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Zou Q. The Generalized Relative Pairs IBD Distribution: Its Use in the Detection of Linkage. Front Public Health 2016; 4:259. [PMID: 27933287 PMCID: PMC5120125 DOI: 10.3389/fpubh.2016.00259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 11/02/2016] [Indexed: 11/13/2022] Open
Abstract
I introduce a novel approach to derive the distribution of disease affectional status given alleles identical by descent (IBD) sharing through ITO method. My approach tremendously simplifies the calculation of the affectional status distribution compared to the conventional method, which requires the parental mating information, and could be applied to disease with both dichotomous trait and quantitative trait locus (QTL). This distribution is shown to be independent of relative relationship and be employed to develop the marker IBD distributions for relative relationship. In addition, three linkage tests: the proportion, the mean test, and the LOD score test are proposed for different relative pairs based on their marker IBD distributions. Among all three tests, the mean test for sib pair requires the least sample size, thus, has the highest power. Finally, I evaluate the significance of different relative relationships by a Monte-Carlo simulation approach.
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Affiliation(s)
- Quan Zou
- Department of Statistics, The George Washington University , Washington, DC , USA
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2
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Nolte MA, van der Meer JWM. Inflammatory responses to infection: the Dutch contribution. Immunol Lett 2014; 162:113-20. [PMID: 25455597 PMCID: PMC7132409 DOI: 10.1016/j.imlet.2014.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
At any given moment, our body is under attack by a large variety of pathogens, which aim to enter and use our body to propagate and disseminate. The extensive cellular and molecular complexity of our immune system enables us to efficiently eliminate invading pathogens or at least develop a condition in which propagation of the microorganism is reduced to a minimum. Yet, the evolutionary pressure on pathogens to circumvent our immune defense mechanisms is immense, which continuously leads to the development of novel pathogenic strains that challenge the health of mankind. Understanding this battle between pathogen and the immune system has been a fruitful area of immunological research over the last century and will continue to do so for many years. In this review, which has been written on the occasion of the 50th anniversary of the Dutch Society for Immunology, we provide an overview of the major contributions that Dutch immunologists and infection biologists have made in the last decades on the inflammatory response to viral, bacterial, fungal or parasitic infections. We focus on those studies that have addressed both the host and the pathogen, as these are most interesting from an immunological point of view. Although it is not possible to completely cover this comprehensive research field, this review does provide an interesting overview of Dutch research on inflammatory responses to infection.
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Affiliation(s)
- Martijn A Nolte
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
| | - Jos W M van der Meer
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
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3
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Hill AVS. Evolution, revolution and heresy in the genetics of infectious disease susceptibility. Philos Trans R Soc Lond B Biol Sci 2012; 367:840-9. [PMID: 22312051 PMCID: PMC3267114 DOI: 10.1098/rstb.2011.0275] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Infectious pathogens have long been recognized as potentially powerful agents impacting on the evolution of human genetic diversity. Analysis of large-scale case–control studies provides one of the most direct means of identifying human genetic variants that currently impact on susceptibility to particular infectious diseases. For over 50 years candidate gene studies have been used to identify loci for many major causes of human infectious mortality, including malaria, tuberculosis, human immunodeficiency virus/acquired immunodeficiency syndrome, bacterial pneumonia and hepatitis. But with the advent of genome-wide approaches, many new loci have been identified in diverse populations. Genome-wide linkage studies identified a few loci, but genome-wide association studies are proving more successful, and both exome and whole-genome sequencing now offer a revolutionary increase in power. Opinions differ on the extent to which the genetic component to common disease susceptibility is encoded by multiple high frequency or rare variants, and the heretical view that most infectious diseases might even be monogenic has been advocated recently. Review of findings to date suggests that the genetic architecture of infectious disease susceptibility may be importantly different from that of non-infectious diseases, and it is suggested that natural selection may be the driving force underlying this difference.
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Affiliation(s)
- Adrian V S Hill
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
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KANAZAWA N, MIKITA N, LI HJ, NAKATANI Y, OZAKI M, KOSAKA M, ISHII N, NISHIMURA H, FURUKAWA F. Genetic involvement of bacterial sensor molecules in Japanese leprosy. ACTA ACUST UNITED AC 2009; 78:255-61. [DOI: 10.5025/hansen.78.255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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6
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Scollard DM, Adams LB, Gillis TP, Krahenbuhl JL, Truman RW, Williams DL. The continuing challenges of leprosy. Clin Microbiol Rev 2006; 19:338-81. [PMID: 16614253 PMCID: PMC1471987 DOI: 10.1128/cmr.19.2.338-381.2006] [Citation(s) in RCA: 498] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Leprosy is best understood as two conjoined diseases. The first is a chronic mycobacterial infection that elicits an extraordinary range of cellular immune responses in humans. The second is a peripheral neuropathy that is initiated by the infection and the accompanying immunological events. The infection is curable but not preventable, and leprosy remains a major global health problem, especially in the developing world, publicity to the contrary notwithstanding. Mycobacterium leprae remains noncultivable, and for over a century leprosy has presented major challenges in the fields of microbiology, pathology, immunology, and genetics; it continues to do so today. This review focuses on recent advances in our understanding of M. leprae and the host response to it, especially concerning molecular identification of M. leprae, knowledge of its genome, transcriptome, and proteome, its mechanisms of microbial resistance, and recognition of strains by variable-number tandem repeat analysis. Advances in experimental models include studies in gene knockout mice and the development of molecular techniques to explore the armadillo model. In clinical studies, notable progress has been made concerning the immunology and immunopathology of leprosy, the genetics of human resistance, mechanisms of nerve injury, and chemotherapy. In nearly all of these areas, however, leprosy remains poorly understood compared to other major bacterial diseases.
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Affiliation(s)
- D M Scollard
- Laboratory Research Branch, National Hansen's Disease Programs, LSU-SVM, Skip Bertman Dr., Baton Rouge, LA 70803, USA.
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7
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Mira MT. Genetic host resistance and susceptibility to leprosy. Microbes Infect 2006; 8:1124-31. [PMID: 16513393 DOI: 10.1016/j.micinf.2005.10.024] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2005] [Accepted: 10/19/2005] [Indexed: 10/25/2022]
Abstract
Leprosy is a chronic infectious disease that affects 600,000 new individuals worldwide every year. This article summarizes some of the advances achieved over the past decades towards the description of the exact number, location and nature of the genetic variants responsible for the well established genetic component controlling leprosy susceptibility in humans.
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Affiliation(s)
- Marcelo Távora Mira
- Pontifical Catholic University of Paraná, Graduate Program in Health Sciences, Rua Imaculada Conceição, 1155, CCBS, PPGCS, CEP 80215-901, Curitiba, Paraná, Brazil.
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8
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Abstract
The affected-sib-pair (ASP) method for detecting linkage between a disease locus and marker loci was first established 50 years ago, and since then numerous modifications have been made. We modify two identity-by-state (IBS) test statistics of Lange (Lange, 1986a, 1986b) to allow for inbreeding in the population. We evaluate the power and false positive rates of the modified tests under three disease models, using simulated data. Before estimating false positive rates, we demonstrate that IBS tests are tests of both linkage and linkage disequilibrium between marker and disease loci. Therefore, the null hypothesis of IBS tests should be no linkage and no LD. When the population inbreeding coefficient is large, the false positive rates of Lange's tests become much larger than the nominal value, while those of our modified tests remain close to the nominal value. To estimate power with a controlled false positive rate, we choose the cutoff values based on simulated datasets under the null hypothesis, so that both Lange's tests and the modified tests generate same false positive rate. The powers of Lange's z-test and our modified z-test are very close and do not change much with increasing inbreeding. The power of the modified chi-square test also stays stable when the inbreeding coefficient increases. However, the power of Lange's chi-square test increases with increasing inbreeding, and is larger than that of our modified chi-square test for large inbreeding coefficients. The power is high under a recessive disease model for both Lange's tests and the modified tests, though the power is low for additive and dominant disease models. Allowing for inbreeding is therefore appropriate, at least for diseases known to be recessive.
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Affiliation(s)
- W Liu
- Department of Health Education Sciences, Penn State College of Medicine, 600 Centerview Drive, Hershey, PA 17033-0855, USA.
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Mira MT, Alcais A, di Pietrantonio T, Thuc NV, Phuong MC, Abel L, Schurr E. Segregation of HLA/TNF region is linked to leprosy clinical spectrum in families displaying mixed leprosy subtypes. Genes Immun 2003; 4:67-73. [PMID: 12595904 DOI: 10.1038/sj.gene.6363911] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Each year an estimated 600000 new leprosy cases are diagnosed worldwide. The spectrum of the disease varies widely from limited tuberculoid forms to extensive lepromatous forms. A measure of the risk to develop lepromatous forms of leprosy is provided by the extent of skin reactivity to lepromin (Mitsuda reaction). To address a postulated oligogenic control of leprosy pathogenesis, we investigated in the present study linkage of leprosy susceptibility, leprosy clinical subtypes, and extent of the Mitsuda reaction to six chromosomal regions carrying known or suspected leprosy susceptibility loci. The only significant result obtained was linkage of leprosy clinical subtype to the HLA/TNF region on human chromosome 6p21 (P(corrected)=0.00126). In addition, we established that within the same family different HLA/TNF haplotypes segregate into patients with different leprosy subtypes directly demonstrating the importance of this genome region for the control of clinical leprosy presentation.
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Affiliation(s)
- M T Mira
- Departments of Human Genetics, Medicine and Biochemistry, McGill University, Montreal, PQ, Canada
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10
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Abstract
The ancient disease of leprosy can cause severe disability and disfigurement and is still a major health concern in many parts of the world. Only a subset of those individuals exposed to the pathogen will go on to develop clinical disease and there is a broad clinical spectrum amongst leprosy sufferers. The outcome of infection is in part due to host genes that influence control of the initial infection and the host's immune response to that infection. Identification of the host genes that influence host susceptibility/resistance will enable a greater understanding of disease pathogenesis. In turn, this should facilitate development of more effective therapeutics and vaccines. So far at least a dozen genes have been implicated in leprosy susceptibility and a genome-wide linkage study has lead to the identification of at least one positional candidate. These findings are reviewed here.
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Affiliation(s)
- J Fitness
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK.
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Wibawa T, Soebono H, Matsuo M. Association of a missense mutation of the laminin alpha2 gene with tuberculoid type of leprosy in Indonesian patients. Trop Med Int Health 2002; 7:631-6. [PMID: 12100448 DOI: 10.1046/j.1365-3156.2002.00908.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Leprosy, an infection caused by Mycobacterium leprae, has a specific tropism for the myelinating Schwann cells of peripheral nerves. Recently, the G domain of laminin alpha2 has been shown to be a mediator for M. leprae to bind to alpha-dystroglycan in Schwann cells. In order to analyse the association of leprosy with the mediator, three genetic polymorphisms encoding the G domain of the laminin alpha2 chain were analysed by direct sequencing in 53 leprosy patients and 58 healthy contact individuals from Indonesia. There was no significant difference in the incidence of the polymorphisms between patients and non-patients. Remarkably, it was found that a missense mutation (T7809C) substituting valine with alanine (V2587A) was found to be more frequent in the tuberculoid type than in the lepromatous type leprosy. It is supposed that this missense mutation is one of the determinant factors in the early onset of peripheral nerve damage in Indonesian tuberculoid leprosy patients.
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Affiliation(s)
- Tri Wibawa
- Division of Molecular Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
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12
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Abstract
Humans are exposed to a variety of environmental mycobacteria (EM), and most children are inoculated with live Bacille Calmette-Guérin (BCG) vaccine. In addition, most of the world's population is occasionally exposed to human-borne mycobacterial species, which are less abundant but more virulent. Although rarely pathogenic, mildly virulent mycobacteria, including BCG and most EM, may cause a variety of clinical diseases. Mycobacterium tuberculosis, M. leprae, and EM M. ulcerans are more virulent, causing tuberculosis, leprosy, and Buruli ulcer, respectively. Remarkably, only a minority of individuals develop clinical disease, even if infected with virulent mycobacteria. The interindividual variability of clinical outcome is thought to result in part from variability in the human genes that control host defense. In this well-defined microbiological and clinical context, the principles of mouse immunology and the methods of human genetics can be combined to facilitate the genetic dissection of immunity to mycobacteria. The natural infections are unique to the human model, not being found in any of the animal models of experimental infection. We review current genetic knowledge concerning the simple and complex inheritance of predisposition to mycobacterial diseases in humans. Rare patients with Mendelian disorders have been found to be vulnerable to BCG, a few EM, and M. tuberculosis. Most cases of presumed Mendelian susceptibility to these and other mycobacterial species remain unexplained. In the general population leprosy and tuberculosis have been shown to be associated with certain human genetic polymorphisms and linked to certain chromosomal regions. The causal vulnerability genes themselves have yet to be identified and their pathogenic alleles immunologically validated. The studies carried out to date have been fruitful, initiating the genetic dissection of protective immunity against a variety of mycobacterial species in natural conditions of infection. The human model has potential uses beyond the study of mycobacterial infections and may well become a model of choice for the investigation of immunity to infectious agents.
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Affiliation(s)
- Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Université René Descartes-INSERM U550, Necker Medical School, 156 rue de Vaugirard, 75015 Paris, France.
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13
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Abstract
A genetic basis for interindividual variation in susceptibility to human infectious diseases has been indicated by twin, adoptee, pedigree, and candidate gene studies. This has led to the identification of a small number of strong genetic associations with common variants for malaria, HIV infection, and infectious prion diseases. Numerous other genes have shown less strong associations with these and some other infectious diseases, such as tuberculosis, leprosy, and persistent hepatitis viral infections. Many immunogenetic loci influence susceptibility to several infectious pathogens. Recent genetic linkage analyses of measures of infection as well as of infectious disease, including some genome-wide scans, have found convincing evidence of genetic linkage to chromosomal regions wherein susceptibility genes have yet to be identified. These studies indicate a highly polygenic basis for susceptibility to many common infectious diseases, with some emerging examples of interaction between variants of specific polymorphic host and pathogen genes.
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Affiliation(s)
- A V Hill
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom.
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Shaw MA, Donaldson IJ, Collins A, Peacock CS, Lins-Lainson Z, Shaw JJ, Ramos F, Silveira F, Blackwell JM. Association and linkage of leprosy phenotypes with HLA class II and tumour necrosis factor genes. Genes Immun 2001; 2:196-204. [PMID: 11477474 DOI: 10.1038/sj.gene.6363754] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2000] [Revised: 03/01/2001] [Accepted: 03/01/2001] [Indexed: 11/08/2022]
Abstract
Previous analyses indicate major gene control of susceptibility to leprosy per se and the HLA class II region has been implicated in determining susceptibility and control of clinical phenotype. Segregation analysis using data from 76 Brazilian leprosy multi-case pedigrees (1166 individuals) supported a two locus model as the best fit: a recessive major gene and a recessive modifier gene(s) (single locus vs two locus model, P = 0.0007). Combined segregation and linkage analysis to the major locus, showed strong linkage to HLA class II (HLA-DQB1 P = 0.000002, HLA-DQA1 P = 0.000002, HLA-DRB1 P = 0.0000003) and tumour necrosis factor genes (TNF P = 0.00002, LTA P = 0.003). Extended transmission disequilibrium testing, using multiple affected family members, demonstrated that the common allele TNF*1 of the -308 promoter region polymorphism showed linkage and/or association with disease per se, at a high level of significance (P < 0.0001). Two locus transmission disequilibrium testing suggested susceptibility (TNF*1/LTA*2) and protective (TNF*2/LTA*2) haplotypes in the class iii region. Taken together the segregation and HLA analyses suggest the possibility of more than one susceptibility locus in the MHC.
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Affiliation(s)
- M A Shaw
- Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Addenbrookes Hospital, Hills Road, Cambridge CB2 2XY,
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15
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Abstract
Methods of model-free linkage analysis do not require a detailed specification for the mode of inheritance of the trait locus being linked. Beginning with methods proposed by Penrose in the 1930s, which allowed detection of linkage only, these methods now allow one to use multipoint analysis both to locate trait genes and to estimate variance components that give information on the genetic mechanism underlying the trait. The newer methods can utilize data on multiple types of pairs of relatives other than just sibpairs, and they can detect multiple trait loci. In combination with special sampling schemes, these methods give hope that they may play a crucial role in unraveling the genetic etiology of multifactorial traits, regardless of whether epistatic interactions are present. The results of such analyses can guide the use of more powerful model-based linkage analyses.
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Affiliation(s)
- R C Elston
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio 44101, USA
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Abel L, Alcais A, Mallet A. Comparison of four sib-pair linkage methods for analyzing sibships with more than two affecteds: interest of the binomial maximum likelihood approach. Genet Epidemiol 2000; 15:371-90. [PMID: 9671987 DOI: 10.1002/(sici)1098-2272(1998)15:4<371::aid-gepi4>3.0.co;2-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Family samples collected for sib-pair linkage studies usually include some sibships with more than two affecteds (multiplex sibships). Several methods have been proposed to take into account these multiplex sibships, and four of them are discussed in this work. Two methods, which are the most widely used, are based on the number of alleles shared by the sib-pairs constitutive of the multiplex sibship, with the first using the total number of these shared alleles ("all possible pairs" method) and the second considering a weighted number of these alleles (weighted method). The two other approaches considered the sibship as a whole, with in particular a likelihood method based on a binomial distribution of parental alleles among affected offspring. We theoretically show that, in the analysis of sibships with two affecteds, this likelihood method is expected to be more powerful than the classical mean test when a common asymptotic type I error is used. The variation of the sibship informativeness (assessed by the proportion of heterozygous parents) according to the number of affected sibs is investigated under various genetic models. Simulations under the null hypothesis of no linkage indicate that the "all possible pairs" is anticonservative, especially for type I errors < or = 0.001, whereas the weighted method generally provides satisfactory results. The likelihood method shows very consistent results in terms of type I errors, whatever the sample size, and provides power levels similar to those of the other methods. This binomial likelihood approach, which accounts in a natural way for multiplex sibships and provides a simple likelihood-ratio test for linkage involving a single parameter, appears to be a quite interesting alternative to analyze sib-pair studies.
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Affiliation(s)
- L Abel
- INSERM U.436 Mathematical and Statistical Modeling in Biology and Medicine, Hôpital Pitié-Salpêtrière, Paris, France.
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Dias MF, Pereira AC, Pereira A, Alves MS. The role of HLA antigens in the development of paracoccidioidomycosis. J Eur Acad Dermatol Venereol 2000; 14:166-71. [PMID: 11032058 DOI: 10.1046/j.1468-3083.2000.00070.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Paracoccidioidomycosis is a systemic granulomatous disease that involves primarily the lungs and may disseminate to other organs and systems. It is caused by Paracoccidioides brasiliensis, a fungus that exhibits reversible thermal dimorphism and whose natural habitat is presently unknown. There are two main clinical forms: the acute (subacute) juvenile form and the chronic adult form. The former runs a more rapid course and is more severe than the latter. This mycosis is found throughout Latin America. Brazil accounts for 80% of reported cases. Presumably P. brasiliensis thrives in humid and hot places, especially near forests or farms. The infection is endemic in certain areas, especially in Brazil, Colombia and Venezuela, where nearly 100% of the population show cutaneous paracoccidioidina positive skin tests, indicating previous contact with the fungus, although a small percentage show clinical manifestations of the disease. METHODS We compared the expression of HLA class I antigens in a healthy group (control) and in a group of patients with paracoccidioidomycosis (chronic adult form) using the Terasaki lymphocytotoxicity test modified by Amos for HLA antigen analysis. AIMS To discover indications of whether or not individual susceptibility to P. brasiliensis might depend on some specific immunological defect. RESULTS There is no evidence of association between a specific HLA antigen and paracoccidioidomycosis in the subjects studied. Further investigations are recommended.
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Affiliation(s)
- M F Dias
- Depto de Dermatologia, Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Brasil.
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Knight JC, Kwiatkowski D. Inherited variability of tumor necrosis factor production and susceptibility to infectious disease. PROCEEDINGS OF THE ASSOCIATION OF AMERICAN PHYSICIANS 1999; 111:290-8. [PMID: 10417736 DOI: 10.1046/j.1525-1381.1999.99237.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Tumor necrosis factor (TNF) is a critical mediator of host defense against infection but may cause severe pathology when produced in excess. Individuals vary in the amount of TNF produced when their peripheral blood mononuclear cells are stimulated in vitro, and family studies indicate that much of this variability is genetically determined. Since the TNF response to infection is partly regulated at the transcriptional level, TNF promoter polymorphisms have been the subject of intense interest as potential determinants of disease susceptibility. A single nucleotide polymorphism at nucleotide -308 relative to the transcriptional start site has been associated with susceptibility to severe malaria, leishmaniasis, scarring trachoma, and lepromatous leprosy. Some experimental data indicate that this polymorphism acts to upregulate TNF transcription, but this remains controversial. Detailed analysis of multiple genetic markers at this locus and more sophisticated investigations of TNF transcriptional regulation, in different cell types and with a wide range of stimuli, are required to understand the molecular basis of these disease associations.
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Affiliation(s)
- J C Knight
- Molecular Infectious Diseases Group, Institute of Molecula Medicine, University of Oxford, UK
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Shaw MA, Collins A, Peacock CS, Miller EN, Black GF, Sibthorpe D, Lins-Lainson Z, Shaw JJ, Ramos F, Silveira F, Blackwell JM. Evidence that genetic susceptibility to Mycobacterium tuberculosis in a Brazilian population is under oligogenic control: linkage study of the candidate genes NRAMP1 and TNFA. TUBERCLE AND LUNG DISEASE : THE OFFICIAL JOURNAL OF THE INTERNATIONAL UNION AGAINST TUBERCULOSIS AND LUNG DISEASE 1998; 78:35-45. [PMID: 9666961 DOI: 10.1016/s0962-8479(97)90014-9] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
SETTING A study of multicase tuberculosis pedigrees from Northern Brazil. OBJECTIVE To determine the model of inheritance for genetic susceptibility to tuberculosis, and to test the hypothesis that TNFA and NRAMP1 are candidate susceptibility genes. DESIGN The study sample included 98 pedigrees, 704 individuals and 205 nuclear families. Segregation analyses were performed using the programs POINTER and COMDS. Combined segregation and linkage analysis was carried out within COMDS. Non-parametric linkage analyses were performed using BETA. RESULTS A sporadic model for disease distribution in families was strongly rejected, as were polygenic and multifactorial models. A codominant single gene model provided the best fit (P < 0.001) to the data using POINTER. COMDS extended the analysis to compare single-gene and two-gene models. A general two-locus model for disease control was marginally favoured (0.01 < P < 0.05) over the codominant single-gene model. No evidence was found for linkage between susceptibility to disease per se and the TNF gene cluster. Weak linkage was observed using COMDS for genes (IL8RB, P = 0.039; D2S1471, P = 0.025) tightly linked (< 150 kb) to NRAMP1, but not for NRAMP1 itself. CONCLUSIONS Tuberculosis susceptibility in this region of Brazil is under oligogenic control. Although a minor role for TNFA and NRAMP1 cannot be excluded, our data suggest that neither is a major gene involved in this oligogenic control.
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Affiliation(s)
- M A Shaw
- Department of Medicine, University of Cambridge Clinical School, Addenbrookes Hospital, UK
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20
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Abstract
Twin and adoptee studies have indicated that host genetic factors are major determinants of susceptibility to infectious disease in humans. Twin studies have also found high heritabilities for many humoral and cellular immune responses to pathogen antigens, with most of the genetic component mapping outside of the major histocompatibility complex. Candidate gene studies have implicated several immunogenetic polymorphisms in human infectious diseases. HLA variation has been associated with susceptibility or resistance to malaria, tuberculosis, leprosy, AIDS, and hepatitis virus persistence. Variation in the tumor necrosis factor gene promoter has also been associated with several infectious diseases. Chemokine receptor polymorphism affects both susceptibility ot HIV-1 infection and the rate of progression to AIDS. Inactivating mutations of the gamma-interferon receptor lead to increased susceptibility to typical mycobacteria and disseminated BCG infection in homozygous children. The active form of vitamin D has immunomodulatory effects, and allelic variants of the vitamin D receptor appear to be associated with differential susceptibility to several infectious diseases. NRAMP1, a macrophage gene identified by positional cloning of its murine homologue, has been implicated in susceptibility to tuberculosis in Africans. Whole genome linkage analysis of multi-case families is now being used to map and identify new loci affecting susceptibility to infectious diseases. It is likely that susceptibility to most microorganisms is determined by a large number of polymorphic genes, and identification of these should provide insights into protective and pathogenic mechanisms in infectious diseases.
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Affiliation(s)
- A V Hill
- Wellcome Trust Centre for Human Genetics, University of Oxford, United Kingdom.
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21
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Population Genetics: Description and Dynamics. Hum Genet 1997. [DOI: 10.1007/978-3-662-03356-2_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Hypothesis Testing and Categorical Data. MATHEMATICAL AND STATISTICAL METHODS FOR GENETIC ANALYSIS 1997. [DOI: 10.1007/978-1-4757-2739-5_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Abstract
The identification of large numbers of candidates genes and the introduction of methodologies for whole-genome screening have provided new opportunities for elucidating the molecular basis of variable susceptibility to major infectious diseases. 12 genes have been implicated in variable susceptibility to malaria and susceptibility/resistance genes for several other infectious diseases are beginning to be identified. Recent work suggests that large-scale family linkage and population association studies will be a more successful route to human disease genes than extrapolation from mouse models of infection.
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Affiliation(s)
- A V Hill
- Wellcome Trust Centre for Human Genetics, University of Oxford, UK
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24
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Abstract
BACKGROUND The presence of a genetic factor in the determination of leprosy has long been debated. This study tests whether the HLA-linked control of susceptibility to leprosy and/or for the types of leprosy could be confirmed. MATERIALS AND METHODS In 15 multicase families, the method of DeVries et al., 1976, was used to detect nonrandom segregation of parental HLA haplotypes in their affected and healthy siblings. Linkage analyses, for two and three alleles were performed by the computer program LIPED: RESULTS For the affected siblings, the segregations of the parental HLA haplotype were significantly nonrandom from the healthy parents and random from the affected parents, indicating that affected siblings were sharing their HLA haplotypes (segregated from the healthy parents) more than expected. The segregations to the healthy siblings from both the healthy and affected parents were random. Healthy siblings inherited the haplotypes shared among the leprosy siblings randomly as expected. There were excess DR2/DR2 homozygote individuals among tuberculoid siblings. The highest lod score was achieved when we considered our suggested three-alleles model for the susceptibility to the different types of leprosy. CONCLUSIONS A closely HLA-linked gene on chromosome number 6 with multiple alleles (3 or more) in recombination fraction between 0.05 and 0.1 with 70 to 100% penetrance may be responsible for the susceptibility to the different types of leprosy, whereas the susceptibility to leprosy per se maybe the responsibility of non-HLA linked gene/s. DR2/DR2 homozygote individuals may be relatively at high risk of developing leprosy or tuberculoid leprosy.
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Affiliation(s)
- M W Dessoukey
- Department of Dermatology, Al-Jazeira Hospital, Abu-Dhabi, United Arab Emirates
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25
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Hill AV. Genetic susceptibility to malaria and other infectious diseases: from the MHC to the whole genome. Parasitology 1996; 112 Suppl:S75-84. [PMID: 8684839 DOI: 10.1017/s003118200007668x] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
There is substantial evidence that host genetic factors play a major role in determining the outcome of infection with many pathogens. Detailed analysis of malaria has identified twelve genes that affect susceptibility in various human populations. However, less attention has been paid to other major infectious diseases where twin studies have identified an important host genetic component to susceptibility. Recent progress in the analysis of the human genome offers exciting prospects for the mapping and identification of new susceptibility and resistance genes for common infectious diseases. Screening of the whole genome in affected sibling pair studies is now feasible by employing highly informative microsatellite markers. In addition, many polymorphic candidate genes have become available for analysis in case-control studies. It is proposed that these new genetic tools offer a powerful approach to the epidemiological analysis of many infectious diseases in humans and supersede traditional genetic approaches to identifying susceptibility genes in mouse models. Progress in characterizing the role of major histocompatibility genes in susceptibility to malaria and other infectious diseases is reviewed before outlining the methodologies for and progress in identifying non-MHC susceptibility genes.
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Affiliation(s)
- A V Hill
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, U.K
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26
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Abstract
Improved genotyping technology has made it feasible to use a genetic approach to map genes involved in the etiology of common human diseases. We discuss here recent developments in several different statistical approaches to linkage analysis of these traits, including affected-sib-pair methods, the affected-pedigree-member method, regressive models and linkage-disequilibrium-based approaches. We discuss advantages and disadvantages of the various approaches, as well as factors influencing study design and the ability to detect loci. Statistical methodology in this area is advancing rapidly and will help enable the mapping and cloning of loci involved in susceptibility to common multifactorial diseases.
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Affiliation(s)
- D E Weeks
- Wellcome Trust Centre for Human Genetics, University of Oxford, UK
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27
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Converse PJ, Haines VL, Wondimu A, Craig LE, Meyers WM. Infection of SCID mice with Mycobacterium leprae and control with antigen-activated "immune" human peripheral blood mononuclear cells. Infect Immun 1995; 63:1047-54. [PMID: 7868226 PMCID: PMC173108 DOI: 10.1128/iai.63.3.1047-1054.1995] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The SCID (severe combined immunodeficient) mouse lacks both B and T cells and tolerates injected mononuclear cells from humans, the principal hosts of Mycobacterium leprae. A SCID mouse model of leprosy could be useful to investigate potential vaccine strategies using human cells in a context in which the growth of the organism is monitored. Initial experiments determined that SCID mice are more susceptible than normal mice to infection and dissemination of M. leprae. Cells from humans, either BCG vaccinated or from countries where leprosy is endemic, were stimulated in vitro with a number of mycobacterial antigens--whole M. leprae, M. leprae cell walls, purified protein derivative of M. tuberculosis, and Mycobacterium bovis BCG--and tested for proliferation and production of interleukin-6, tumor necrosis factor alpha, and gamma interferon. Cell walls were the most efficient and consistent in inducing all of these activities. In vitro-activated human cells retain function better after injection into SCID mice than nonactivated cells. To test the ability of cells to affect the growth of M. leprae in the footpads of SCID mice, cells from a known responder to mycobacterial antigens and from a nonresponder were activated by M. leprae cell wall antigens. The cells were harvested and coinjected with fresh M. leprae into the right hind footpads of SCID mice. After 3 months, there was no growth of M. leprae in the footpads of mice coinjected with cells from the mycobacterial antigen responder, while growth was uninhibited in mice receiving cells from the nonresponder. Future experiments will determine requirements for antigen specificity in inhibiting M. leprae multiplication.
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Affiliation(s)
- P J Converse
- Department of Molecular Microbiology and Immunology, Johns Hopkins University School of Hygiene and Public Health, Baltimore, Maryland 21205
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28
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Abstract
Arthritis is a common feature of leprosy and contributes to disability. Direct invasion of joints and bones by mycobacteria may lead to a destructive arthritis in lepromatous disease. The infective process may involve few or many joints. Reactional states may occur spontaneously but usually after the initiation of anti-mycobacterial treatment. In both the type 1 reaction of borderline case and the type 2 reaction of the lepromatous disease, intense inflammation may occur at sites of infection. The immunology of the reactions is different but they share clinical features including a polyarthritis which may resemble rheumatoid disease. The joint disease may be chronic or relapsing, affecting the wrists and small joints of the hands in particular. Radiological erosions may occur. Mycobacterium leprae is not found in the synovium in this pattern of arthritis. Further study of this phenomenon might yield useful information above the mechanism of joint inflammation in other rheumatic diseases.
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29
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Lustbader ED, Rebbeck TR, Buetow KH. Using loss of heterozygosity data in affected pedigree member linkage tests. Genet Epidemiol 1995; 12:339-50. [PMID: 8536951 DOI: 10.1002/gepi.1370120402] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Linkage analysis can be used to test the hypothesis that a marker locus of known location segregates independently from a presumed disease gene. One way to test this hypothesis is to measure the similarity of marker alleles among pairs of relatives affected with the disease. When the disease under consideration is cancer, it is possible to take advantage of the marker alleles in tumors to revise the similarity measure obtained from the observations made in constitutional tissue. Only cancers that arise through the model of recessive oncogenesis are amenable to this revised analysis. This model postulates that cancer is caused by somatic genetic changes which result in the loss of one or both copies of a normal allele at a tumor suppressor locus. If an individual's inherited genotype is heterozygous at the marker locus, the model of recessive oncogenesis suggests that we may observe loss of constitutional heterozygosity at the marker locus in the tumor. In this report, we how how to incorporate this loss of heterozygosity data into affected pedigree member linkage tests. The revised procedure is illustrated using data obtained from relatives with breast cancer. Substantial improvement in the power to reject the different chromosome hypothesis is obtained when loss of heterozygosity is observed in multiple relatives with the same marker alleles retained in the tumors.
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Affiliation(s)
- E d Lustbader
- Division of Population Science, Fox Chase Cancer Center, Philadelphia, Pennsylvania. 19111, USA
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30
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Thomson G. HLA disease associations: models for the study of complex human genetic disorders. Crit Rev Clin Lab Sci 1995; 32:183-219. [PMID: 7598790 DOI: 10.3109/10408369509084684] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The genes of the human leukocyte antigen (HLA) region, the major histocompatibility complex (MHC) of humans, control a variety of functions involved in immune response and influence susceptibility to over 40 diseases. Theoretical studies in the development of models to determine the modes of inheritance of the HLA-associated diseases have led to a better understanding of the inheritance patterns in insulin-dependent diabetes mellitus (IDDM), rheumatoid arthritis, multiple sclerosis, ankylosing spondylitis, hemochromatosis, celiac disease, and others. It is now clear that many of the HLA-associated diseases involve heterogeneity in their HLA components, as well as non-HLA genetic factors. This review is presented using HLA-associated diseases, and in particular IDDM, as the example of interest, but the observations and techniques presented have direct relevance to the study of all human diseases with a complex genetic component. Three methods for localizing disease-predisposing genes are presented: (1) association studies, including population, family, and relative predispositional effects, (2) affected sib pair and other affected-relative methods, and (3) lod score analysis. A variety of complementary methods for studying the mode(s) of inheritance of the alleles at the disease-predisposing locus and for identifying the alleles and amino acids directly involved in the disease process also are presented.
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Affiliation(s)
- G Thomson
- Department of Integrative Biology, University of California, Berkeley 94720-3140, USA
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31
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Abel L, Vu DL, Oberti J, Nguyen VT, Van VC, Guilloud-Bataille M, Schurr E, Lagrange PH. Complex segregation analysis of leprosy in southern Vietnam. Genet Epidemiol 1995; 12:63-82. [PMID: 7713401 DOI: 10.1002/gepi.1370120107] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
To investigate the nature of the genetic component controlling susceptibility to leprosy and its subtypes, 402 nuclear families were ascertained through a leprosy patient followed at the Dermatology Hospital in Ho Chi Minh City, Vietnam; 285 families were of Vietnamese origin and 117 were of Chinese origin with a higher proportion of lepromatous forms among Chinese patients. Segregation analyses were conducted using the model developed by Abel and Bonney [(1990) Genet Epidemiol 7:391-407], which accounted for variable age of onset and time-dependent covariates. Three phenotypes were considered: leprosy per se (all forms of leprosy together), nonlepromatous leprosy, and lepromatous leprosy. For each of this phenotype, analyses were performed on the whole sample and separately on the Vietnamese and the Chinese families. The results showed that a single Mendelian gene could not account for the familial distributions of leprosy per se and its two subtypes in the whole sample. However, these results were different according to the ethnic origin of the families. In the Vietnamese subsample, there was evidence for a codominant major gene with residual familial dependences for the leprosy per se phenotype, and borderline rejection of the Mendelian transmission hypothesis for the nonlepromatous phenotype. In Chinese families, strong rejection of Mendelian transmission was obtained in the analysis of leprosy per se, and no evidence for a familial component in the distribution of the nonlepromatous phenotype was observed. For the lepromatous phenotype, the discrimination between models was poor, and no definitive conclusion could be reached. Referring to immunological data, we suggest that these results could be explained by a heterogeneity in the definition of the lepromatous phenotype. It is likely that progress in the understanding of the genetic components involved in the expression of leprosy will come from a better definition of the phenotype under study, and immunological studies are ongoing in this population to investigate this hypothesis.
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Affiliation(s)
- L Abel
- INSERM U. 194, Hôpital St. Louis, Paris, France
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32
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Abstract
There is now a considerable body of literature which describes and analyses various methods of testing for the presence of disease susceptibility genes by examining the degree of HLA haplotype sharing of parental haplotypes over random expectations amongst affected siblings. We here survey a number of improvements, generalizations and extensions of the earlier reported methods with the aim of bringing them to the attention of those who are collecting HLA or other haplotype data on familial disease.
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Affiliation(s)
- S Shah
- Statistics and Computational Mathematics Department, University of Liverpool
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33
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Abstract
Four methods using identity by state (IBS) data from affected sib pairs are compared for their ability to detect linkage between a diallelic marker and disease. A joint null hypothesis of no linkage and no linkage disequilibrium between the marker and disease must be considered. Two tests have undesirable properties in the case of linkage disequilibrium. Which of the other two tests has more power is dependent on the presence or not of linkage disequilibrium. The procedure of choice when possible is to type parents of affected sib pairs: the null hypothesis of no linkage can then be tested using identity by descent (IBD) values from informative parents, and the null hypothesis of no marker association with disease (linkage equilibrium) can be tested independently using the marker allele frequencies in the affected sib pairs.
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Affiliation(s)
- G Thomson
- Department of Integrative Biology, University of California, Berkeley 94720
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34
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Shaw MA, Atkinson S, Dockrell H, Hussain R, Lins-Lainson Z, Shaw J, Ramos F, Silveira F, Mehdi SQ, Kaukab F. An RFLP map for 2q33-q37 from multicase mycobacterial and leishmanial disease families: no evidence for an Lsh/Ity/Bcg gene homologue influencing susceptibility to leprosy. Ann Hum Genet 1993; 57:251-71. [PMID: 7910002 DOI: 10.1111/j.1469-1809.1993.tb00899.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The mycobacterial diseases leprosy and tuberculosis (TB) and the leishmaniases are characterized by a wide spectrum of disease phenotypes, and by the fact that the majority of individuals exposed to the causative organisms Mycobacterium leprae, M. tuberculosis and Leishmania sp. become infected but do not present with clinical disease. In order to determine whether a human homologue to the murine macrophage resistance gene Lsh/Ity/Bcg influences susceptibility to human disease, multicase families for all three diseases have been collected, and linkage analysis performed using a panel of markers in the region of human chromosome 2q33-q37 known to be conserved with the Lsh/Ity/Bcg-containing region of murine chromosome 1. Because of the paucity of available polymorphic markers/linkage information for 2q33-q37, data from 35 multicase leprosy, TB and visceral leishmaniasis families (310 individuals) were first pooled to produce a detailed RFLP map of the region. Peak LOD scores well in excess of 3 were observed for linkage between adjacent pairs of a more proximal (2q33-q35) set of markers CRYGP1, MAP2, FN1, TNP1, VIL1 and DES, and between adjacent pairs of a more distal (2q35-q37) set COL6A3, D2S55 and D2S3. These peak LOD scores and the corresponding values for theta were used in the MAP92 program to generate a multiple two-point map with gene order/map intervals (cM) of: CRYGP1-4.65-MAP2-3.45-FN1-5.95-TNP1-3.41-VIL1-3. 01- DES-20.14-COL6A-10.91-D2S55-3.67-D2S3. Although local support for the placement of loci in this order was weak (LOD < 2, except for DES-COL6A3 where LOD = 6.02), the map is consistent with the gene order for those loci (Cryg, Fn-1, Tp-1, Vil, Des, Col6a3) previously mapped in the mouse. Data from 17 multicase leprosy families (149 individuals) were further analysed for linkage between a putative disease susceptibility locus (DSL) controlling susceptibility to leprosy per se and each of the marker loci. Assuming 100% penetrance for the susceptibility allele, no positive LOD score was obtained for linkage between the DSL and any of the marker genes. Instead, the data provide convincing evidence (LOD scores < -2) that a DSL does not fall within 10-20 cM of CRYGP1, MAP2, TNP1, VIL1, DES or D2S55, or within 5-10 cM of FN1, COL6A3 or D2S3. This effectively excludes a putative DSL controlling susceptibility to leprosy per se from the entire region 2q33-q37.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- M A Shaw
- Department of Medicine, University of Cambridge Clinical School, UK
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35
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Taneja V, Mehra NK, Anand C, Malaviya AN. HLA-linked susceptibility to rheumatoid arthritis. A study of forty-one multicase families from northern India. ARTHRITIS AND RHEUMATISM 1993; 36:1380-6. [PMID: 8216398 DOI: 10.1002/art.1780361009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
OBJECTIVE To analyze segregation of rheumatoid arthritis (RA) with HLA-DR4 and/or other alleles in multicase RA families and to compare the segregation patterns among affected and unaffected sibs. METHODS Forty-one multicase families (22 multiplex and 19 simplex) of northern Indian origin were studied for HLA haplotype segregation. RESULTS HLA haplotype sharing among affected sibs was observed more often than expected in families in which both parents were healthy (P < 0.05). RA cosegregated with a DR4 haplotype among offspring only in multiplex families in which both parents were unaffected (P < 0.05), while in simplex families, the disease segregated with DR4 only when the allele was from the affected DR4-heterozygous parent. In DR4-negative affected sib pairs, DR1, DR6, and DR10 were inherited from healthy parents more often than expected. CONCLUSION Dissimilar modes of inheritance are seen among multiplex and simplex RA families. The results of segregation analysis are compatible with the hypothesis that an epitope, rather than an individual DR antigen(s), is responsible for increased risk for development of RA.
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Affiliation(s)
- V Taneja
- Histocompatibility and Immunogenetics Unit, All India Institute of Medical Sciences, New Delhi
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36
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Ulrich M, Zulueta AM, Cáceres-Dittmar G, Sampson C, Pinardi ME, Rada EM, Aranzazu N. Leprosy in women: characteristics and repercussions. Soc Sci Med 1993; 37:445-56. [PMID: 8211257 DOI: 10.1016/0277-9536(93)90280-h] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
"Health is often measured in terms of low mortality; nevertheless, merely being alive is not a measure of the quality of life" H. Méndez Castellanos. Physiological, socioeconomic and cultural factors play important roles in the response of women to Mycobacterium leprae and in the impact of leprosy on their lives. They appear to develop stronger immunological responses to M. leprae than men, as suggested by lower incidence and less severe clinical forms of disease in most areas of the world, as well as stronger reactions of cell-mediated immunity after prophylactic vaccination. Genetic factors and physiological status including pregnancy, intercurrent infection and malnutrition might be among the factors which modulate this response. Women in leprosy-endemic areas of the world, with few exceptions, suffer from marked economic and social dependency and inferiority which can only be heightened by the social stigma associated with leprosy. Nevertheless, they bear an enormous responsibility for the health of their families, often as head of the household, and they often possess a unique capacity to influence community opinion. With the introduction of multidrug therapy, leprosy control throughout the world is no longer an unrealistic goal. Active vaccination may constitute the other factor necessary for eventual eradication of the disease. The incorporation of women at all levels into active roles in health care programs may constitute one of the decisive factors in the success or failure of leprosy control.
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Affiliation(s)
- M Ulrich
- Instituto de Biomedicina, Caracas, Venezuela
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37
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Abstract
There are several tests available for use with family studies to test if there is significant evidence of association with a particular disease gene locus, especially of HLA. We have used large simulations to compare the powers of tests using criteria N, R, T, PR, WP and some new tests involving both affecteds and unaffecteds in a sibship. It was found that tests using both affected and unaffected siblings were often more powerful.
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Affiliation(s)
- J R Green
- Statistics and Computational Mathematics Department, Liverpool University
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38
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Abstract
An improved sib-pair test for linkage is introduced which is superior to the previously proposed tests. The test is derived from the standard chi-squared goodness of fit statistic by restricting the alternative hypothesis to the genetically possible. Critical values are given and exact power comparisons are made with the previously proposed tests. The new test is shown to be more powerful for finite samples as well as being asymptotically uniformly most powerful.
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Affiliation(s)
- J J Faraway
- Department of Statistics, University of Michigan, Ann Arbor 48109
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39
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Abstract
The N-test of haplotype concordance among siblings affected by some disease under investigation is used to decide whether there is a disease susceptibility gene linked to a marker locus or chromosomal region. The use of this test and appropriate modifications of it is briefly reviewed. The power of the ordinary N-test is then derived as a function of several parameters. The sample size needed to attain a given power is then derived. Some of the parameters are specified and the required sample sizes are given in tables for different values of the main unknown parameters.
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Affiliation(s)
- J R Green
- Statistics and Computational Mathematics Department, Liverpool University
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40
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Affiliation(s)
- R R de Vries
- Department of Immunohematology and Blood Bank, University Hospital, Leiden, The Netherlands
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41
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Schauf V, Holobaugh P, Miller P, Mittal K. Sensitization in vitro of human peripheral blood mononuclear cells to phenolic glycolipid 1 of Mycobacterium leprae in liposomes. Cell Immunol 1991; 137:81-7. [PMID: 1884400 DOI: 10.1016/0008-8749(91)90058-j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Study of primary immune responses in leprosy has been limited, since disease becomes manifest long after infection or is not detectable. To study primary immune responses, we immunized in vitro human peripheral blood mononuclear cells from unexposed individuals using phenolic glycolipid 1 (PGL-1), an important water-insoluble antigenic constituent of Mycobacterium leprae. PGL-1, encapsulated in liposomes, induced lymphoproliferation or, less frequently, suppression of lymphoproliferation in 11-day lymphocyte cultures. The primary lymphocyte responses resembled those elicited with keyhole limpet hemocyanin (KLH). HLA-DR2 expression, associated with tuberculoid leprosy, did not influence the outcome of in vitro sensitization. The association of HLA-DR2 and tuberculoid leprosy is not explained by differential ability to generate primary lymphoproliferative responses to PGL-1 or KLH. We have extended in vitro sensitization methodology to include a water-insoluble antigen in antigen-bearing liposomes. This methodology is potentially useful for studies of immunogenetics and immunopathology, and for vaccine research.
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Affiliation(s)
- V Schauf
- Department of Pediatrics, School of Medicine, State University of New York, Stony Brook
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42
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Abstract
This review, the third in the series on cellular immune reactivity to tubercle bacilli in the centenary year of Koch's classical paper describing this phenomenon and its possible implications, represents an immunogenetic point of view. In fact this will be quite a broad point of view by an immunogeneticist who is not hampered by specific knowledge on therapy or prevention of tuberculosis. In this respect I probably do not differ very much from Robert Koch 100 years ago! An important difference, however, is that we think we now understand a great deal of the cellular and molecular basis of the immunological phenomena observed by Koch. Immunogenetics has contributed considerably to our current understanding and I will try to review that contribution here. Because thus far my main research interest has been in another mycobacterium, namely Mycobacterium leprae, I will use M. leprae and leprosy as an example to illustrate some ideas. The message of this review is that there is a reason for optimism: the knowledge recently gained by cellular and molecular immunologists as well as immunogeneticists has straightforward implications for the rational development of subunit vaccines and immunotherapeutic strategies.
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Affiliation(s)
- R R De Vries
- Department of Immunohaematology and Blood Bank, University Hospital, Leiden, The Netherlands
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43
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Lara ML, Layrisse Z, Scorza JV, Garcia E, Stoikow Z, Granados J, Bias W. Immunogenetics of human American cutaneous leishmaniasis. Study of HLA haplotypes in 24 families from Venezuela. Hum Immunol 1991; 30:129-35. [PMID: 2022495 DOI: 10.1016/0198-8859(91)90081-j] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Twenty-four families with one or multiple cases of localized cutaneous leishmaniasis (LCL) from an endemic region with the highest incidence of LCL in Venezuela were typed from HLA-ABC, DR, DQ antigens and complement factors. The parental HLA haplotypes segregated at random among healthy and affected siblings but in backcross families significantly higher frequencies of HLA-A28 (p = 0.0018), -Bw22 (p = 0.0122), or -DQw8 (p = 0.0364) were present in affected compared to healthy siblings. HLA-B15 showed a higher frequency (p = 0.0062) among the latter group. Haplotypes Bw22CF31 (p = 0.0076) and Bw22DRw11DQw7 (p = 0.0163) were also significantly more frequent in affected compared to healthy siblings and A2Cw- (p = 0.0445) among the latter. No HLA genetic linkage with a putative LCL susceptibility gene(s) could be demonstrated in this study. A case/control comparison of 26 unrelated LCL patients (one proband from each family) and healthy individuals of the same ethnic origin confirmed the association of HLA-Bw22 (pc = 0.048) and -DQw3 (pc = 0.036) with LCL. The relative risk reached 12.5 for Bw22 and 4.25 for DQw3 with ethiologic factors of 0.17 and 0.64, respectively. HLA-DQw3 apparently makes the major contribution as a genetic risk factor for LCL at the population level.
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Affiliation(s)
- M L Lara
- Centro de Medicina Experimental, Instituto Venezolano de Investigaciones, Caracas
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44
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Abstract
Cases of interest using affected sib-pair methods to distinguish between recessive and additive (dominant) modes of inheritance of a disease-predisposing gene involve goodness-of-fit tests with a small expected number in the "share-zero parental haplotypes" category, as well as an unknown parameter, the frequency of the disease-predisposing allele. Our simulations demonstrate that the real significance level of the chi-square test using the three-haplotype-sharing IBD values (share 2, 1, and 0 parental haplotypes) is close to the assumed (.05) level in these cases, so that the haplotype-sharing classes do not have to be lumped, which would leave no degrees of freedom for a statistical test. The validity of the chi-square approximation in cases of small expected frequencies has previously been described, but the situations that have been considered do not cover the very small values in the share-zero category that are often expected in the affected sib-pair analysis, nor do they involve estimation of an unknown parameter. Although including IBD values from affected kin pairs other than sibs can be a very powerful tool in demonstrating linkage of a marker and disease, these pairs do not add power, in fact they reduce the power, of the chi-square tests of goodness-of-fit of modes of inheritance.
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Affiliation(s)
- U Motro
- Department of Integrative Biology, University of California, Berkeley 94720
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45
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Khomenko AG, Litvinov VI, Chukanova VP, Pospelov LE. Tuberculosis in patients with various HLA phenotypes. TUBERCLE 1990; 71:187-92. [PMID: 2238125 DOI: 10.1016/0041-3879(90)90074-i] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Tuberculosis patients and healthy subjects from six ethnic groups of the Soviet Union were HLA-A, -B, -C, and DR typed. The frequencies of the HLA-A, -B and -C antigens differed amongst the ethnic groups. With all groups, however, patients with tuberculosis showed a significantly increased frequency of HLA-DR2 and a reduced frequency of HLA-DR3 type. Unfavourable dynamics of tuberculosis was significantly associated with an increased incidence of B15 and DR2 and a reduced incidence of B27 and DR3. Family studies revealed that the inheritance of susceptibility to tuberculosis (from parent to offspring) is associated with the inheritance of certain HLA haplotypes. Tuberculosis patients bearing the DR2 antigen had increased levels of IgG antibodies to PPD and the frequency of B7 and, more particularly, DR2 was higher in anergic patients.
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Affiliation(s)
- A G Khomenko
- Central Tuberculosis Research Institute, Moscow, USSR
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46
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Pal N, Majumder PP. On a test of non-random segregation under linkage for autosomal recessive diseases. Stat Med 1990; 9:573-82. [PMID: 2349406 DOI: 10.1002/sim.4780090510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
To test the null hypothesis of random segregation of marker haplotypes from an unaffected parent to affected offspring for a one-locus autosomal recessive disease, Majumder proposed a test statistic which was shown to be locally most powerful against the alternative hypothesis of non-random segregation due to linkage between the disease and marker loci. The test procedure relied on a chi-squared approximation to the null distribution of the test statistic. In the present study, we show that the chi-squared approximation is poor for most practical situations and derive the exact null distribution of a function of the test statistic. We illustrate the method using published data on tuberculoid leprosy and HLA. We show that the test procedure is invariant, and extend the method to the case of a two-locus recessive disease.
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Affiliation(s)
- N Pal
- Department of Statistics, University of Southwestern Louisiana, Lafayette
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47
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Schaid DJ, Nick TG. Sib-pair linkage tests for disease susceptibility loci: common tests vs. the asymptotically most powerful test. Genet Epidemiol 1990; 7:359-70. [PMID: 2253870 DOI: 10.1002/gepi.1370070506] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Several statistical tests for linkage between a disease susceptibility locus and a marker locus for sib-pair data are examined analytically. Two common statistics, a test based on the mean number of marker alleles shared identical by descent by sib-pairs, and a test based on the proportion of sib-pairs sharing exactly two marker alleles, are shown to be special cases of a more general statistic. We use this more general statistic to derive the asymptotically most powerful statistic for a given genetic alternative hypothesis, and then compare this statistic with the "mean" statistic and the "proportion" statistic. Results indicate that the "mean" statistic generally compares well with the most powerful statistic. However, in some instances the "mean" statistic may lose power, relative to the most powerful. To guard against this, a new statistic (the maximum of the "mean" and "proportions" statistics) is considered and its asymptotic distribution is derived. Results indicate that this new statistic performs well.
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Affiliation(s)
- D J Schaid
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905
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Sheehy MJ, Meske LM, Emler CA, Rowe JR, Neme de Gimenez MH, Ingle CA, Chan A, Trucco M, Mak TW. Allelic T-cell receptor alpha complexes have little or no influence on susceptibility to type 1 diabetes. Hum Immunol 1989; 26:261-71. [PMID: 2573589 DOI: 10.1016/0198-8859(89)90004-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We performed a multiple-affected-sib study to determine if T-cell receptor alpha-chain alleles affect susceptibility to insulin-dependent diabetes mellitus. Restriction fragment length polymorphisms were used to follow the segregation of allelic T-cell receptor alpha complexes within the families. The segregation of T-cell receptor alpha alleles in 29 multiplex families revealed no significant tendency for affected sibs to share T-cell receptor alpha-chain alleles more often than would be expected by chance alone (p greater than 0.2). In contrast, the same type of analysis for HLA alleles easily detected the well-known linkage of insulin-dependent diabetes mellitus susceptibility to the HLA complex (p = 0.003). We suggest that the importance of HLA alleles in insulin-dependent diabetes mellitus susceptibility and the lack of importance of T-cell receptor alpha alleles result from the different strategies by which HLA and T-cell receptor molecules achieve antigen-binding diversity: multiple loci and allelic diversity in the case of HLA; combinatorial, junctional, and N-region diversity in the case of the T-cell receptor. In this paper we also describe three new restriction fragment length polymorphisms of the T-cell receptor alpha complex and a new method for testing the significance of linkage in multiple-affected-sib studies.
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Affiliation(s)
- M J Sheehy
- American Red Cross Blood Services, Madison, WI 53705
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49
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Affiliation(s)
- V N Sehgal
- Department of Dermatology and Venereology, Maulana Azad Medical College, New Delhi, India
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50
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van Eden W, Hogervorst EJ, Hensen EJ, van der Zee R, van Embden JD, Cohen IR. A cartilage-mimicking T-cell epitope on a 65K mycobacterial heat-shock protein: adjuvant arthritis as a model for human rheumatoid arthritis. Curr Top Microbiol Immunol 1989; 145:27-43. [PMID: 2680295 DOI: 10.1007/978-3-642-74594-2_3] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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