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Thomson G. An overview of the genetic analysis of complex diseases, with reference to type 1 diabetes. Best Pract Res Clin Endocrinol Metab 2001; 15:265-77. [PMID: 11554770 DOI: 10.1053/beem.2001.0145] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Despite extensive efforts by many groups, progress in the mapping of complex diseases has been exceedingly slow, only a few genes and some genetic regions having been identified. The general picture is one of difficulty in locating disease genes and in the replication of linkages. This results from the role in disease of a large number of genes, many with a relatively minor effect and many involving common genetic variation. A multi-strategy approach to the mapping of complex diseases is required: no single method is sufficient or optimal. The role of human leukocyte antigens in type 1 diabetes has been known for nearly 30 years, and the associations, linkage and genetic contribution to disease are all strong, but all the human leukocyte antigen region genes involved in the disease process have not yet been identified. The methods used in study of this component to type 1 diabetes are a model for all complex diseases.
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Jones S, Love C, Thomson G, Green R, Howden-Chapman P. Second-hand smoke at work: the exposure, perceptions and attitudes of bar and restaurant workers to environmental tobacco smoke. Aust N Z J Public Health 2001; 25:90-3. [PMID: 11297311 DOI: 10.1111/j.1467-842x.2001.tb00557.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVES To investigate the knowledge of, and perceptions, attitudes and exposure to second-hand smoke (SHS) of staff in the New Zealand hospitality industry. METHOD Face-to-face interviews with bar staff, waiters, and bar and eating-place managers and owners in Wellington during the 1999-2000 summer. An analysis was made of the 1999 New Zealand Electoral Roll to find the number of those most exposed to SHS. RESULTS 435 interviews with full data recovery were completed at 364 locations; 59% of interviewees were exposed to SHS, including 77% of those at licensed premises. More than half of those exposed to workplace smoke reported irritation from SHS to their throat or lungs. Less than a third were aware of the risk of strokes from SHS. Three-quarters of interviewees wanted some sort of smoking restriction in bars. CONCLUSIONS The majority of interviewees were at risk of premature death and disease because of exposure to workplace smoke, and had an incomplete knowledge of the dangers to which they were exposed. More than 5,000 similar workers in New Zealand appear to share this risk. IMPLICATIONS This industry needs legislation to make it smoke free.
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Hollenbach JA, Thomson G, Cao K, Fernandez-Vina M, Erlich HA, Bugawan TL, Winkler C, Winter M, Klitz W. HLA diversity, differentiation, and haplotype evolution in Mesoamerican Natives. Hum Immunol 2001; 62:378-90. [PMID: 11295471 DOI: 10.1016/s0198-8859(01)00212-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Genetic variation of the Human Leukocyte Antigen region (HLA) in three Amerindian populations from the Southern Mexican state of Oaxaca, the Zapotec, Mixtec and the Mixe is examined. Individuals were typed using PCR-SSOP for four class II loci (DRB1, DQA1, DQB1, DPB1) and three class I loci (HLA-A, -B, and -C). Based on known HLA distributions, European admixture ranged from 1% to 10%. Individuals with European alleles were excluded from subsequent analysis. New alleles were revealed at each of the class I loci. In general, genotype frequencies were in Hardy-Weinberg equilibrium, although some deviations were detected. Allele frequency distributions at the DRB1, DQA1, DQB1 and HLA-A loci in all populations were more even than expected under neutrality, supporting a model of balancing selection at these loci. A history of directional selection for DPB1 in all three populations was indicated, as homozygosity values were significantly above expected values. Allele frequency distributions at HLA-B and HLA-C did not differ significantly from neutrality expectations. The data also provide evidence from linkage disequilibrium that strong haplotypic associations are present across the entire HLA region in each of the populations. Significant overall linkage disequilibrium exists between all pairs of loci typed in these populations, except those which include the DPB1 locus. These associations exist despite the fact that the recombination fraction between HLA-A, in the class I region, and DQB1, in the class II region, may exceed 0.02. One explanation is that selective pressures are maintaining the relationships between particular alleles at these loci in these populations. These relationships are maintained in general across the entire HLA region in the Oaxacan Amerindians, with the exception of DPB1.
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Abstract
Genome-wide linkage scans using affected sibpair families are being conducted on many complex diseases, such as type 1 and type 2 diabetes, multiple sclerosis, rheumatoid arthritis, schizophrenia, asthma, cardiovascular diseases, obesity, and alcoholism. Despite extensive efforts by many groups, progress has been exceedingly slow, and only a few genes and some genomic regions involved in complex diseases have been identified. The general picture is one of difficulty in locating disease genes and replication of reported linkages. This results from the fact that complex diseases and traits may result principally from genetic variation that is relatively common in the general population involving a large number of genes, environmental factors, and their interactions. Genome-wide association studies are now feasible through the use of PCR methodologies with pooled DNA samples and microsatellite variation, and more recently single-nucleotide polymorphism (SNP) variation. Issues relating to significance levels in genome-wide linkage and association scans are discussed, and suggestions for dealing with false positive (type I) errors proposed.
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Wilson N, Thomson G. Pacific peoples killed by New Zealand tobacco industry exports. THE NEW ZEALAND MEDICAL JOURNAL 2001; 114:49-50. [PMID: 11277483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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Meyer D, Thomson G. How selection shapes variation of the human major histocompatibility complex: a review. Ann Hum Genet 2001; 65:1-26. [PMID: 11415519 DOI: 10.1046/j.1469-1809.2001.6510001.x] [Citation(s) in RCA: 259] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2000] [Indexed: 11/20/2022]
Abstract
The nature of polymorphism and molecular sequence variation in the genes of the human major histocompatibility complex (MHC) provides strong support for the idea that these genes are under selection. With the understanding that selection shapes MHC variation new questions have become the focus of study. What is the mode of selection that accounts for MHC polymorphism? Is variation maintained by pathogen pressure or by reproductive mechanisms? Discerning between these requires drawing on information from studies on association between HLA genes and infectious diseases, reproductive success and mating preferences relative to HLA genotypes, and theoretical studies that compare the outcomes of different selection regimes. The pattern that has emerged suggests that several types of selection are plausible for the maintenance of HLA polymorphism.
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Rigby AS, MacGregor AJ, Thomson G. HLA haplotype sharing in rheumatoid arthritis sibships: risk estimates subdivided by proband genotype. Genet Epidemiol 2000; 15:403-18. [PMID: 9671989 DOI: 10.1002/(sici)1098-2272(1998)15:4<403::aid-gepi6>3.0.co;2-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
There is a well-known association between rheumatoid arthritis (RA) and HLA-DR4. Recent research has indicated that both DR4 haplotypes are important in disease predisposition (favoring a recessive mode of inheritance). Others have suggested that certain combinations of genotypes, in particular Dw4/Dw14 heterozygotes, may be more important than others. We examined the mode of inheritance of RA using data from the Arthritis and Rheumatism Council's national repository of family material [Worthington et al. (1994) Br J Rheumatol 33:970-976]. There were 85 affected sibships consisting of 77 sib pairs, 6 trios, 1 quintuplet, and 1 sextuplet. The affected sibs shared two, one, and zero parental HLA haplotypes in a ratio of 0.42:0.43:0.15, which was significantly different from random expectations (P = 0.00009). Risk estimates for RA to sibs were calculated based on an overall sibling recurrence risk of 3.9%. Risks for those sharing two, one, and zero parental HLA haplotypes were 6.5% [95% confidence interval (CI) = 5.1-7.9%], 3.3% (95% CI = 2.6-4.0%), and 2.5% (95% CI = 1.5-3.5%), respectively. We also examined the risk of RA based on the DRbeta1 genotype status of sib and proband. After excluding genotypic combinations with small numbers, the highest genotype-specific risks were seen for sibs sharing two haplotypes with either a DRbeta1*0401/DRbeta1*0404 (12.5%, 95% CI = 6.9-15.2%) or a DRbeta1*0401/DRbeta1*0408 (11.1%, 95% CI = 4.5-15.1%) proband. An independent assessment based on the AGFAP methodology confirmed the increase in risk for these genotypes, in particular for DRbeta1*0401/DRbeta1*0408. The excess being due to *0401/*0408 rather than to *0401/*0404 may explain why the Dw4/Dw14 effect is not always observed.
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Thomson G, Wilson N. Tobacco tax and Maori and low-income families. THE NEW ZEALAND MEDICAL JOURNAL 2000; 113:197. [PMID: 10917088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
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Adams EJ, Cooper S, Thomson G, Parham P. Common chimpanzees have greater diversity than humans at two of the three highly polymorphic MHC class I genes. Immunogenetics 2000; 51:410-24. [PMID: 10866107 DOI: 10.1007/s002510050639] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
MHC class I polymorphism improves the defense of vertebrate species against viruses and other intracellular pathogens. To see how polymorphism at the same class I genes can evolve in different species we compared the MHC-A, MHC-B, and MHC-C loci of common chimpanzees and humans. Diversity in 23 Patr-A, 32 Patr-B, and 18 Patr-C alleles obtained from study of 48 chimpanzees was compared to diversity in 66 HLA-A, 149 HLA-B, and 41 HLA-C alleles obtained from a study of over 1 million humans. At each locus, alleles group hierarchically into families and then lineages. No alleles or families are shared by the two species, commonality being seen only at the lineage level. The overall nucleotide sequence diversity of MHC class I is estimated to be greater for modern chimpanzees than humans. Considering the numbers of lineages, families, and alleles, Patr-B and Patr-C have greater diversity than the HLA-B and HLA-C, respectively. In contrast, Patr-A has less polymorphism than HLA-A, due to the absence of A2 lineage alleles. The results are consistent with ancestral humans having passed through a narrower population bottleneck than chimpanzees, and with pathogen-mediated selection having favored either preservation of A2 lineage alleles on the human line and/or their extinction on the chimpanzee line.
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Abstract
Testing for random mating in human populations is difficult due to confounding factors such as ethnic preference and population stratification. With HLA, the high level of polymorphism is an additional problem since it is rare for couples to share the same haplotype. Focus on an ethnically homogeneous population, where levels of polymorphism at HLA loci are more limited, may provide the best situation in which to detect non-random mating. However, such populations are often genetic isolates where there may be inbreeding to an extent that is difficult to quantify and account for. We have developed a test for random mating at a multiallelic locus that is robust to stratification and inbreeding. This test relies on the availability of genotypic information from the parents of both spouses. The focus of the test is on families where there is allele sharing between the parents of both spouses, so that potential spouses could share an allele. Denoting the shared allele at the locus of interest by A, then under the assumption of random mating, heterozygous parents AX should transmit allele A equally as frequently as allele X to their offspring. When there is positive (negative) assortative mating, A will be transmitted more (less) often than X. The power of the test has been computed in a number of situations. Data on high resolution HLA haplotypes from the Hutterite population were reinvestigated by the proposed test. The test detects significant negative assortative mating when the parental origin of the shared haplotype is taken into account.
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Abstract
HLA-DPB1 genotypes were determined for samples from 269 multiplex Caucasian families from the Human Biological Data Interchange. DRB1 and DQB1 loci were also characterized, allowing assignment of DPB1 alleles to haplotypes and calculation of linkage disequilibrium values. Frequencies for several DPB1 alleles differed significantly between patients and affected family-based control subjects. Some differences were attributable to linkage disequilibrium with DR and DQ alleles, whereas others were not. DPB1*0301 and DPB1*0202 alleles are predisposing for type 1 diabetes in these data, not only in analyses of individual alleles, but also in genotype analyses. DPB1*0402 appears protective; however, stratification analysis indicates that its protective effect is specific for DR3 haplotypes. A protective role for DPB1*0401 is suggested by genotype analysis. For increased statistical power, DPB1 alleles were pooled into three categories: susceptible, neutral, and protective after removal of effects due to linkage disequilibrium with DR-DQ. Analysis of these pools suggests that DPB1 primarily affects susceptibility to, rather than protection from, type 1 diabetes in a dominant fashion. This effect is more apparent in patients with genotypes other than the highest risk DR3/DR4-DQB1*0302 genotype. These data support a role for the DPB1 locus in conferring susceptibility to type 1 diabetes.
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Valdes AM, McWeeney SK, Thomson G. Evidence for linkage and association to alcohol dependence on chromosome 19. Genet Epidemiol 1999; 17 Suppl 1:S367-72. [PMID: 10597464 DOI: 10.1002/gepi.1370170762] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
An association study on markers showing suggestive evidence for linkage to severe alcoholism was performed on the Collaborative Study on the Genetics of Alcoholism (COGA) data set. Our linkage study was restricted to the autosomal markers on chromosomes 2, 3, 4, 13, and 19, with low homozygosity (below 30%) and high identity-by-state sharing in affected sib pairs (ASPs). We used a strict phenotype definition, only individuals diagnosed as affected both on the ALDX1 (COGA criterion) and ALDX2 (ICD-10) scales were used in the analyses. Linkage was assessed by excess identity-by-descent allele sharing in ASPs. The strongest evidence of linkage was detected on chromosome 19, in particular at markers D19S49 (p < 0.0001) and D19S431 (p < 0.002). An association study of allele and haplotype data was then carried out on chromosome 19 markers using affected-family-based controls. A haplotype defined by alleles at markers D19S49, D19S43, and D19S200 in chromosome 19 shows significant association (p < 0.003, odds ratio 2.82). Further, significant differences were observed in the distribution of the harm avoidance subscale among genotypes defined by D19S49 (p < 0.0001). These results provide evidence for the existence of a locus in chromosome 19 potentially involved in alcohol dependence susceptibility.
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Chen JJ, Hollenbach JA, Trachtenberg EA, Just JJ, Carrington M, Rønningen KS, Begovich A, King MC, McWeeney S, Mack SJ, Erlich HA, Thomson G. Hardy-Weinberg testing for HLA class II (DRB1, DQA1, DQB1, and DPB1) loci in 26 human ethnic groups. TISSUE ANTIGENS 1999; 54:533-42. [PMID: 10674966 DOI: 10.1034/j.1399-0039.1999.540601.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Testing the fit of population data to Hardy-Weinberg proportions is crucial in the validation of many current approaches in population genetic studies. In this paper, we tested fit to Hardy-Weinberg proportions using exact approaches for both the overall and individual heterozygote genotype data of four HLA Class II loci: DRB1, DQA1, DQB1, and DPB1, from 26 human populations. Eighty of 99 overall tests fit the Hardy-Weinberg expectation (73% for DRB1, 89% for DQA1, 81% for DQB1 and 81% for DPB1). Deviations from Hardy-Weinberg proportions were both locus and group specific. Although we could not rule out other mechanisms at work, the individual test results indicated that the departure was possibly partly due to recent admixture. Evidence for selection and other sources of deviation are also discussed.
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Thomson G, Esposito MS. The genetics of complex diseases. Trends Cell Biol 1999; 9:M17-20. [PMID: 10611674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Genetic factors influence virtually every human disorder, determining disease susceptibility or resistance and interactions with environmental factors. Our recent successes in the genetic mapping and identification of the molecular basis of mendelian traits have been remarkable. Now, attention is rapidly shifting to more-complex, and more-prevalent, genetic disorders and traits that involve multiple genes and environmental effects, such as cardiovascular disease, diabetes, rheumatoid arthritis and schizophrenia. Rather than being due to specific and relatively rare mutations, complex diseases and traits result principally from genetic variation that is relatively common in the general population. Unfortunately, despite extensive efforts by many groups, only a few genetic regions and genes involved in complex diseases have been identified. Completion of the human genome sequence will be a seminal accomplishment, but it will not provide an immediate solution to the genetics of complex traits.
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Abstract
It is of interest to detect the deviation from Hardy-Weinberg proportion (HWP) for a particular heterozygote. Hernández and Weir (1989, Biometrics 45, 53-70) suggested a disequilibrium coefficient approach and proposed a 1-d.f. chi2 test. This note derives the appropriate variance under the null hypothesis for performing this individual HWP test. Examples of applying the test to human genetic disease data are presented.
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Wilson N, Thomson G. Content analysis and publication outcomes of projects by public health medicine registrars. Aust N Z J Public Health 1999; 23:541-2. [PMID: 10575781 DOI: 10.1111/j.1467-842x.1999.tb01315.x] [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: 11/28/2022] Open
Abstract
OBJECTIVE To examine the content of the project work of public health medicine registrars in New Zealand and identify publication outcomes. METHOD All projects submitted during 1987-97 were examined and key aspects captured on a database. Literature searches using Medline, Health Star, Index New Zealand and the NZ National Library catalogue were undertaken. RESULTS A total of 355 registrar projects produced by 91 registrars were identified. Only 29% of these projects were associated with one or more publications that could be identified in electronic databases commonly available to New Zealanders and only 16% of them were associated with an article in the Medline-indexed literature. A possible cause for concern is the relatively small amount of project work (6% of projects) that was directly on Maori and/or Pacific Peoples' health. There also appears to be a relative lack of project work on chronic disease epidemiology and control, tobacco control and the socio-economic determinants of health. CONCLUSIONS Given the relatively high quality of registrar project work, a publication rate of only 29% is probably suboptimal. The subject matter of registrar projects appears to infrequently address certain major areas of public health importance including Maori and Pacific Peoples' health. IMPLICATIONS Consideration should be given to addressing these issues by those involved in public health medicine training.
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Adams EJ, Thomson G, Parham P. Evidence for an HLA-C-like locus in the orangutan Pongo pygmaeus. Immunogenetics 1999; 49:865-71. [PMID: 10436180 DOI: 10.1007/s002510050566] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
HLA-B and C are related class I genes which are believed to have arisen by duplication of a common ancestor. Previous study showed the presence of orthologues for both HLA-B and C in African apes but only for HLA-B in Asian apes. These observations suggested that the primate C locus evolved subsequent to the divergence of the Pongidae and Hominidae. From an analysis of orangutan Tengku two HLA-C-like alleles (Popy C*0101 and Popy C*0201) were defined as well as three HLA-B-like (Popy-B) alleles. By contrast, no Popy-C alleles were obtained from orangutan Hati, although three Popy-B alleles were defined. Thus an HLA-C-like locus exists in the orangutan (as well as a duplicated B locus), implying that the primate C locus evolved prior to the divergence of the Pongidae and Hominidae and is at least 12-13 million years old. Uncertain is whether all orangutan MHC haplotypes contain a C locus, as the failure to find C alleles in some individuals could be due to a mispairing of HLA-C-specific primers with certain Popy-C alleles. These results raise the possibilities that other primate species have a C locus and that the regulation of natural killer cells by C allotypes evolved earlier in primate evolution than has been thought.
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Abstract
In this study, we report type 1 diabetes age-of-onset association with HLA class II (DRB1, DQB1, and DPB1) and class I (A) genes in 222 multiplex families from the Human Biological Data Interchange. Linear regression showed a small (R2 = 0.26) but significant correlation in the ages of onset among sib pairs. A strong association in age of onset between members of sib pairs was observed when the analysis was performed using contingency tables that split sibs into three age-at-onset ranges (0-10, 11-20, and 21-36 years). The association is strongest for sib pairs that share both haplotypes and is nonsignificant for sib pairs that do not share any DR-DQ haplotypes. A goodness-of-fit test revealed that DR-DQ haplotype sharing cannot account for all the association in age of onset among sib pairs. The age-of-onset distribution of DR-DQ haplotypes is affected by the DPB1 and A alleles present. The strongest associations were found with the A locus: DR3/DR4 genotype frequency decreases with age of onset in this data set only among A*0101- individuals, and A*2402 is strongly associated with younger age of onset in many DR-DQ haplotypes.
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Costello C, Thomson G, Soni N, Henry K. Images in haematology. Overwhelming cryptococcal infection detected by bone marrow examination. Br J Haematol 1999; 105:851. [PMID: 10554792 DOI: 10.1046/j.1365-2141.1999.105004851.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Guédez Y, Kotby A, El-Demellawy M, Galal A, Thomson G, Zaher S, Kassem S, Kotb M. HLA class II associations with rheumatic heart disease are more evident and consistent among clinically homogeneous patients. Circulation 1999; 99:2784-90. [PMID: 10351973 DOI: 10.1161/01.cir.99.21.2784] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Discrepancies in reported HLA class II associations with rheumatic heart disease (RHD) may have been due to inaccuracies of serological typing reagents and/or lack of defined clinical classification of patients analyzed. The molecular association between HLA and RHD was investigated in patients with defined clinical outcome. METHODS AND RESULTS Class II allele/haplotype distribution was determined in 2 groups of RHD patients (n=88) and a control group (n=59). Patients were divided into the mitral valve disease (MVD) category (ie, those with mitral regurgitation with or without mitral stenosis) and the multivalvular lesions (MVL) category, with impairment of aortic and/or tricuspid valves in addition to mitral valve damage. The MVD category (n=65) accounted for 74% of patients and included significantly fewer recurrent RF episodes compared with MVL patients (P=0.002). CONCLUSIONS Significant increases in DRB1*0701 and DQA1*0201 alleles and DRB1*0701-DQA1*0201 haplotypes were found in patients. Removal of the MVL patients from analysis increased the strength of HLA associations among the MVD sample. The frequency of DQA1*0103 allele was decreased and the DQB1*0603 allele was absent from the patient group, suggesting that these alleles may confer protective effects against RHD. DQ alleles in linkage disequilibrium with DR alleles appear to influence risk/protection effect: whereas the DRB1*13-DQA1*0501-3-DQB1*0301 haplotype showed a trend toward risk, the DRB1*13-DQA1*0103-DQB1*0603 haplotype was absent in the RHD sample. Our data indicate that certain class II alleles/haplotypes are associated with risk or protection from RHD and that these associations appear to be stronger and more consistent when analyzed in patients with relatively more homogeneous clinical manifestations.
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Salamon H, Klitz W, Easteal S, Gao X, Erlich HA, Fernandez-Viña M, Trachtenberg EA, McWeeney SK, Nelson MP, Thomson G. Evolution of HLA class II molecules: Allelic and amino acid site variability across populations. Genetics 1999; 152:393-400. [PMID: 10224269 PMCID: PMC1460587 DOI: 10.1093/genetics/152.1.393] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Analysis of the highly polymorphic beta1 domains of the HLA class II molecules encoded by the DRB1, DQB1, and DPB1 loci reveals contrasting levels of diversity at the allele and amino acid site levels. Statistics of allele frequency distributions, based on Watterson's homozygosity statistic F, reveal distinct evolutionary patterns for these loci in ethnically diverse samples (26 populations for DQB1 and DRB1 and 14 for DPB1). When examined over all populations, the DQB1 locus allelic variation exhibits striking balanced polymorphism (P < 10(-4)), DRB1 shows some evidence of balancing selection (P < 0.06), and while there is overall very little evidence for selection of DPB1 allele frequencies, there is a trend in the direction of balancing selection (P < 0.08). In contrast, at the amino acid level all three loci show strong evidence of balancing selection at some sites. Averaged over polymorphic amino acid sites, DQB1 and DPB1 show similar deviation from neutrality expectations, and both exhibit more balanced polymorphic amino acid sites than DRB1. Across ethnic groups, polymorphisms at many codons show evidence for balancing selection, yet data consistent with directional selection were observed at other codons. Both antigen-binding pocket- and non-pocket-forming amino acid sites show overall deviation from neutrality for all three loci. Only in the case of DRB1 was there a significant difference between pocket- and non-pocket-forming amino acid sites. Our findings indicate that balancing selection at the MHC occurs at the level of polymorphic amino acid residues, and that in many cases this selection is consistent across populations.
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Thomson G, Wilson N. Tobacco control in New Zealand from 1945 to 1961. THE NEW ZEALAND MEDICAL JOURNAL 1999; 112:101-3. [PMID: 10210298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
The 1945 to 1961 period was characterised by a significant increase in the international scientific knowledge of the health risks of smoking. Despite this, there was relatively little response by the New Zealand Government, the New Zealand medical profession and other local agencies. Specific tobacco control activities were virtually limited to some episodic and low profile publicity measures, and an incidental increase in tobacco taxation. This limited response may have partly been due to the slow diffusion of the health risk information to health professionals in this country and the presence of other more obvious health concerns (such as polio epidemics). Other reasons may have been the absence of a New Zealand research base, the lack of focused advocacy groups, political wariness about using tobacco taxation, a minimalist approach by government to product safety regulation and the major extent to which smoking was normalised within New Zealand society. Britain and the US led to further research. Reports linking lung cancer to smoking were published in 1950 by Doll and Hill in Britain, and by Wynder and Graham in the US. As a result of subsequent prospective studies, the American Cancer Society and the British Medical Research Council produced in 1954, independent reports that death rates were higher for cigarette smokers. A number of further studies on smoking and health were published in Britain and the US during the 1950s (e.g. by Doll and Hill in 1954), and the Medical Research Council and the United States Surgeon General gave further strong warnings. However, the unease of some parts of the medical world with the new science of epidemiology was reflected in the confusion by public and politicians over the conclusiveness of the evidence. Nevertheless, by the late 1950s there was evidence of declining tobacco consumption amongst US doctors, partly at least because of concern about health risks such as lung cancer.
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Mu H, Chen JJ, Jiang Y, King MC, Thomson G, Criswell LA. Tumor necrosis factor a microsatellite polymorphism is associated with rheumatoid arthritis severity through an interaction with the HLA-DRB1 shared epitope. ARTHRITIS AND RHEUMATISM 1999; 42:438-42. [PMID: 10088765 DOI: 10.1002/1529-0131(199904)42:3<438::aid-anr7>3.0.co;2-f] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
OBJECTIVE To determine whether tumor necrosis factor microsatellite a (TNFa) polymorphism is associated with severity of rheumatoid arthritis (RA), and to examine the evidence for interaction between TNFa and the HLA-DRB1 shared epitope (SE). METHODS One hundred seventy-one community-based white female RA patients were genotyped for both TNFa and HLA-DRB1 alleles. We performed pairwise association analyses, stratified analyses, and multivariate logistic regressions to determine whether TNFa was associated with 4 measures of RA severity, and whether there was significant interaction between TNFa and the HLA-DRB1 SE. RESULTS Simple pairwise analyses did not reveal significant association between TNFa polymorphism and RA severity. However, when the data were stratified by the presence versus absence of the SE, striking associations were observed between TNFa allele 11 (TNFa11) and RA severity. These analyses also demonstrated significant interaction between TNFa11 and the SE (P = 0.07-0.005), and this was confirmed in our multivariate regressions. Specifically, the most severe outcomes were observed among individuals who had inherited both TNFa11 and the SE (61-71% had severe RA based on 1 of the 4 outcomes). In contrast, individuals who had inherited TNFa11 in the absence of the SE had the best outcomes (8-21% with severe RA). The odds ratios comparing these 2 groups ranged from 8.8 to 22.7 for the 4 severity measures. The differential effect of TNFa11 according to the presence versus absence of the SE (and vice versa) illustrated their interaction with respect to RA severity. CONCLUSION The data suggest that TNFa is associated with RA severity through an interaction with the HLA-DRB1 SE.
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Valdes AM, McWeeney SK, Meyer D, Nelson MP, Thomson G. Locus and population specific evolution in HLA class II genes. Ann Hum Genet 1999; 63:27-43. [PMID: 10738519 DOI: 10.1046/j.1469-1809.1999.6310027.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The population genetics of the HLA class II loci was studied with reference to variation in the frequency of (a) alleles at a locus and (b) amino acids at specific sites. Variation was surveyed at 4 loci (DRB1, DQA1, DQB1, and DPB1) in 22 populations from the Twelfth International Histocompatibility Workshop (Saint-Malo, 1996). Allele and amino acid variation was measured by computing heterozygosity and the effective number of alleles. Substantial variations in polymorphism were observed among the various populations and loci studied. In the majority of the populations, DRB1 has the highest heterozygosity and effective number of alleles. As previously shown, the Amerindian populations have lower levels of allelic diversity when compared to other populations. At the amino acid level, DRB1 antigen recognition sites (ARS) have the highest heterozygosities and effective number of alleles. For the other loci (DPB1, DQA1, and DQB1) for which there is no crystal structure and for which ARS sites were inferred from DRB1, non-ARS sites were often among the sites with highest levels of variation. It is possible that these putative non-ARS sites do play a role in antigen presentation. The homozygosity test for neutrality was applied to allele and amino acid data. Of the four HLA class II loci studied, only DPB1 failed to show evidence of balancing selection. DQB1 and DQA1 depart significantly from neutrality in the largest number of populations. Genetic distances between populations were computed based on frequency of alleles and amino acids at ARS sites.
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Grote MN, Klitz W, Thomson G. Constrained disequilibrium values and hitchhiking in a three-locus system. Genetics 1998; 150:1295-307. [PMID: 9799280 PMCID: PMC1460391 DOI: 10.1093/genetics/150.3.1295] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Positive selection on a new mutant allele can increase the frequencies of closely linked alleles (through hitchhiking), as well as create linkage disequilibrium between them. Because this disequilibrium is induced by the selected allele, one may be able to identify loci under selection by measuring the influence of a candidate locus on pairwise disequilibrium values at nearby loci. The constrained disequilibrium values (CDV) method approaches this problem by examining differences in pairwise disequilibrium values, which have been normalized for two- and three-locus systems, respectively. We have investigated in detail the reliability of inferences based on CDV, using simulation and analytical methods. Our main results are (i) in some circumstances, CDV may not distinguish well between a selected locus and a neighboring neutral locus, but (ii) CDV seldom indicates "selection" in neutral haplotypes with moderate to large 4Nc. We conclude that, although the CDV method does not appear to precisely locate selected alleles, it can be used to screen for regions in which hitchhiking is a plausible hypothesis. We present a microsatellite data set from human chromosome 6, in which constrained disequilibrium values suggest the action of selection in a region containing the human leukocyte antigen (HLA)-A and myelin oligodendrocyte glycoprotein (MOG) loci. The connection between hitchhiking and disequilibrium has received relatively little attention, so our investigation presents opportunities to address more general issues.
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