverse PCR sequence-specific oligonucleotide (PCR-SSO) method. An initial GWAS screen displayed a strong HLA class II region signal. The HLA-DRB1*15 haplotype was strongly negatively associated to JCV sero-status in Scandinavian MS cases (OR = 0.42, p = 7×10−15) and controls (OR = 0.53, p = 2×10−5). In contrast, the DQB1*06:03 haplotype was positively associated with JCV sero-status, in Scandinavian MS cases (OR = 1.63, p = 0.006), and controls (OR = 2.69, p = 1×10−5). The German dataset confirmed these findings (OR = 0.54, p = 1×10−4 and OR = 1.58, p = 0.03 respectively for these haplotypes). HLA class II restricted immune responses, and hence CD4+ T cell immunity is pivotal for JCV infection control. Alleles within the HLA-DR1*15 haplotype are associated with a protective effect on JCV infection. Alleles within the DQB1*06:03 haplotype show an opposite association. These associations between JC virus antibody response and human leucocyte antigens supports the notion that CD4+ T cells are crucial in the immune defence to JCV and lays the ground for risk stratification for PML and development of therapy and prevention. JC virus infection can lead to progressive multifocal leukoencephalopathy in individuals with a compromised immune system, such as during HIV infections or when treated with immunosuppressive or immunomodulating therapies. Progressive multifocal leukoencephalopathy is a rare but potentially fatal disease characterized by progressive damage of the brain white matter at multiple locations. It is therefore of importance to understand the host genetic control of response to JC virus in order to identify patients that can be treated with immunomodulating therapies, common treatments for autoimmune diseases, without increased risk for progressive multifocal leukoencephalopathy. This may also lead to development of preventative or curative anti-JC virus therapies. We here identify genetic variants being associated with JC virus antibody development; a negative association with the human leucocyte antigen DRB1*15-DQA1*01:02-DQB1*06:02 haplotype and a positive association with the DRB1*13-DQA1*01:03-DQB1*06:03 haplotype among controls and patients with multiple sclerosis from Scandinavia. We confirmed the associations in patients with multiple sclerosis from Germany. These associations between JC virus antibody response and human leucocyte antigens imply that CD4+ T cells are crucial in the immune defence and lay the ground for development of therapy and prevention.
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Affiliation(s)
- Emilie Sundqvist
- Neuroimmunology Unit, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Dorothea Buck
- Department of Neurology, Technische Universität München, Munich, Germany
| | - Clemens Warnke
- The Multiple Sclerosis Research Group, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Eva Albrecht
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Mohsen Khademi
- Neuroimmunology Unit, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Izaura Lima Bomfim
- Neuroimmunology Unit, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Anna Fogdell-Hahn
- The Multiple Sclerosis Research Group, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Jenny Link
- The Multiple Sclerosis Research Group, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Lars Alfredsson
- Institute for Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Helle Bach Søndergaard
- Danish Multiple Sclerosis Center, Department of Neurology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Jan Hillert
- The Multiple Sclerosis Research Group, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | | | - Annette B. Oturai
- Danish Multiple Sclerosis Center, Department of Neurology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Bernhard Hemme
- Department of Neurology, Technische Universität München, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Ingrid Kockum
- Neuroimmunology Unit, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
| | - Tomas Olsson
- Neuroimmunology Unit, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
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31
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Pillai NE, Okada Y, Saw WY, Ong RTH, Wang X, Tantoso E, Xu W, Peterson TA, Bielawny T, Ali M, Tay KY, Poh WT, Tan LWL, Koo SH, Lim WY, Soong R, Wenk M, Raychaudhuri S, Little P, Plummer FA, Lee EJD, Chia KS, Luo M, De Bakker PIW, Teo YY. Predicting HLA alleles from high-resolution SNP data in three Southeast Asian populations. Hum Mol Genet 2014; 23:4443-51. [DOI: 10.1093/hmg/ddu149] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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32
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Genotyping of human leukocyte antigen (HLA) ancestral haplotypes as prognostic marker in cancer using PCR analysis. Methods Mol Biol 2014; 1102:353-66. [PMID: 24258987 DOI: 10.1007/978-1-62703-727-3_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The major histocompatibility complex (MHC) comprises a set of genes that are essential to immunity and surveillance against neoplastic transformation. MHC antigens not only regulate antitumor immune responses in experimental animal models but also directly correlate with survival and prognosis of patients with various types of cancers. Effective recognition of tumor cells by effector T cells may be affected by the genotype and the extent of expression of human leukocyte antigen (HLA)-peptide complexes. Therefore, MHC antigens may serve as potential biomarkers for prognosis and allow selection of cancer patients for specific therapy. We describe PCR-based method to determine the HLA genotype in healthy individuals and patients using blood and tumor tissue as DNA source.
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da Silva JS, Wowk PF, Poerner F, Santos PSC, Bicalho MDG. Absence of strong linkage disequilibrium between odorant receptor alleles and the major histocompatibility complex. Hum Immunol 2013; 74:1619-23. [DOI: 10.1016/j.humimm.2013.08.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 07/22/2013] [Accepted: 08/10/2013] [Indexed: 01/03/2023]
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Patel JS, Patel MM, Koringa PG, Shah TM, Patel AK, Tripathi AK, Mathew A, Rajapurkar MM, Joshi CG. Human leukocyte antigen alleles, genotypes and haplotypes frequencies in renal transplant donors and recipients from West Central India. INDIAN JOURNAL OF HUMAN GENETICS 2013; 19:219-32. [PMID: 24019626 PMCID: PMC3758731 DOI: 10.4103/0971-6866.116122] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
BACKGROUND: Human leukocyte antigen (HLA) is comprised of a highly polymorphic set of genes which determines the histocompatibility of organ transplantation. The present study was undertaken to identify HLA class I and class II allele, genotype and haplotype frequencies in renal transplant recipients and donors from West Central India. MATERIALS AND METHODS: HLA typing was carried out using Polymerase Chain Reaction-Sequence Specific Primer in 552 live related and unrelated renal transplant recipients and donors. RESULTS: The most frequent HLA class I and class II alleles and their frequencies in recipients were HLA-AFNx0101 (0.1685) and AFNx0102 (0.1649), HLA-BFNx0135 (0.1322), and HLA-DR beta 1 (DRB 1)FNx0115 (0.2192), whereas in donors, these were HLA-AFNx0102 (0.1848) and AFNx0101 (0.1667), HLA-BFNx0135 (0.1359), and HLA-DRB1FNx0115 (0.2409). The two-locus haplotype statistical analysis revealed HLA-AFNx0102-B61 as the most common haplotype with the frequency of 0.0487 and 0.0510 in recipients and donors, respectively. Further, among the three locus haplotypes HLA-AFNx0133-BFNx0144-DRB1FNx0107 and HLA-AFNx0102-BFNx0161-DRB1FNx0115 were the most common haplotypes with frequencies 0.0362 and 0.0326, respectively in recipients and 0.0236 and 0.0323, respectively in donors. Genotype frequency revealed a high prevalence of genotype HLA-AFNx0102/AFNx0124 in recipients (0.058) compared to donors (0.0109) whereas low prevalence of HLA-AFNx0101/AFNx0102 in recipients (0.0435) than in donors (0.0797). The phylogenetic and principal component analysis of HLA allele and haplotype frequency distribution revealed genetic similarities of various ethnic groups. Further, case control analysis provides preliminary evidence of association of HLA-A genotype (P < 0.05) with renal failure. CONCLUSION: This study will be helpful in suitable donor search besides providing valuable information for population genetics and HLA disease association analysis.
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Affiliation(s)
- Jaina S Patel
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, India
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Urayama KY, Chokkalingam AP, Metayer C, Hansen H, May S, Ramsay P, Wiemels JL, Wiencke JK, Trachtenberg E, Thompson P, Ishida Y, Brennan P, Jolly KW, Termuhlen AM, Taylor M, Barcellos LF, Buffler PA. SNP association mapping across the extended major histocompatibility complex and risk of B-cell precursor acute lymphoblastic leukemia in children. PLoS One 2013; 8:e72557. [PMID: 23991122 PMCID: PMC3749982 DOI: 10.1371/journal.pone.0072557] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 07/12/2013] [Indexed: 02/01/2023] Open
Abstract
The extended major histocompatibility complex (xMHC) is the most gene-dense region of the genome and harbors a disproportionately large number of genes involved in immune function. The postulated role of infection in the causation of childhood B-cell precursor acute lymphoblastic leukemia (BCP-ALL) suggests that the xMHC may make an important contribution to the risk of this disease. We conducted association mapping across an approximately 4 megabase region of the xMHC using a validated panel of single nucleotide polymorphisms (SNPs) in childhood BCP-ALL cases (n=567) enrolled in the Northern California Childhood Leukemia Study (NCCLS) compared with population controls (n=892). Logistic regression analyses of 1,145 SNPs, adjusted for age, sex, and Hispanic ethnicity indicated potential associations between several SNPs and childhood BCP-ALL. After accounting for multiple comparisons, one of these included a statistically significant increased risk associated with rs9296068 (OR=1.40, 95% CI=1.19-1.66, corrected p=0.036), located in proximity to HLA-DOA. Sliding window haplotype analysis identified an additional locus located in the extended class I region in proximity to TRIM27 tagged by a haplotype comprising rs1237485, rs3118361, and rs2032502 (corrected global p=0.046). Our findings suggest that susceptibility to childhood BCP-ALL is influenced by genetic variation within the xMHC and indicate at least two important regions for future evaluation.
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Affiliation(s)
- Kevin Y Urayama
- School of Public Health, University of California, Berkeley, Berkeley, California, USA.
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Genomic evolution and polymorphism: Segmental duplications and haplotypes at 108 regions on 21 chromosomes. Genomics 2013; 102:15-26. [DOI: 10.1016/j.ygeno.2013.02.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 02/13/2013] [Accepted: 02/27/2013] [Indexed: 11/21/2022]
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Fuerst D, Parmar S, Schumann C, Rüdiger S, Boeck S, Heinemann V, Kaechele V, Stiebel K, Paul T, Seufferlein T, Mytilineos J, Stingl JC. HLA polymorphisms influence the development of skin rash arising from treatment with EGF receptor inhibitors. Pharmacogenomics 2013; 13:1469-76. [PMID: 23057547 DOI: 10.2217/pgs.12.122] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM Development of a skin rash under treatment with EGF receptor (EGFR) inhibitors (EGFRIs) has been linked to a favorable prognosis in some studies, suggesting a possible immunological role for EGFRIs in addition to direct antagonistic downstream effects. The present study aimed to investigate whether particular HLA polymorphisms found in cancer patients treated with EGFRIs are associated with the development of skin rash and overall survival rates. PATIENTS & METHODS HLA typing was performed on 105 cancer patients and the development of skin rash was rated during the first 4 weeks of therapy with EGFRIs. RESULTS A significantly lower incidence of skin rash was found in patients carrying the HLA-A*02:01 or HLA-A*03:01 alleles (hazard ratio: 0.277; 95% CI: 0.121-0.634; p = 0.002 and hazard ratio: 0.292; 95% CI: 0.113-0.752; p = 0.011, respectively); however, no association with worse survival was seen. CONCLUSION The chances of developing a skin rash in patients treated with EGFRIs may be lower in patients that carry the HLA-A*02:01 or HLA-A*03:01 alleles, while the antitumor efficacy of EGFRIs does not seem to be significantly impaired in these patients.
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Affiliation(s)
- Daniel Fuerst
- German Red Cross Blood Transfusion Service, Baden-Wuerttemberg-Hessen, Ulm, Germany
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Kumar N, Kaur G, Tandon N, Kanga U, Mehra NK. Genomic evaluation of HLA-DR3+ haplotypes associated with type 1 diabetes. Ann N Y Acad Sci 2013; 1283:91-6. [PMID: 23387390 DOI: 10.1111/nyas.12019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We have defined three sets of HLA-DR3(+) haplotypes that provide maximum risk of type 1 disease development in Indians: (1) a diverse array of B8-DR3 haplotypes, (2) A33-B58-DR3 haplotype, and (3) A2-B50-DR3 occurring most predominantly in this population. Further analysis has revealed extensive diversity in B8-DR3 haplotypes, particularly at the HLA-A locus, in contrast to the single fixed HLA-A1-B8-DR3 haplotype (generally referred to as AH8.1) reported in Caucasians. However, the classical AH8.1 haplotype was rare and differed from the Caucasian counterpart at multiple loci. In our study, HLA-A26-B8-DR3 (AH8.2) was the most common B8-DR3 haplotype constituting >50% of the total B8-DR3 haplotypes. Further, A2-B8-DR3 contributed the maximum risk (RR = 48.7) of type 1 diabetes, followed by A2-B50-DR3 (RR = 9.4), A33-B58-DR3 (RR = 6.6), A24-B8-DR3 (RR = 4.5), and A26-B8-DR3 (RR = 4.2). Despite several differences, the disease-associated haplotypes in Indian and Caucasian populations share a frozen DR3-DQ2 block, suggesting a common ancestor from which multiple haplotypes evolved independently.
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Affiliation(s)
- Neeraj Kumar
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
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Kawashima M, Ohashi J, Nishida N, Tokunaga K. Evolutionary analysis of classical HLA class I and II genes suggests that recent positive selection acted on DPB1*04:01 in Japanese population. PLoS One 2012; 7:e46806. [PMID: 23056460 PMCID: PMC3463557 DOI: 10.1371/journal.pone.0046806] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 09/10/2012] [Indexed: 01/01/2023] Open
Abstract
The human leukocyte antigen (HLA) genes exhibit the highest degree of polymorphism in the human genome. This high degree of variation at classical HLA class I and class II loci has been maintained by balancing selection for a long evolutionary time. However, little is known about recent positive selection acting on specific HLA alleles in a local population. To detect the signature of recent positive selection, we genotyped six HLA loci, HLA-A, HLA-B, HLA-C, HLA-DRB1, HLA-DQB1, and HLA-DPB1 in 418 Japanese subjects, and then assessed the haplotype homozygosity (HH) of each HLA allele. There were 120 HLA alleles across the six loci. Among the 80 HLA alleles with frequencies of more than 1%, DPB1*04∶01, which had a frequency of 6.1%, showed exceptionally high HH (0.53). This finding raises the possibility that recent positive selection has acted on DPB1*04∶01. The DPB1*04∶01 allele, which was present in the most common 6-locus HLA haplotype (4.4%), A*33∶03-C*14∶03-B*44∶03-DRB1*13∶02-DQB1*06∶04-DPB1*04∶01, seems to have flowed from the Korean peninsula to the Japanese archipelago in the Yayoi period. A stochastic simulation approach indicated that the strong linkage disequilibrium between DQB1*06∶04 and DPB1*04∶01 observed in Japanese cannot be explained without positive selection favoring DPB1*04∶01. The selection coefficient of DPB1*04∶01 was estimated as 0.041 (95% credible interval 0.021–0.077). Our results suggest that DPB1*04∶01 has recently undergone strong positive selection in Japanese population.
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Affiliation(s)
- Minae Kawashima
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- * E-mail: (MK); (JO)
| | - Jun Ohashi
- Molecular and Genetic Epidemiology, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
- * E-mail: (MK); (JO)
| | - Nao Nishida
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa, Chiba, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Baker PR, Nanduri P, Gottlieb PA, Yu L, Klingensmith GJ, Eisenbarth GS, Barker JM. Predicting the onset of Addison's disease: ACTH, renin, cortisol and 21-hydroxylase autoantibodies. Clin Endocrinol (Oxf) 2012; 76:617-24. [PMID: 22066755 PMCID: PMC4963152 DOI: 10.1111/j.1365-2265.2011.04276.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
CONTEXT Autoantibodies to 21-hydroxylase (21OH-AA) precede onset of autoimmune Addison's disease (AD). Progression to AD can take months to years, and early detection of metabolic decompensation may prevent morbidity and mortality. OBJECTIVE To define optimal methods of predicting progression to overt AD (defined by subnormal peak cortisol response to Cosyntropin) in 21OH-AA+ individuals. DESIGN, SETTING AND PARTICIPANTS Individuals were screened for 21OH-AA at the Barbara Davis Center from 1993 to 2011. Subjects positive for 21OH-AA (n = 87) were tested, and the majority prospectively followed for the development of Addison's disease, including seven diagnosed with AD upon 21OH-AA discovery (discovered), seven who progressed to AD (progressors) and 73 nonprogressors. MAIN OUTCOME MEASURED Plasma renin activity (PRA), ACTH, baseline cortisol, peak cortisol and 21OH-AA were measured at various time points relative to diagnosis of AD or last AD-free follow-up. RESULTS Compared with nonprogressors, in the time period 2 months-2 years prior to the onset of AD, progressors were significantly more likely to have elevated ACTH (11-22 pM, P < 1E-4), with no significant differences in mean PRA (P = 0·07) or baseline cortisol (P = 0·08), and significant but less distinct differences seen with 21OH-AA levels (P < 1E-4) and poststimulation cortisol levels (P = 6E-3). CONCLUSION Moderately elevated ACTH is a more useful early indicator of impending AD than 21OH-AA, PRA or peak cortisol, in the 2 months-2 years preceding the onset of AD.
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Affiliation(s)
- Peter R. Baker
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Aurora, CO, USA
| | - Priyaanka Nanduri
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Aurora, CO, USA
| | - Peter A. Gottlieb
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Aurora, CO, USA
| | - Liping Yu
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Aurora, CO, USA
| | | | - George S. Eisenbarth
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Aurora, CO, USA
| | - Jennifer M. Barker
- Department of Pediatric Endocrinology, University of Colorado Denver, Aurora, CO, USA
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Keller MC, Simonson MA, Ripke S, Neale BM, Gejman PV, Howrigan DP, Lee SH, Lencz T, Levinson DF, Sullivan PF. Runs of homozygosity implicate autozygosity as a schizophrenia risk factor. PLoS Genet 2012; 8:e1002656. [PMID: 22511889 PMCID: PMC3325203 DOI: 10.1371/journal.pgen.1002656] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Accepted: 02/27/2012] [Indexed: 11/19/2022] Open
Abstract
Autozygosity occurs when two chromosomal segments that are identical from a common ancestor are inherited from each parent. This occurs at high rates in the offspring of mates who are closely related (inbreeding), but also occurs at lower levels among the offspring of distantly related mates. Here, we use runs of homozygosity in genome-wide SNP data to estimate the proportion of the autosome that exists in autozygous tracts in 9,388 cases with schizophrenia and 12,456 controls. We estimate that the odds of schizophrenia increase by ~17% for every 1% increase in genome-wide autozygosity. This association is not due to one or a few regions, but results from many autozygous segments spread throughout the genome, and is consistent with a role for multiple recessive or partially recessive alleles in the etiology of schizophrenia. Such a bias towards recessivity suggests that alleles that increase the risk of schizophrenia have been selected against over evolutionary time.
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Affiliation(s)
- Matthew C Keller
- Department of Psychology and Neuroscience, University of Colorado at Boulder, Boulder, Colorado, United States of America.
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Baschal EE, Jasinski JM, Boyle TA, Fain PR, Eisenbarth GS, Siebert JC. Congruence as a measurement of extended haplotype structure across the genome. J Transl Med 2012; 10:32. [PMID: 22369243 PMCID: PMC3310717 DOI: 10.1186/1479-5876-10-32] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 02/27/2012] [Indexed: 02/01/2023] Open
Abstract
Background Historically, extended haplotypes have been defined using only a few data points, such as alleles for several HLA genes in the MHC. High-density SNP data, and the increasing affordability of whole genome SNP typing, creates the opportunity to define higher resolution extended haplotypes. This drives the need for new tools that support quantification and visualization of extended haplotypes as defined by as many as 2000 SNPs. Confronted with high-density SNP data across the major histocompatibility complex (MHC) for 2,300 complete families, compiled by the Type 1 Diabetes Genetics Consortium (T1DGC), we developed software for studying extended haplotypes. Methods The software, called ExHap (Extended Haplotype), uses a similarity measurement we term congruence to identify and quantify long-range allele identity. Using ExHap, we analyzed congruence in both the T1DGC data and family-phased data from the International HapMap Project. Results Congruent chromosomes from the T1DGC data have between 96.5% and 99.9% allele identity over 1,818 SNPs spanning 2.64 megabases of the MHC (HLA-DRB1 to HLA-A). Thirty-three of 132 DQ-DR-B-A defined haplotype groups have > 50% congruent chromosomes in this region. For example, 92% of chromosomes within the DR3-B8-A1 haplotype are congruent from HLA-DRB1 to HLA-A (99.8% allele identity). We also applied ExHap to all 22 autosomes for both CEU and YRI cohorts from the International HapMap Project, identifying multiple candidate extended haplotypes. Conclusions Long-range congruence is not unique to the MHC region. Patterns of allele identity on phased chromosomes provide a simple, straightforward approach to visually and quantitatively inspect complex long-range structural patterns in the genome. Such patterns aid the biologist in appreciating genetic similarities and differences across cohorts, and can lead to hypothesis generation for subsequent studies.
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Affiliation(s)
- Erin E Baschal
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Denver, CO 80045, USA
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Abstract
Type 1 diabetes mellitus (T1DM) is an autoimmune disease affecting approximately one in 300 individuals in the United States. The majority of genetic research to date has focused on the heritability that predisposes to islet autoimmunity and T1DM. The evidence so far points to T1DM being a polygenic, common, complex disease with major susceptibility lying in the major histocompatibility complex (MHC) on chromosome 6 with other smaller effects seen in loci outside of the MHC. With recent advances in technology, novel means of exploring the human genome have given way to new information in the development of T1DM. The newest technologies, namely high-throughput polymorphism typing and sequencing, have led to a paradigm shift in studying common diseases such as T1DM. In this review we highlight the advances in genetic associations in T1DM in the last several decades and how they have led to a better understanding of T1DM pathogenesis.
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Affiliation(s)
- Peter R Baker
- The Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Aurora, CO 80045-6511, USA
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Williamson JF, McLure CA, Guymer RH, Baird PN, Millman J, Cantsilieris S, Dawkins RL. Almost total protection from age-related macular degeneration by haplotypes of the Regulators of Complement Activation. Genomics 2011; 98:412-21. [PMID: 21855625 DOI: 10.1016/j.ygeno.2011.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Revised: 07/25/2011] [Accepted: 08/01/2011] [Indexed: 11/16/2022]
Abstract
Age-related macular degeneration (AMD) is the leading cause of blindness in developed countries. It has been proposed that the polymorphism encoding Y402H (T1277C) in the complement factor H gene (CFH) is one of the main determinants of disease. We genotyped the polymorphism at a number of loci in the region encompassing the Regulators of Complement Activation (RCA) on chromosome 1, including T1277C SNP, in 187 patients and 146 controls. Haplotypes have been classified as protective (P) or susceptible (S) with respect to AMD. This included the identification of an S haplotype with a T at 1277. The results show that no single locus should be assumed to be directly responsible for AMD, but rather argue for the existence of RCA haplotypes, which can be assigned meaningful predictive values for AMD. We conclude that the critical sequences are within a region 450 kb centromeric to 128 kb telomeric of CFH.
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Affiliation(s)
- Joseph F Williamson
- C.Y. O'Connor ERADE Village Foundation, Canning Vale, Western Australia, Australia
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Baschal EE, Baker PR, Eyring KR, Siebert JC, Jasinski JM, Eisenbarth GS. The HLA-B 3906 allele imparts a high risk of diabetes only on specific HLA-DR/DQ haplotypes. Diabetologia 2011; 54:1702-9. [PMID: 21533899 PMCID: PMC3110277 DOI: 10.1007/s00125-011-2161-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Accepted: 03/29/2011] [Indexed: 12/05/2022]
Abstract
AIMS/HYPOTHESIS We investigated the risk associated with HLA-B*39 alleles in the context of specific HLA-DR/DQ haplotypes. METHODS We studied a readily available dataset from the Type 1 Diabetes Genetics Consortium that consists of 2,300 affected sibling pair families genotyped for both HLA alleles and 2,837 single nucleotide polymorphisms across the major histocompatibility complex region. RESULTS The B*3906 allele significantly enhanced the risk of type 1 diabetes when present on specific HLA-DR/DQ haplotypes (DRB1 0801-DQB1 0402: p = 1.6 × 10(-6), OR 25.4; DRB1 0101-DQB1 0501: p = 4.9 × 10(-5), OR 10.3) but did not enhance the risk of DRB1 0401-DQB1 0302 haplotypes. In addition, the B 3901 allele enhanced risk on the DRB1 1601-DQB1 0502 haplotype (p = 3.7 × 10(-3), OR 7.2). CONCLUSIONS/INTERPRETATION These associations indicate that the B 39 alleles significantly increase risk when present on specific HLA-DR/DQ haplotypes, and HLA-B typing in concert with specific HLA-DR/DQ genotypes should facilitate genetic prediction of type 1 diabetes, particularly in a research setting.
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Affiliation(s)
- E. E. Baschal
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, 1775 Aurora Ct, Box B140, Aurora, CO 80045-6511 USA
| | - P. R. Baker
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, 1775 Aurora Ct, Box B140, Aurora, CO 80045-6511 USA
| | - K. R. Eyring
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, 1775 Aurora Ct, Box B140, Aurora, CO 80045-6511 USA
| | | | - J. M. Jasinski
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, 1775 Aurora Ct, Box B140, Aurora, CO 80045-6511 USA
| | - G. S. Eisenbarth
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, 1775 Aurora Ct, Box B140, Aurora, CO 80045-6511 USA
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Baker PR, Baschal EE, Fain PR, Nanduri P, Triolo TM, Siebert JC, Armstrong TK, Babu SR, Rewers MJ, Gottlieb PA, Barker JM, Eisenbarth GS. Dominant suppression of Addison's disease associated with HLA-B15. J Clin Endocrinol Metab 2011; 96:2154-62. [PMID: 21565792 PMCID: PMC3135206 DOI: 10.1210/jc.2010-2964] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CONTEXT Autoimmune Addison's disease (AD) is the major cause of primary adrenal failure in developed nations. Autoantibodies to 21-hydroxylase (21OH-AA) are associated with increased risk of progression to AD. Highest genetic risk is associated with the Major Histocompatibility region (MHC), specifically human leukocyte antigen (HLA)-DR3 haplotypes (containing HLA-B8) and HLA-DR4. OBJECTIVE The objective of the study was the further characterization of AD risk associated with MHC alleles. DESIGN, SETTING, AND PARTICIPANTS MHC genotypes were determined for HLA-DRB1, DQA1, DQB1, MICA, HLA-B, and HLA-A in 168 total individuals with 21OH-AA (85 with AD at referral and 83 with positive 21OH-AA but without AD at referral). MAIN OUTCOME MEASURE(S) Genotype was evaluated in 21OH-AA-positive individuals. Outcomes were compared with general population controls and type 1 diabetes patients. RESULTS In HLA-DR4+ individuals, HLA-B15 was found in only one of 55 (2%) with AD vs. 24 of 63 (40%) 21OH-AA-positive nonprogressors (P = 2 × 10(-7)) and 518 of 1558 (33%) HLA-DR4 patients with type 1 diabetes (P = 1 × 10(-8)). On prospective follow-up, none of the HLA-B15-positive, 21-hydroxylase-positive individuals progressed to AD vs. 25% non-HLA-B15 autoantibody-positive individuals by life table analysis (P = 0.03). Single nucleotide polymorphism analysis revealed the HLA-DR/DQ region associated with risk and HLA-B15 were separated by multiple intervening single-nucleotide polymorphism haplotypes. CONCLUSIONS HLA-B15 is not associated with protection from 21OH-AA formation but is associated with protection from progression to AD in 21OH-AA-positive individuals. To our knowledge, this is one of the most dramatic examples of genetic disease suppression in individuals who already have developed autoantibodies and of novel dominant suppression of an autoimmune disease by a class I HLA allele.
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Affiliation(s)
- Peter R Baker
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Aurora, Colorado 80045-6511, USA
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Williamson JF, Steele EJ, Lester S, Kalai O, Millman JA, Wolrige L, Bayard D, McLure C, Dawkins RL. Genomic evolution in domestic cattle: ancestral haplotypes and healthy beef. Genomics 2011; 97:304-12. [PMID: 21338665 DOI: 10.1016/j.ygeno.2011.02.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Revised: 02/07/2011] [Accepted: 02/09/2011] [Indexed: 11/25/2022]
Abstract
We have identified numerous Ancestral Haplotypes encoding a 14-Mb region of Bota C19. Three are frequent in Simmental, Angus and Wagyu and have been conserved since common progenitor populations. Others are more relevant to the differences between these 3 breeds including fat content and distribution in muscle. SREBF1 and Growth Hormone, which have been implicated in the production of healthy beef, are included within these haplotypes. However, we conclude that alleles at these 2 loci are less important than other sequences within the haplotypes. Identification of breeds and hybrids is improved by using haplotypes rather than individual alleles.
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Affiliation(s)
- Joseph F Williamson
- C.Y. O'Connor ERADE Village Foundation, Canning Vale, Western Australia, Australia
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Conditional meta-analysis stratifying on detailed HLA genotypes identifies a novel type 1 diabetes locus around TCF19 in the MHC. Hum Genet 2010; 129:161-76. [PMID: 21076979 PMCID: PMC3020293 DOI: 10.1007/s00439-010-0908-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Accepted: 10/26/2010] [Indexed: 10/25/2022]
Abstract
The human leukocyte antigen (HLA) class II genes HLA-DRB1, -DQA1 and -DQB1 are the strongest genetic factors for type 1 diabetes (T1D). Additional loci in the major histocompatibility complex (MHC) are difficult to identify due to the region's high gene density and complex linkage disequilibrium (LD). To facilitate the association analysis, two novel algorithms were implemented in this study: one for phasing the multi-allelic HLA genotypes in trio families, and one for partitioning the HLA strata in conditional testing. Screening and replication were performed on two large and independent datasets: the Wellcome Trust Case-Control Consortium (WTCCC) dataset of 2,000 cases and 1,504 controls, and the T1D Genetics Consortium (T1DGC) dataset of 2,300 nuclear families. After imputation, the two datasets have 1,941 common SNPs in the MHC, of which 22 were successfully tested and replicated based on the statistical testing stratifying on the detailed DRB1 and DQB1 genotypes. Further conditional tests using the combined dataset confirmed eight novel SNP associations around 31.3 Mb on chromosome 6 (rs3094663, p = 1.66 × 10(-11) and rs2523619, p = 2.77 × 10(-10) conditional on the DR/DQ genotypes). A subsequent LD analysis established TCF19, POU5F1, CCHCR1 and PSORS1C1 as potential causal genes for the observed association.
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Lind C, Ferriola D, Mackiewicz K, Heron S, Rogers M, Slavich L, Walker R, Hsiao T, McLaughlin L, D'Arcy M, Gai X, Goodridge D, Sayer D, Monos D. Next-generation sequencing: the solution for high-resolution, unambiguous human leukocyte antigen typing. Hum Immunol 2010; 71:1033-42. [DOI: 10.1016/j.humimm.2010.06.016] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 06/15/2010] [Accepted: 06/22/2010] [Indexed: 11/16/2022]
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Baker PR, Baschal EE, Fain PR, Triolo TM, Nanduri P, Siebert JC, Armstrong TK, Babu SR, Rewers MJ, Gottlieb PA, Barker JM, Eisenbarth GS. Haplotype analysis discriminates genetic risk for DR3-associated endocrine autoimmunity and helps define extreme risk for Addison's disease. J Clin Endocrinol Metab 2010; 95:E263-70. [PMID: 20631027 PMCID: PMC3050098 DOI: 10.1210/jc.2010-0508] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CONTEXT Multiple autoimmune disorders (e.g. Addison's disease, type 1 diabetes, celiac disease) are associated with HLA-DR3, but it is likely that alleles of additional genes in linkage disequilibrium with HLA-DRB1 contribute to disease. OBJECTIVE The objective of the study was to characterize major histocompatability complex (MHC) haplotypes conferring extreme risk for autoimmune Addison's disease (AD). DESIGN, SETTING, AND PARTICIPANTS Eighty-six 21-hydroxylase autoantibody-positive, nonautoimmune polyendocrine syndrome type 1, Caucasian individuals collected from 1992 to 2009 with clinical AD from 68 families (12 multiplex and 56 simplex) were genotyped for HLA-DRB1, HLA-DQB1, MICA, HLA-B, and HLA-A as well as high density MHC single-nucleotide polymorphism (SNP) analysis for 34. MAIN OUTCOME MEASURES AD and genotype were measured. RESULT Ninety-seven percent of the multiplex individuals had both HLA-DR3 and HLA-B8 vs. 60% of simplex AD patients (P = 9.72 × 10(-4)) and 13% of general population controls (P = 3.00 × 10(-19)). The genotype DR3/DR4 with B8 was present in 85% of AD multiplex patients, 24% of simplex patients, and 1.5% of control individuals (P = 4.92 × 10(-191)). The DR3-B8 haplotype of AD patients had HLA-A1 less often (47%) than controls (81%, P = 7.00 × 10(-5)) and type 1 diabetes patients (73%, P = 1.93 × 10(-3)). Analysis of 1228 SNPs across the MHC for individuals with AD revealed a shorter conserved haplotype (3.8) with the loss of the extended conserved 3.8.1 haplotype approximately halfway between HLA-B and HLA-A. CONCLUSION Extreme risk for AD, especially in multiplex families, is associated with haplotypic DR3 variants, in particular a portion (3.8) but not all of the conserved 3.8.1 haplotype.
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Affiliation(s)
- Peter R Baker
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Aurora, Colorado 80045-6511, USA
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