1
|
Henriksen EKK, Viken MK, Wittig M, Holm K, Folseraas T, Mucha S, Melum E, Hov JR, Lazaridis KN, Juran BD, Chazouillères O, Färkkilä M, Gotthardt DN, Invernizzi P, Carbone M, Hirschfield GM, Rushbrook SM, Goode E, Ponsioen CY, Weersma RK, Eksteen B, Yimam KK, Gordon SC, Goldberg D, Yu L, Bowlus CL, Franke A, Lie BA, Karlsen TH. HLA haplotypes in primary sclerosing cholangitis patients of admixed and non-European ancestry. HLA 2017; 90:228-233. [PMID: 28695657 DOI: 10.1111/tan.13076] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Revised: 05/26/2017] [Accepted: 06/12/2017] [Indexed: 12/19/2022]
Abstract
Primary sclerosing cholangitis (PSC) is strongly associated with several human leukocyte antigen (HLA) haplotypes. Due to extensive linkage disequilibrium and multiple polymorphic candidate genes in the HLA complex, identifying the alleles responsible for these associations has proven difficult. We aimed to evaluate whether studying populations of admixed or non-European descent could help in defining the causative HLA alleles. When assessing haplotypes carrying HLA-DRB1*13:01 (hypothesized to specifically increase the susceptibility to chronic cholangitis), we observed that every haplotype in the Scandinavian PSC population carried HLA-DQB1*06:03. In contrast, only 65% of HLA-DRB1*13:01 haplotypes in an admixed/non-European PSC population carried this allele, suggesting that further assessments of the PSC-associated haplotype HLA-DRB1*13:01-DQA1*01:03-DQB1*06:03 in admixed or multi-ethnic populations could aid in identifying the causative allele.
Collapse
Affiliation(s)
- E K K Henriksen
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Research Institute of Internal Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway.,K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - M K Viken
- K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Immunology, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - M Wittig
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - K Holm
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Research Institute of Internal Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway.,K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - T Folseraas
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Research Institute of Internal Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway.,K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Section of Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - S Mucha
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - E Melum
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Research Institute of Internal Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway.,K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Section of Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - J R Hov
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Research Institute of Internal Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway.,K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Section of Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - K N Lazaridis
- Center for Basic Research in Digestive Diseases, Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - B D Juran
- Center for Basic Research in Digestive Diseases, Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - O Chazouillères
- Hôpital Saint-Antoine, Service d'Hépatologie, INSERM, UMR_S 938, CDR Saint-Antoine, and Sorbonne Universités, UPMC Univ Paris 06, Paris, France
| | - M Färkkilä
- Helsinki University and Clinic of Gastroenterology, Helsinki University Hospital, Helsinki, Finland
| | - D N Gotthardt
- Department of Gastroenterology, Infectious Diseases and Intoxications, University Hospital of Heidelberg, Heidelberg, Germany
| | - P Invernizzi
- Program for Autoimmune Liver Diseases, International Center for Digestive Health, Department of Medicine and Surgery, University of Milan-Bicocca, Milan, Italy
| | - M Carbone
- Program for Autoimmune Liver Diseases, International Center for Digestive Health, Department of Medicine and Surgery, University of Milan-Bicocca, Milan, Italy
| | - G M Hirschfield
- Centre for Liver Research and NIHR Birmingham Liver Biomedical Research Unit, Institute of Biomedical Research, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - S M Rushbrook
- The Department of Gastroenterology, Norfolk and Norwich University Hospitals NHS Foundation Trust, Norfolk, UK
| | - E Goode
- Wellcome Trust Sanger Institute, Hinxton and Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | | | - C Y Ponsioen
- Department of Gastroenterology and Hepatology, Academic Medical Center, Amsterdam, the Netherlands
| | - R K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - B Eksteen
- Snyder Institute for Chronic Diseases, Division of Gastroenterology, University of Calgary, Calgary, Canada
| | - K K Yimam
- Division of Hepatology and Liver Transplantation, California Pacific Medical Center, San Francisco, California
| | - S C Gordon
- Division of Gastroenterology and Hepatology, Henry Ford Health System, Detroit, Michigan
| | - D Goldberg
- Division of Gastroenterology, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - L Yu
- Department of Medicine, University of Washington, Seattle, Washington
| | - C L Bowlus
- Division of Gastroenterology and Hepatology, University of California Davis School of Medicine, Sacramento, California
| | - A Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - B A Lie
- K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Immunology, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Department of Medical Genetics, University of Oslo and Oslo University Hospital Ullevål, Oslo, Norway
| | - T H Karlsen
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Research Institute of Internal Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway.,K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Section of Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
| |
Collapse
|
2
|
Refinement of the MHC risk map in a scandinavian primary sclerosing cholangitis population. PLoS One 2014; 9:e114486. [PMID: 25521205 PMCID: PMC4270690 DOI: 10.1371/journal.pone.0114486] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 11/09/2014] [Indexed: 11/29/2022] Open
Abstract
Background Genetic variants within the major histocompatibility complex (MHC) represent the strongest genetic susceptibility factors for primary sclerosing cholangitis (PSC). Identifying the causal variants within this genetic complex represents a major challenge due to strong linkage disequilibrium and an overall high physical density of candidate variants. We aimed to refine the MHC association in a geographically restricted PSC patient panel. Methodology/Principal Findings A total of 365 PSC cases and 368 healthy controls of Scandinavian ancestry were included in the study. We incorporated data from HLA typing (HLA-A, -B, -C, -DRB3, -DRB1, -DQB1) and single nucleotide polymorphisms across the MHC (n = 18,644; genotyped and imputed) alongside previously suggested PSC risk determinants in the MHC, i.e. amino acid variation of DRβ, a MICA microsatellite polymorphism and HLA-C and HLA-B according to their ligand properties for killer immunoglobulin-like receptors. Breakdowns of the association signal by unconditional and conditional logistic regression analyses demarcated multiple PSC associated MHC haplotypes, and for eight of these classical HLA class I and II alleles represented the strongest association. A novel independent risk locus was detected near NOTCH4 in the HLA class III region, tagged by rs116212904 (odds ratio [95% confidence interval] = 2.32 [1.80, 3.00], P = 1.35×10−11). Conclusions/Significance Our study shows that classical HLA class I and II alleles, predominantly at HLA-B and HLA-DRB1, are the main risk factors for PSC in the MHC. In addition, the present assessments demonstrated for the first time an association near NOTCH4 in the HLA class III region.
Collapse
|
3
|
Folseraas T, Melum E, Franke A, Karlsen TH. Genetics in primary sclerosing cholangitis. Best Pract Res Clin Gastroenterol 2011; 25:713-26. [PMID: 22117637 DOI: 10.1016/j.bpg.2011.09.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2011] [Accepted: 09/30/2011] [Indexed: 01/31/2023]
Abstract
Primary sclerosing cholangitis (PSC) is a chronic and severe inflammatory disease leading to fibrotic bile duct destruction and in most cases liver cirrhosis. As in other complex genetic diseases, the sibling risk of PSC is more than ten times that of the general population. Recent genome-wide association studies have consistently identified several genetic susceptibility loci. The overlap of these loci with susceptibility loci in other chronic inflammatory diseases is considerable, and offers intriguing opportunities for transfer of pathogenetic knowledge and potentially treatment options. In the present article we summarise the present knowledge on PSC genetics with a particular emphasis on the major histocompatibility complex (MHC). We discuss the clinical relevance of the risk loci and elaborate on the insight that may be obtained from associated inflammatory conditions and existing murine knock-out models.
Collapse
Affiliation(s)
- Trine Folseraas
- Norwegian PSC Research Center, Clinic for Specialized Medicine and Surgery, Oslo University Hospital, Rikshospitalet, 0027 Oslo, Norway
| | | | | | | |
Collapse
|
4
|
Hov JR, Kosmoliaptsis V, Traherne JA, Olsson M, Boberg KM, Bergquist A, Schrumpf E, Bradley JA, Taylor CJ, Lie BA, Trowsdale J, Karlsen TH. Electrostatic modifications of the human leukocyte antigen-DR P9 peptide-binding pocket and susceptibility to primary sclerosing cholangitis. Hepatology 2011; 53:1967-76. [PMID: 21413052 PMCID: PMC3128712 DOI: 10.1002/hep.24299] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Accepted: 03/07/2010] [Indexed: 12/29/2022]
Abstract
UNLABELLED The strongest genetic risk factors for primary sclerosing cholangitis (PSC) are found in the human leukocyte antigen (HLA) complex at chromosome 6p21. Genes in the HLA class II region encode molecules that present antigen to T lymphocytes. Polymorphisms in these genes are associated with most autoimmune diseases, most likely because they contribute to the specificity of immune responses. The aim of this study was to analyze the structure and electrostatic properties of the peptide-binding groove of HLA-DR in relation to PSC. Thus, four-digit resolution HLA-DRB1 genotyping was performed in 356 PSC patients and 366 healthy controls. Sequence information was used to assign which amino acids were encoded at all polymorphic positions. In stepwise logistic regressions, variations at residues 37 and 86 were independently associated with PSC (P = 1.2 × 10(-32) and P = 1.8 × 10(-22) in single-residue models, respectively). Three-dimensional modeling was performed to explore the effect of these key residues on the HLA-DR molecule. This analysis indicated that residue 37 was a major determinant of the electrostatic properties of pocket P9 of the peptide-binding groove. Asparagine at residue 37, which was associated with PSC, induced a positive charge in pocket P9. Tyrosine, which protected against PSC, induced a negative charge in this pocket. Consistent with the statistical observations, variation at residue 86 also indirectly influenced the electrostatic properties of this pocket. DRB1*13:01, which was PSC-associated, had a positive P9 pocket and DRB1*13:02, protective against PSC, had a negative P9 pocket. CONCLUSION The results suggest that in patients with PSC, residues 37 and 86 of the HLA-DRβ chain critically influence the electrostatic properties of pocket P9 and thereby the range of peptides presented.
Collapse
Affiliation(s)
- Johannes R Hov
- Norwegian PSC Research Center, Clinic for Specialized Medicine and Surgery, Oslo University Hospital RikshospitaletOslo, Norway,Research Institute for Internal Medicine, Oslo University Hospital RikshospitaletOslo, Norway,Institute of Immunology, Oslo University HospitalOslo, Norway,Faculty of Medicine, University of OsloOslo, Norway
| | - Vasilis Kosmoliaptsis
- Tissue Typing Laboratory, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's HospitalCambridge, United Kingdom,Department of Surgery, University of Cambridge, Addenbrooke's HospitalCambridge, United Kingdom
| | - James A Traherne
- Division of Immunology, Department of Pathology, University of Cambridge and Cambridge Institute for Medical Research, University of CambridgeCambridge, United Kingdom
| | - Marita Olsson
- Mathematical Sciences, Chalmers University of TechnologyGothenburg, Sweden
| | - Kirsten M Boberg
- Norwegian PSC Research Center, Clinic for Specialized Medicine and Surgery, Oslo University Hospital RikshospitaletOslo, Norway
| | - Annika Bergquist
- Department of Gastroenterology and Hepatology, Karolinska University HospitalHuddinge, Stockholm, Sweden
| | - Erik Schrumpf
- Norwegian PSC Research Center, Clinic for Specialized Medicine and Surgery, Oslo University Hospital RikshospitaletOslo, Norway,Faculty of Medicine, University of OsloOslo, Norway
| | - J Andrew Bradley
- Department of Surgery, University of Cambridge, Addenbrooke's HospitalCambridge, United Kingdom
| | - Craig J Taylor
- Tissue Typing Laboratory, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's HospitalCambridge, United Kingdom
| | - Benedicte A Lie
- Institute of Immunology, Oslo University HospitalOslo, Norway
| | - John Trowsdale
- Division of Immunology, Department of Pathology, University of Cambridge and Cambridge Institute for Medical Research, University of CambridgeCambridge, United Kingdom
| | - Tom H Karlsen
- Norwegian PSC Research Center, Clinic for Specialized Medicine and Surgery, Oslo University Hospital RikshospitaletOslo, Norway
| |
Collapse
|
5
|
Butler MO, Ansén S, Tanaka M, Imataki O, Berezovskaya A, Mooney MM, Metzler G, Milstein MI, Nadler LM, Hirano N. A panel of human cell-based artificial APC enables the expansion of long-lived antigen-specific CD4+ T cells restricted by prevalent HLA-DR alleles. Int Immunol 2010; 22:863-73. [PMID: 21059769 DOI: 10.1093/intimm/dxq440] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Many preclinical experiments have attested to the critical role of CD4(+) T cell help in CD8(+) cytotoxic T lymphocyte (CTL)-mediated immunity. Recent clinical trials have demonstrated that reinfusion of CD4(+) T cells can induce responses in infectious diseases and cancer. However, few standardized and versatile systems exist to expand antigen-specific CD4(+) T(h) for clinical use. K562 is a human erythroleukemic cell line, which lacks expression of HLA class I and class II, invariant chain and HLA-DM but expresses adhesion molecules such as intercellular adhesion molecule-1 and leukocyte function-associated antigen-3. With this unique immunologic phenotype, K562 has been tested in clinical trials of cancer immunotherapy. Previously, we created a K562-based artificial antigen-presenting cell (aAPC) that generates ex vivo long-lived HLA-A2-restricted CD8(+) CTL with a central/effector memory phenotype armed with potent effector function. We successfully generated a clinical version of this aAPC and conducted a clinical trial where large numbers of anti-tumor CTL are reinfused to cancer patients. In this article, we shifted focus to CD4(+) T cells and developed a panel of novel K562-derived aAPC, where each expresses a different single HLA-DR allele, invariant chain, HLA-DM, CD80, CD83 and CD64; takes up soluble protein by endocytosis and processes and presents CD4(+) T-cell peptides. Using this aAPC, we were able to determine novel DR-restricted CD4(+) T-cell epitopes and expand long-lived CD4(+) T-cells specific for multiple antigens without growing bystander Foxp3(+) regulatory T cells. Our results suggest that K562-based aAPC may serve as a translatable platform to generate both antigen-specific CD8(+) CTL and CD4(+) T(h).
Collapse
Affiliation(s)
- Marcus O Butler
- Department of Medical Oncology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Bowlus CL, Li CS, Karlsen TH, Lie BA, Selmi C. Primary sclerosing cholangitis in genetically diverse populations listed for liver transplantation: unique clinical and human leukocyte antigen associations. Liver Transpl 2010; 16:1324-30. [PMID: 21031548 PMCID: PMC2967453 DOI: 10.1002/lt.22161] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Primary sclerosing cholangitis (PSC) is well characterized in European populations. We aimed to characterize clinical characteristics and human leukocyte antigen (HLA) associations in a population of European American, Hispanic, and African American PSC patients listed for liver transplantation (LT). Population-stratified demographic, clinical, and HLA data from 6767 LT registrants of the United Network for Organ Sharing who had a diagnosis of PSC (4.7% of the registrants) were compared to data from registrants with other diagnoses. Compared to European Americans and Hispanics, African Americans were significantly younger (46.6 ± 13.7, 42.3 ± 15.9, and 39.7 ± 13.1 years, respectively; P = 0.002) and were listed with a higher Model for End-Stage Liver Disease score (15.2 ± 7.5, 14.9 ± 7.6, and 18.1 ± 9.3, respectively; P = 0.001); they were also less frequently noted to have inflammatory bowel disease in comparison with European Americans (71.4% versus 60.5%, P < 0.01). In multivariate analysis, African origin was a significant factor associated with listing for LT with PSC (odds ratio with respect to European Americans = 1.325, 95% confidence interval = 1.221-1.438). HLA associations in European Americans, Hispanics, and African Americans with PSC versus alcoholic liver disease were detected for HLA-B8, HLA-DR13, and protective HLA-DR4. However, HLA-DR3, which is in linkage disequilibrium with HLA-B8, showed associations only in European Americans and Hispanics. In conclusion, African Americans with PSC who are listed for LT differ clinically from European Americans and Hispanics. The association with HLA-B8 but not HLA-DR3 in African Americans should make possible the refinement of the HLA associations in PSC.
Collapse
Affiliation(s)
| | - Chin-Shang Li
- Department of Public Health Sciences, Division of Biostatistics, University of California Davis
| | - Tom H. Karlsen
- Norwegian PSC research center, Clinic for Specialized Medicine and Surgery, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Benedicte A. Lie
- Institute of Immunology, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Carlo Selmi
- Division of Rheumatology, Allergy and Clinical Immunology, University of California Davis, IRCCS Istituto Clinico Humanitas, University of Milan, Italy
| |
Collapse
|
7
|
|
8
|
Rybicki BA, Sinha R, Iyengar S, Gray-McGuire C, Elston RC, Iannuzzi MC. Genetic linkage analysis of sarcoidosis phenotypes: the sarcoidosis genetic analysis (SAGA) study. Genes Immun 2007; 8:379-86. [PMID: 17476268 DOI: 10.1038/sj.gene.6364396] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The sarcoidosis genetic analysis (SAGA) study previously identified eight chromosomal regions with suggestive evidence for linkage to sarcoidosis susceptibility in African-American sib pairs. Since the clinical course of sarcoidosis is variable and likely under genetic control, we used the affected relative pair portion of the SAGA sample (n=344 pairs) to perform multipoint linkage analyses with covariates based on pulmonary and organ involvement phenotypes. Chest radiographic resolution was the pulmonary phenotype with the highest LOD (logarithm of the backward odds, or likelihood ratio) score of 5.11 at D1S3720 on chromosome 1p36 (P=4 x 10(-5)). In general, higher LOD scores were attained for covariates that modeled clustered organ system involvement rather than individual organ systems, with the cardiac/renal group having the highest LOD score of 6.65 at chromosome 18q22 (P=2 x 10(-5)). The highest LOD scores for the other three organ involvement groups of liver/spleen/bone marrow, neuro/lymph and ocular/skin/joint were 3.72 at 10p11 (P=0.0004), 5.16 at 7p22 (P=4 x 10(-5)) and 2.93 at 10q26 (P=0.001), respectively. Most of the phenotype linkages did not overlap with the regions previously found linked to susceptibility. Our results suggest that genes influencing clinical presentation of sarcoidosis in African Americans are likely to be different from those that underlie disease susceptibility.
Collapse
Affiliation(s)
- B A Rybicki
- Department of Biostatistics and Research Epidemiology, Henry Ford Health System, Detroit, MI 48202, USA.
| | | | | | | | | | | |
Collapse
|
9
|
Leffell MS, Cherikh WS, Land G, Zachary AA. Improved Definition of Human Leukocyte Antigen Frequencies Among Minorities and Applicability to Estimates of Transplant Compatibility. Transplantation 2007; 83:964-72. [PMID: 17460569 DOI: 10.1097/01.tp.0000258588.09356.d7] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND HLA population data can be applied to estimates of waiting time and probabilities of donor compatibility. Registry data were used for derivation of HLA antigen and haplotype frequencies in a 1996 report. At that time there were several instances of significant deviation from Hardy Weinberg Equilibrium (HWE). Because molecular typing has been increasingly used since 1996, analysis of recent donor phenotypes should provide more accurate HLA frequencies. METHODS HLA frequencies were derived from the phenotypes of 12,061 donors entered into the Organ Procurement and Transplantation Network registry from January 1, 2003 to December 31, 2004. Frequencies for HLA-A;B;DR and HLA-A;B, DR, DQ haplotypes were derived from 11,509 and 10,590 donors, respectively. Frequencies of the allele groups encoding serologic antigens were obtained by gene counting and haplotype frequencies were estimated using the expectation maximization algorithm. Fit to HWE was evaluated by an exact test using Markov Chain Monte Carlo methods. RESULTS There was clear evidence of improved definition of rarer HLA antigens and haplotypes, particularly among minorities. The reported frequencies of broad antigens decreased overall for HLA-A, B, and DR, with concomitant increases in split antigens. Allele group genotypes among the major ethnic groups were in HWE with the single exception of HLA-A locus alleles among Asians. Improved HLA definition also permitted the first report of DR;DQ and A;B;DR;DQ haplotypes among U.S. donors. CONCLUSIONS The noted improvements in HLA definition and the overall lack of significant deviation from HWE indicate the accuracy of these HLA frequencies. These frequencies can therefore be applied for representative estimates of the U.S. donor population.
Collapse
Affiliation(s)
- Mary S Leffell
- Immunogenetics Laboratory, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | | | | | | |
Collapse
|
10
|
Tu B, Mack SJ, Lazaro A, Lancaster A, Thomson G, Cao K, Chen M, Ling G, Hartzman R, Ng J, Hurley CK. HLA-A, -B, -C, -DRB1 allele and haplotype frequencies in an African American population. ACTA ACUST UNITED AC 2007; 69:73-85. [PMID: 17212710 DOI: 10.1111/j.1399-0039.2006.00728.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sequence-based typing was used to identify human leukocyte antigen (HLA)-A, -B, -C, and -DRB1 alleles from 564 consecutively recruited African American volunteers for an unrelated hematopoietic stem cell registry. The number of known alleles identified at each locus was 42 for HLA-A, HLA-B 67, HLA-C 33, and HLA-DRB1 44. Six novel alleles (A*260104, A*7411, Cw*0813, Cw*1608, Cw*1704, and DRB1*130502) not observed in the initial sequence-specific oligonucleotide probe testing were characterized. The action of balancing selection, shaping more 'even' than expected allele frequency distributions, was inferred for all four loci and significantly so for the HLA-A and DRB1 loci. Two-, three-, and four-locus haplotypes were estimated using the expectation maximization algorithm. Comparisons with other populations from Africa and Europe suggest that the degree of European admixture in the African American population described here is lower than that in other African American populations previously reported, although HLA-A:B haplotype frequencies similar to those in previous studies of African American individuals were also noted.
Collapse
Affiliation(s)
- B Tu
- CW Bill Young Marrow Donor Recruitment and Research Program, Department of Pediatrics, Georgetown University, Washington, DC 20057, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Iannuzzi MC, Rybicki BA. Genetics of sarcoidosis: candidate genes and genome scans. PROCEEDINGS OF THE AMERICAN THORACIC SOCIETY 2007; 4:108-16. [PMID: 17202299 PMCID: PMC2647608 DOI: 10.1513/pats.200607-141jg] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2006] [Accepted: 08/16/2006] [Indexed: 02/07/2023]
Abstract
Human leukocyte antigen class II allele associations and T-cell receptor beta chain bias in sarcoidosis suggest a specific disease-triggering antigen exposure in a genetically susceptible host. The cause of sarcoidosis has been elusive, but genetics provides one of the few promising avenues to further our understanding. We review the association studies and genome scans used to identify the genes involved in sarcoidosis.
Collapse
Affiliation(s)
- Michael C Iannuzzi
- Division of Pulmonary, Critical Care and Sleep Medicine, Mount Sinai School of Medicine, New York, New York, USA.
| | | |
Collapse
|
12
|
Iannuzzi M, Maliarik M, Rybicki B. Genetics of Sarcoidosis. LUNG BIOLOGY IN HEALTH AND DISEASE 2005. [DOI: 10.1201/b13773-10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
13
|
Delaney NL, Esquenazi V, Lucas DP, Zachary AA, Leffell MS. TNF-alpha, TGF-beta, IL-10, IL-6, and INF-gamma alleles among African Americans and Cuban Americans. Report of the ASHI Minority Workshops: Part IV. Hum Immunol 2005; 65:1413-9. [PMID: 15603866 DOI: 10.1016/j.humimm.2004.07.240] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2004] [Revised: 07/21/2004] [Accepted: 07/22/2004] [Indexed: 10/26/2022]
Abstract
Point mutations or single nucleotide substitutions in the regulatory regions of cytokine genes may affect levels of cytokine expression and have been associated with acute and chronic rejection in organ transplantation, severity of graft-versus-host disease in hematopoietic stem cell transplants, and predisposition to autoimmune disorders. Because these cytokine variants have been studied primarily among Caucasians, we defined the alleles and frequencies of five cytokines among 691 unrelated, adult African Americans and 296 Cuban Americans in the American Society for Histocompatibility/National Institutes of Health Minority HLA Workshops. The genotypes of all cytokines, except for transforming growth factor (TGF)-beta among African Americans, were found to be in Hardy-Weinberg's equilibrium. Genotype frequencies among African American and Cuban American participants were compared with those of 75 North American Caucasian bone marrow donors and with published frequencies. Significant differences were observed in all comparisons except between Cuban and Caucasian Americans for alleles of interferon (IFN)-gamma, interleukin (IL)-6, and IL-10. The most notable differences were in genotype frequencies of African Americans compared with those of the two other populations. The frequency of the IFN-gamma genotype A/A, which is associated with low expression, was significantly higher in African Americans than in Caucasian or Cuban Americans (0.66 vs 0.37 and 0.26, respectively; p < 0.0001 for both comparisons). The high-expression G/G genotype for IL-6 was more than twice as prevalent among African Americans as among Caucasians and 1.5 times more frequent than among Cuban Americans (respective frequencies: 0.85 vs 0.38 and 0.49; p < 0.0001 for both comparisons). In African Americans, the frequency of the high-expression genotype for IL-10, GCC/GCC, was approximately half that of the frequency in Cuban and Caucasian Americans (0.10 vs 0.19 and 0.23, respectively; p < 0.0001, p = 0.004). Because levels of expression can affect inflammation and immune regulation, differences in cytokine allele frequencies between racial or ethnic groups may contribute to different incidences of autoimmunity and allograft rejection.
Collapse
Affiliation(s)
- Nancy L Delaney
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | | | | | | |
Collapse
|
14
|
Meulen JT, Badusche M, Satoguina J, Strecker T, Lenz O, Loeliger C, Sakho M, Koulemou K, Koivogui L, Hoerauf A. Old and New World arenaviruses share a highly conserved epitope in the fusion domain of the glycoprotein 2, which is recognized by Lassa virus-specific human CD4+ T-cell clones. Virology 2004; 321:134-43. [PMID: 15033572 DOI: 10.1016/j.virol.2003.12.013] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2003] [Revised: 11/12/2003] [Accepted: 12/04/2003] [Indexed: 11/23/2022]
Abstract
Data from human studies and animal experiments indicate a dominant role of T-cells over antibodies in controlling acute Lassa virus infection and providing immunity to reinfection. Knowledge of the epitopes recognized by T-cells may therefore be crucial to the development of a recombinant Lassa virus vaccine. In order to study human T-cell reactivity to the most conserved structural protein of Lassa virus, the glycoprotein 2 (GP2), seven GP2-specific CD4+ T-cell clones (TCCs) were generated from the lymphocytes of a Lassa antibody positive individual. All TCC displayed high specific proliferation, showed DR-restriction, and produced IFN-gamma upon stimulation with recombinant GP2. The epitope of four of the clones was localized to a short stretch of 13 amino acids located in the N-terminal part of GP2 (aa 289-301, numbering according to sequence of GPC). This epitope is conserved in all strains of Lassa virus and lymphocytic choriomeningitis virus (LCMV), shows >90% similarity in all New World arenaviruses of clade B, and overlaps with the proposed fusion domain of GP2. Peptides with conservative aa exchanges, as they naturally occur in the epitope 289-301 of the Old World arenavirus Mopeia and some New World arenaviruses, continued to effectively stimulate the Lassa-GP2-specific T-cell clones tested. The finding of a human T-helper cell epitope, which is highly conserved between Old and New World arenaviruses, is of importance for the design of arenavirus vaccines.
Collapse
Affiliation(s)
- Jan ter Meulen
- Institute of Virology, Philipps University, 35037 Marburg, Germany.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Leffell MS, Fallin MD, Hildebrand WH, Cavett JW, Iglehart BA, Zachary AA. HLA alleles and haplotypes among the lakota sioux: report of the ASHI minority workshops, part III. Hum Immunol 2004; 65:78-89. [PMID: 14700599 DOI: 10.1016/j.humimm.2003.10.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Human leukocyte antigen (HLA) class I and II alleles were defined for 302 Lakota Sioux American Indians as part of the American Society for Histocompatibility and Immunogenetics coordinated studies on minority populations. The study group was comprised of adult volunteers from the Cheyenne River and Ogala Sioux tribes residing, respectively, on the Cheyenne River and Pine Ridge Reservations in South Dakota. Of the participants, 263 (87%) claimed full American Indian ancestry through both maternal and paternal grandparents. The study group included 25 nuclear families that were informative for genotyping. HLA phenotypes from 202 adults with no other known first-degree relative included in the study were used for calculation of allele and haplotype frequencies by maximum likelihood estimation. HLA-A, -B, and -Cw alleles were found to be in Hardy Weinberg equilibrium. Deviation from equilibrium was observed for DRB1 alleles (p=0.01), but could be attributed to the sample size and the occurrence of some genotypes with low expected frequencies. Polymorphism among the Sioux was limited with four to seven alleles comprising >80% of those observed at each locus. Several alleles were found at high frequency (0.05-0.30) among the Sioux that are also prevalent in other Native Americans and Alaska Natives, including: A*2402, *3101, and *0206; B*3501,*3901, *5101, and *2705; Cw*0702, *0404, and *03041; DRB1*0407, *0404, *1402, and *16021; and DQB1*0301, *0302, and *0402. DRB1*0811, which has been only previously described in Navajo and Tlingit Indians, was found to occur at a frequency of 0.119 among the Sioux. Two new alleles were defined among the Sioux: Cw*0204 and DRB1*040703, which were found in two and four individuals, respectively. In the haplotype analyses, significant linkage disequilibrium (p<0.00001) was seen in all pairwise comparisons of loci and numerous two and three locus haplotypes were found to have strong, positive linkage disequilibrium values. The two most common extended haplotypes among the Sioux, determined by maximum likelihood estimation and genotyping were: A*31012, B*3501, Cw*0404, DRB1*0407; and A*24021, B*3501, Cw*0404, DRB1*0404.
Collapse
Affiliation(s)
- Mary S Leffell
- Department of Medicine, Johns Hopkins University School of Public Health, Baltimore, MD 21205, USA.
| | | | | | | | | | | |
Collapse
|
16
|
Rossman MD, Thompson B, Frederick M, Maliarik M, Iannuzzi MC, Rybicki BA, Pandey JP, Newman LS, Magira E, Beznik-Cizman B, Monos D. HLA-DRB1*1101: a significant risk factor for sarcoidosis in blacks and whites. Am J Hum Genet 2003; 73:720-35. [PMID: 14508706 PMCID: PMC1180597 DOI: 10.1086/378097] [Citation(s) in RCA: 233] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2003] [Accepted: 06/11/2003] [Indexed: 12/27/2022] Open
Abstract
Sarcoidosis is a granulomatous disorder of unknown etiology, associated with an accumulation of CD4+ T cells and a TH1 immune response. Since previous studies of HLA associations with sarcoidosis were limited by serologic or low-resolution molecular identification, we performed high-resolution typing for the HLA-DPB1, HLA-DQB1, HLA-DRB1, and HLA-DRB3 loci and the presence of the DRB4 or DRB5 locus, to define HLA class II associations with sarcoidosis. A Case Control Etiologic Study of Sarcoidosis (ACCESS) enrolled biopsy-confirmed cases (736 total) from 10 centers in the United States. Seven hundred six (706) controls were case matched for age, race, sex, and geographic area. We studied the first 474 ACCESS patients and case-matched controls. The HLA-DRB1 alleles were differentially distributed between cases and controls (P<.0001). The HLA-DRB1*1101 allele was associated (P<.01) with sarcoidosis in blacks and whites and had a population attributable risk of 16% in blacks and 9% in whites. HLA-DRB1-F(47) was the amino acid residue most associated with sarcoidosis and independently associated with sarcoidosis in whites. The HLA-DPB1 locus also contributed to susceptibility for sarcoidosis and, in contrast to chronic beryllium disease, a non-E(69)-containing allele, HLA-DPB1*0101, conveyed most of the risk. Although significant differences were observed in the distribution of HLA class II alleles between blacks and whites, only HLA-DRB1*1501 was differentially associated with sarcoidosis (P<.003). In addition to being susceptibility markers, HLA class II alleles may be markers for different phenotypes of sarcoidosis (DRB1*0401 for eye in blacks and whites, DRB3 for bone marrow in blacks, and DPB1*0101 for hypercalcemia in whites). These studies confirm a genetic predisposition for sarcoidosis and present evidence for the allelic variation at the HLA-DRB1 locus as a major contributor.
Collapse
Affiliation(s)
- Milton D Rossman
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Affiliation(s)
- Russell W Chesney
- Department of Pediatrics, University of Tennessee Health Science Center, LeBonheur Children's Medical Center, Memphis, TN 38103, USA.
| | | |
Collapse
|
18
|
Kuffner T, Whitworth W, Jairam M, McNicholl J. HLA class II and TNF genes in African Americans from the Southeastern United States: regional differences in allele frequencies. Hum Immunol 2003; 64:639-47. [PMID: 12770797 DOI: 10.1016/s0198-8859(03)00056-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Knowledge of population major histocompatibility complex gene frequencies is important for construction of organ donor pools and for studies of disease association. Human leukocyte antigen DRB1 (HLA-DRB1), HLA-DQB1, and TNFalpha -308 (G-A) promoter genetic typing was performed in 112 healthy, unrelated African Americans (AAs) from the southeastern United States. Allele frequencies were compared with published frequency data from other AA populations. Our AA population had the highest frequency of HLA- DRB1*09 (6.7%) reported in any AA population. The frequency of the TNF alpha -308A polymorphism was also high (14.4%), when compared with published frequencies in AAs. Significant regional differences in the distribution of most HLA-DRB1 and HLA-DQB1 alleles were observed in all AA populations examined. The AA HLA-DRB1 and -DQB1 frequencies also differed from published Caucasian frequencies. This is the first report describing the distribution of TNF alpha promoter alleles in the Southeastern United States. The high DRB1*09 and TNF alpha -308A allele frequencies of our population most resemble the frequencies of these alleles in certain West African populations. These varying major histocompatibility complex gene frequencies may reflect different regional population structures among AAs in the United States, which may be due to differences in ancestral origins, migration, and racial admixture.
Collapse
Affiliation(s)
- Tamara Kuffner
- HIV Immunology and Diagnostics Branch, Division of AIDS, STD and TB Laboratory Research, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | | | | | | |
Collapse
|
19
|
Iannuzzi MC, Maliarik MJ, Poisson LM, Rybicki BA. Sarcoidosis susceptibility and resistance HLA-DQB1 alleles in African Americans. Am J Respir Crit Care Med 2003; 167:1225-31. [PMID: 12615619 DOI: 10.1164/rccm.200209-1097oc] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Sarcoidosis, in the United States, more commonly and severely affects African Americans. HLA associations with sarcoidosis have been reported, but most studies used case-control designs, which may produce biased results because of population stratification. We examined transmission of HLA-DQB1 alleles in 225 African American families with at least one offspring with sarcoidosis. Of five low-resolution HLA-DQB1 alleles, *02 and *06 showed significant deviation in transmission patterns to affected offspring. High-resolution typing of these allelic subsets revealed that HLA-DQB1*0201 was transmitted to affected offspring half as often as expected (p = 0.001), whereas DQB1*0602 was transmitted to affected offspring about 20% more often than expected (p = 0.029). Examining interactions between *0201 and *0602 alleles and environmental exposures showed that *0602 varied little with respect to exposure, but sarcoidosis risk associated with *0201 often depended on exposure status. Alternatively, the *0602 allele in affected probands was associated with radiographic disease progression, but the *0201 allele showed no significant correlation with phenotype. Major differences in the amino acid sequences encoded by *0201 and *0602 alleles exist, which may explain the differential effects these alleles have on sarcoidosis susceptibility and progression in African Americans.
Collapse
Affiliation(s)
- Michael C Iannuzzi
- Division of Pulmonary and Critical Care Medicine, Mount Sinai Medical Center, One Gustave Levy Place, Box 1232, NY, NY 10029, USA.
| | | | | | | |
Collapse
|
20
|
Rybicki BA, Maliarik MJ, Poisson LM, Sheffer R, Chen KM, Major M, Chase GA, Iannuzzi MC. The major histocompatibility complex gene region and sarcoidosis susceptibility in African Americans. Am J Respir Crit Care Med 2003; 167:444-9. [PMID: 12554629 DOI: 10.1164/rccm.2112060] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Investigators have intensively evaluated the major histocompatibility (MHC) complex for sarcoidosis susceptibility genes with the majority of reports implicating the human leukocyte antigen (HLA)-DRB1 gene. Because most studies have been performed in white and Asian populations, we sought to determine which MHC genes might be risk factors for sarcoidosis in African Americans. We genotyped six microsatellite markers spanning 11.6 megabases that overlapped the MHC region on chromosome 6p21-22 in 225 nuclear families ascertained by African American probands with a history of sarcoidosis. Using a family-based association methods approach, we performed multiallelic tests of association between each marker and sarcoidosis. A statistically significant association was detected between sarcoidosis and the DQCAR marker (p = 0.002) less than two kilobases telomeric from the HLA-DQB1 gene. Typing two additional markers in this region revealed that DQCAR-G51152 haplotypes, spanning a 38-kilobase region across the HLA-DQB1 gene, were associated with sarcoidosis on a global level (p = 0.022). Analysis of individual DQCAR and G51152 alleles showed that the DQCAR 178 (expected = 21.0; observed = 10; p = 0.0005) and G51152 217 (expected = 25.6; observed = 14; p = 0.0009) alleles were transmitted to affected offspring less often than expected; whereas the DQCAR 182 allele was transmitted more often than expected (expected = 52.6; observed = 66; p = 0.002). Our results indicate that HLA-DQB1 and not HLA-DRB1 plays an important role in sarcoidosis susceptibility in African Americans. Identification of the specific HLA-DQB1 alleles that influence sarcoidosis susceptibility in African Americans and the study of their antigenic-binding properties may reveal why African Americans suffer disproportionately from this disease.
Collapse
Affiliation(s)
- Benjamin A Rybicki
- Department of Biostatistics and Research Epidemiology and Division of Pulmonary and Critical Care Medicine, Henry Ford Health System, Detroit, Michigan 48202, USA.
| | | | | | | | | | | | | | | |
Collapse
|
21
|
Leffell MS, Fallin MD, Erlich HA, Fernandez-Vĩna M, Hildebrand WH, Mack SJ, Zachary AA. HLA antigens, alleles and haplotypes among the Yup'ik Alaska natives: report of the ASHI Minority Workshops, Part II. Hum Immunol 2002; 63:614-25. [PMID: 12072196 DOI: 10.1016/s0198-8859(02)00415-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
As part of the American Society for Histocompatibility and Immunogenetics coordinated studies among minority populations, human leukocyte antigen (HLA) alleles were defined for 460 volunteer Yup'ik Eskimos from the Yukon Kuskokwim delta region of southwestern Alaska. The study group included 252 adults with no other first-degree relatives and 48 informative nuclear families. Full Yupik ancestry through both maternal and paternal grandparents was claimed by 81.1% of participants. HLA-A, -B, -Cw, -DRB1, and -DQB1 alleles were determined by SBT, SSOP, reverse SSOP, and/or RSCA according to the protocols of five participating laboratories. Polymorphism was limited with 3-6 alleles comprising > 80% of the alleles observed at each locus. Homozygosity was high, particularly at the HLA-A and -DQB1 loci, with 36.6% and 44% of individuals having a single allele defined at these respective loci. HLA-A, -B, and -DRB1 alleles were in Hardy-Weinberg equilibrium, whereas HLA-Cw and -DQB1 alleles gave significant deviation (p = 0.002; 0.005). Significant linkage disequilibrium (p < or = 0.00001) was observed in all pairwise evaluations. A new Cw*0806 allele was observed in high linkage disequilibrium with B*4801(Delta = 0.099; Delta(rel) = 1.0). Three extended haplotypes were found to have frequencies > 5%, the most prevalent being A*2402; B*4801; DRB1*0401; DQB1*0301 (0.0933). Comparison of available class I data indicate that the Yup'ik share several common alleles with other Native American populations, including: A*2402, *0206, *6801; B*1501, *2705, *3501, *4002, *4801, *5101; and Cw*0202, *0304, *0401. Comparisons of class II data also confirm a close relationship of the Yup'ik to two other Eskimo populations, Siberian and East Greenland Eskimos. DRB1*0401 and *1101, which occur in high frequency among these Eskimo populations, but not in other Native Americans, were also prevalent among the Yup'ik, with respective frequencies of 0.232 and 0.107.
Collapse
Affiliation(s)
- Mary S Leffell
- Department of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
| | | | | | | | | | | | | |
Collapse
|