701
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Abstract
Coeliac disease has a strong genetic component, higher than for many other common complex diseases. Possession of the HLA-DQ2 variant is required for presentation of disease causing dietary antigens to T cells, although this is also common in the healthy population. Non-HLA genetic factors account for the majority of heritable risk. Linkage studies have identified promising regions on chromosomes 5 and 19, with multiple other loci awaiting definitive confirmation in independent studies. Inherited variants in the tightly clustered chromosome 2q CD28-CTLA4-ICOS region are associated with disease, although of weak effect size. Larger sample sizes are necessary in coeliac disease genetic studies to detect small effects, alternatively meta-analysis offers promise. Newer methods including gene expression analysis and genome wide association studies will advance understanding of genetic susceptibility. Identification of coeliac disease genes may improve diagnostic/prognostic markers, basic understanding of disease aetiology, permit development of novel therapeutics and provide insight into other autoimmune disorders.
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Affiliation(s)
- David A van Heel
- Department of Gastroenterology, Imperial College London, Du Cane Road, London W12 0NN, UK.
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702
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Gambaro G, Vezzoli G, Casari G, Rampoldi L, D'Angelo A, Borghi L. Genetics of hypercalciuria and calcium nephrolithiasis: from the rare monogenic to the common polygenic forms. Am J Kidney Dis 2005; 44:963-86. [PMID: 15558518 DOI: 10.1053/j.ajkd.2004.06.030] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Idiopathic calcium nephrolithiasis is a multifactorial disease with a pathogenesis that involves a complex interaction of environmental and individual factors. This review discusses what is known about monogenic renal calcium stone-related disorders, provides an update on genetic research in calcium nephrolithiasis and such intermediate phenotypes as idiopathic hypercalciuria, discusses the problems that these conditions pose to clinicians and geneticists interested in their pathogenesis, and proposes some method tools potentially useful in this research frame of reference.
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Affiliation(s)
- Giovanni Gambaro
- Department of Biomedical and Surgical Sciences, Division of Nephrology, University of Verona, Verona, Italy.
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703
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Penny MA, McHale D. Pharmacogenomics and the drug discovery pipeline: when should it be implemented? ACTA ACUST UNITED AC 2005; 5:53-62. [PMID: 15727489 DOI: 10.2165/00129785-200505010-00005] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
One of the key factors in developing improved medicines lies in understanding the molecular basis of the complex diseases we treat. Investigation of genetic associations with disease utilizing advances in linkage disequilibrium-based whole genome association strategies will provide novel targets for therapy and define relevant pathways contributing to disease pathogenesis. Genetic studies in conjunction with gene expression, proteomic, and metabonomic analyses provide a powerful tool to identify molecular subtypes of disease. Using these molecular data, pharmacogenomics has the potential to impact on the drug discovery and development process at many stages of the pipeline, contributing to both target identification and increased confidence in the therapeutic rationale. This is exemplified by the identified association of 5-lipoxygenase-activating protein (ALOX5AP/FLAP) with increased risk of myocardial infarction, and of the chemokine receptor 5 (CCR5) with HIV infection and therapy. Pharmacogenomics has already been used in oncology to demonstrate that molecular data facilitates assessment of disease heterogeneity, and thus identification of molecular markers of response to drugs such as imatinib mesylate (Gleevec) and trastuzumab (Herceptin). Knowledge of genetic variation in a target allows early assessment of the clinical significance of polymorphism through the appropriate design of preclinical studies and use of relevant animal models. A focussed pharmacogenomic strategy at the preclinical phase of drug development will produce data to inform the pharmacogenomic plan for exploratory and full development of compounds. Opportunities post-approval show the value of large well-characterized data sets for a systematic assessment of the contribution of genetic determinants to adverse drug reactions and efficacy. The availability of genomic samples in large phase IV trials also provides a valuable resource for further understanding the molecular basis of disease heterogeneity, providing data that feeds back into the drug discovery process in target identification and validation for the next generation of improved medicines.
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Affiliation(s)
- Michelle A Penny
- Clinical Pharmacogenomics, Pfizer Global Research and Development, Sandwich Laboratories (ipc 746), Sandwich, Kent, Ramsgate Road, CT13 9NJ, UK.
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704
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Goodman RS, Ewing J, Evans PC, Craig J, Poulton K, Dyer PA, Marcus RE, Taylor CJ. Donor CD31 genotype and its association with acute graft-versus-host disease in HLA identical sibling stem cell transplantation. Bone Marrow Transplant 2005; 36:151-6. [PMID: 15908974 DOI: 10.1038/sj.bmt.1705013] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
CD31 gene polymorphisms are implicated in the pathogenesis of graft-versus-host disease (GvHD) following haematopoietic stem cell transplantation (HST). We investigated the influence of CD31 genotype on the incidence of GvHD following HST from an human leukocyte antigen (HLA)-identical sibling donor. Donor and recipient CD31 codons 125, 563 and 670 DNA polymorphisms were determined in 85 cases of HLA identical sibling HST from two transplant centres. A correlation between CD31 genotype and acute GvHD was considered significant if observed in patients from both transplant centres independently. A strong correlation was identified between donor CD31 codon 125 genotype and the incidence of acute GvHD. Acute GvHD grades II-IV occurred in 27 of 46 (59%) recipients with a CD31 codon 125 leucine / valine heterozygous donor compared to nine of 39 (23%) recipients with a CD31 codon 125 homozygous donor (P=0.0019, relative-risk 2.45, 95% confidence interval 1.3-4.5). This correlation was significant in patients from both transplant centres (P=0.015 and P=0.019). We suggest that CD31 genotype may influence the function of donor-derived leukocytes and may be informative when there is a choice of comparable donors.
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Affiliation(s)
- R S Goodman
- Tissue Typing Laboratory, Addenbrooke's Cambridge University Teaching Hospital Trust, Cambridge, UK.
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705
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Tan NCK, Heron SE, Scheffer IE, Pelekanos JT, McMahon JM, Vears DF, Mulley JC, Berkovic SF. Failure to confirm association of a polymorphism in ABCB1 with multidrug-resistant epilepsy. Neurology 2005; 63:1090-2. [PMID: 15452306 DOI: 10.1212/01.wnl.0000137051.33486.c7] [Citation(s) in RCA: 145] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Alteration of ATP-binding cassette subfamily B member 1 transporter (ABCB1) can plausibly cause drug-resistant epilepsy as it influences brain penetration of drugs. The CC genotype at the ABCB1 C3435T polymorphism was reported to be associated with multidrug resistance. A replication study in 401 drug-resistant and 208 drug-responsive subjects with epilepsy showed no significant association between the CC genotype and drug-resistant epilepsy. The authors suggest the initial association may have arisen by chance.
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MESH Headings
- ATP Binding Cassette Transporter, Subfamily B, Member 1/genetics
- ATP Binding Cassette Transporter, Subfamily B, Member 1/physiology
- Alleles
- Amino Acid Substitution
- Anticonvulsants/pharmacology
- Anticonvulsants/therapeutic use
- Drug Resistance, Multiple/genetics
- Epilepsy, Temporal Lobe/drug therapy
- Epilepsy, Temporal Lobe/genetics
- Exons/genetics
- Gene Frequency
- Genotype
- Haplotypes/genetics
- Hippocampus/pathology
- Mutation, Missense
- Polymorphism, Genetic
- Polymorphism, Single Nucleotide
- Reproducibility of Results
- Sclerosis
- Victoria/epidemiology
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Affiliation(s)
- N C K Tan
- Epilepsy Research Centre and Department of Medicine (Neurology), University of Melbourne, USA
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706
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Davey Smith G, Ebrahim S. What can mendelian randomisation tell us about modifiable behavioural and environmental exposures? BMJ 2005; 330:1076-9. [PMID: 15879400 PMCID: PMC557238 DOI: 10.1136/bmj.330.7499.1076] [Citation(s) in RCA: 322] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/04/2005] [Indexed: 11/04/2022]
Abstract
Using genetic variants as a proxy for modifiable environmental factors that are associated with disease can circumvent some of the problems of observational studies
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707
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Lewis SJ, Zammit S, Gunnell D, Smith GD. A meta-analysis of the MTHFR C677T polymorphism and schizophrenia risk. Am J Med Genet B Neuropsychiatr Genet 2005; 135B:2-4. [PMID: 15729744 DOI: 10.1002/ajmg.b.30170] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Epigenetic mechanisms such as methylation of DNA, could lead to abnormal neurodevelopment and may be important in the etiology of schizophrenia. Maternal dietary folate intake may play a role in determining methylation levels. The MTHFR gene C677T polymorphism influences folate metabolism and intracellular availability of folate metabolites for methylation. We carried out a meta-analysis of MTHFR C677T genotype and schizophrenia risk, and found that TT homozygotes had a significantly increased risk, OR 1.48 (1.18-1.86). This supports the hypothesis that folate status is a determinant of schizophrenia risk. Larger studies of this issue are required, together with studies of maternal genotype which could identify whether maternal folate status during pregnancy is important.
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Affiliation(s)
- Sarah J Lewis
- Department of Social Medicine, University of Bristol, Bristol, United Kingdom.
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708
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Powell BL, Haddad L, Bennett A, Gharani N, Sovio U, Groves CJ, Rush K, Goh MJ, Conway GS, Ruokonen A, Martikainen H, Pouta A, Taponen S, Hartikainen AL, Halford S, Zeggini E, Järvelin MR, Franks S, McCarthy MI. Analysis of multiple data sets reveals no association between the insulin gene variable number tandem repeat element and polycystic ovary syndrome or related traits. J Clin Endocrinol Metab 2005; 90:2988-93. [PMID: 15705917 DOI: 10.1210/jc.2004-2485] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CONTEXT Variation at the insulin gene VNTR (variable number tandem repeat) minisatellite has been reported to be associated with polycystic ovary syndrome (PCOS), but findings have been inconsistent and all studies have featured small sample sizes. OBJECTIVE To gain a robust understanding of the role of the INS-VNTR in PCOS susceptibility. DESIGN Case-control, family-based association and quantitative trait analyses. SETTING AND PARTICIPANTS A UK population comprising 255 parent-offspring trios, 185 additional cases, and 1062 control subjects (cases and controls all British/Irish) as well as 1599 women from a northern Finland population-based birth cohort characterized for PCO symptomatology and testosterone levels. VNTR class was inferred from genotyping of the -23HphI variant. INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) INS-VNTR genotype frequencies between subject groups, body mass index, and testosterone levels by genotype. RESULTS Case-control analyses in both UK and Finnish samples failed to confirm previously reported class III allele associations with PCOS (UK, P = 0.43, Finnish, P = 0.31; Kruskal-Wallis chi2). Transmission analysis in trios showed no excess transmission of either allele (P = 0.62), regardless of parent of origin (maternal: P = 0.73; paternal: P = 0.66). No association between genotype and testosterone levels was seen in any sample (UK PCOS subjects, P = 0.95; Finnish symptomatic cases, P = 0.38; Finnish control women, P = 0.58). CONCLUSIONS Despite the strong biological candidacy and supportive data from previous studies, we conclude that variation at the INS-VNTR has no major role in the development of PCOS.
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Affiliation(s)
- Brenda L Powell
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
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709
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Manly KF. Conventional P-values fail to assure reproducibility for genetic association tests. Trends Genet 2005; 21:268-9; author reply 269-71. [PMID: 15851061 DOI: 10.1016/j.tig.2005.02.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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710
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Abstract
Few areas in modern medicine provide a better example of evidence-based data than the anatomic pathologists' classification of fully developed malignancies. Beginning with the Papanicolaou (Pap) smear, morphologic tools also were applied to specimens obtained in cancer screening programs directed at large, asymptomatic patient populations. The Papanicolaou test was quickly responsible for a reduction in the incidence of invasive squamous cell carcinoma of the cervix, proving the concept that screening could interdict the development of advanced malignancy. Other screening programs followed the Papanicolaou test initiative, producing a revolutionary change in the specimens submitted to pathologists. Cancer screening generates specimens containing morphologic deviations from normal that are thought to put currently healthy patients at risk of future malignancy. However, translating morphologic findings in such samples into risk estimates raises a number of statistical and ethical problems. When diagnostic thresholds are set to favor specificity, unwanted false-negative results accrue. Conversely, aiming at sensitivity over specificity is associated with biologically false-positive results, which are likewise undesirable. Pathologists interpreting these specimens find themselves facing a screening paradox. These screening programs attempt to discover the very earliest changes of neoplastic transformation, but these same earliest changes are inherently the most difficult to identify with precision and accuracy. This paper discusses these challenges.
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711
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Le Marchand L. The Predominance of the Environment over Genes in Cancer Causation: Implications for Genetic Epidemiology. Cancer Epidemiol Biomarkers Prev 2005; 14:1037-9. [PMID: 15894649 DOI: 10.1158/1055-9965.epi-04-0816] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Loïc Le Marchand
- Cancer Research Center of Hawaii, University of Hawaii, 1236 Lauhala Street, Suite 407, Honolulu, HI 96813, USA.
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712
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Strange RC, El-Genidy N, Ramachandran S, Lovatt TJ, Fryer AA, Smith AG, Lear JT, Wong C, Jones PW, Ichii-Jones F, Hoban PR. Susceptibility to basal cell carcinoma: associations with PTCH polymorphisms. Ann Hum Genet 2005; 68:536-45. [PMID: 15598212 DOI: 10.1046/j.1529-8817.2004.00132.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Loss of function of the human patched gene (PTCH) is common and critical in basal cell carcinoma (BCC) development. Indirect evidence suggests polymorphism in PTCH mediates BCC risk. We studied 659 BCC cases and 300 controls to determine if exon 2(318), 3(429), 11(1552), 12(1665), 12(1686), 14(2199) and 23(3944) and intron 9(1336-135) and 15(2560+9)PTCH variants were sufficiently common for use in case-control studies, and if selected markers were associated with risk. Intron 15(2560+9) and exon 23(3944) variants were studied further. Their genotype frequencies were not significantly different in controls and cases, though frequency of the G(2560+9)-C(3944) haplotype was lower in all cases (odds ratio=0.44, p=0.009) and those stratified by BCC site and rate of development of further tumours. This association was not mediated by the extent of UVR exposure. We confirmed the robustness of these findings by showing these associations demonstrated similar odds ratios in two groups of randomly selected cases and controls, and using the false positive report probability (FPRP) approach described by Wacholder et al. (2004). The FPRP value (0.168) was in the noteworthy category. These data, showing for the first time that PTCH polymorphism mediates susceptibility, are compatible with reports showing that PTCH haploinsufficiency influences development of BCC precursor lesions.
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Affiliation(s)
- R C Strange
- Human Genomics Research Group, Institute for Science and Technology in Medicine, Keele University School of Medicine, University Hospital of North Staffordshire, Hartshill, Stoke-on-Trent ST4 7QB Staffordshire, England
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713
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Molony CM, Fitzgerald AP, Shields DC. Overdispersion of allele frequency differences between populations: implications for meta-analyses of genotypic disease associations. Eur J Hum Genet 2005; 13:79-85. [PMID: 15470368 DOI: 10.1038/sj.ejhg.5201275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Methods correcting case-control studies of genetic polymorphisms for unmeasured genetic population substructure by modelling the variation at a number of variant loci provide no standard and easily implemented approach to meta-analysis, which is a key to understanding the effects of minor genotypic risks on complex diseases. A correction of the odds ratio estimate and its confidence interval is shown to be easy to implement using a mixed effects logistic regression. The method is shown to substantially reduce bias and to give accurate coverage even when there is substantial overdispersion of allele frequency differences between populations. Major sequence classes of single-nucleotide polymorphism (SNP) are likely to act as valid controls for each other, since CpG SNPs did not differ in the extent of population structure from other SNPs. Agreement among investigators and journals to provide these straightforward statistics in publications of polymorphism studies will enhance the ability of future investigators to perform meta-analyses of weak genetic effects across accumulated studies that allow for population structure.
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Affiliation(s)
- Cliona M Molony
- Department of Clinical Pharmacology, Royal College of Surgeons in Ireland, Dublin, Ireland
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714
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Matullo G, Berwick M, Vineis P. Gene-environment interactions: how many false positives? J Natl Cancer Inst 2005; 97:550-1. [PMID: 15840871 DOI: 10.1093/jnci/dji122] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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715
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Frodsham AJ. Host genetics and the outcome of hepatitis B viral infection. Transpl Immunol 2005; 14:183-6. [PMID: 15982561 DOI: 10.1016/j.trim.2005.03.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2005] [Indexed: 12/31/2022]
Abstract
Hepatitis B Virus (HBV) infection can result in numerous different clinical outcomes. A complex combination of environment, and viral and host genetic factors play a critical role in determining both susceptibility to HBV persistence and the course of infection. Evidence is presented that suggests that host genetic factors play an important role in determining the outcome of HBV infection. This data from various groups demonstrates that multiple genes play a role in determining hepatitis B viral clearance or persistence. However, to identify all the relevant variants that affect the outcome of infection, alternative strategies such as genome-wide association studies with large sample sizes will be required to define the majority of the relevant polygenes.
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Affiliation(s)
- Angela J Frodsham
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.
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716
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Abstract
Studies of gene-environment interactions aim to describe how genetic and environmental factors jointly influence the risk of developing a human disease. Gene-environment interactions can be described by using several models, which take into account the various ways in which genetic effects can be modified by environmental exposures, the number of levels of these exposures and the model on which the genetic effects are based. Choice of study design, sample size and genotyping technology influence the analysis and interpretation of observed gene-environment interactions. Current systems for reporting epidemiological studies make it difficult to assess whether the observed interactions are reproducible, so suggestions are made for improvements in this area.
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Affiliation(s)
- David J Hunter
- Department of Epidemiology, Harvard School of Public Health, 677 Huntington Avenue, Boston, Massachusetts 02115, USA.
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717
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McBride KL, Fernbach S, Menesses A, Molinari L, Quay E, Pignatelli R, Towbin JA, Belmont JW. A family-based association study of congenital left-sided heart malformations and 5,10 methylenetetrahydrofolate reductase. ACTA ACUST UNITED AC 2005; 70:825-30. [PMID: 15390319 DOI: 10.1002/bdra.20049] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
BACKGROUND Aortic valve stenosis (AVS), coarctation of the aorta (CoA), and hypoplastic left heart syndrome (HLHS) are obstructive malformations of the left ventricular outflow tract that account for a significant proportion of infant mortality. Two previous small case-control studies suggested methylenetetrahydrofolate reductase (MTHFR) polymorphisms may be associated with this group of malformations. METHODS We used a family-based association design with inclusion criteria of nonsyndromic diagnosis of AVS, CoA, and HLHS, powered to detect an odds ratio for the heterozygote of <1.5. A total of 207 affected offspring-parent trios were genotyped by restriction fragment length polymorphisms at the two common polymorphic loci C677T and A1298C. RESULTS Error rate estimation based on replicate samples was 0.76%. Mendelian inconsistency at either polymorphism was noted in 10 trios, for a calculated undetected error rate of 1.95%. A total of 197 trios were analyzed using the transmission disequilibrium test. Significant association was not found between both the C677T or A1298C polymorphisms and presence of a heart defect, whether analyzed as a group, or by sex, ethnicity, or specific diagnosis. A log-linear analysis did not find increased relative risk based on the maternal genotype. CONCLUSIONS We were unable to replicate previous association studies and concluded that neither the affected nor the maternal MTHFR genotype, by itself, is a major risk factor for congenital left ventricular outflow tract malformations.
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Affiliation(s)
- Kim L McBride
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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718
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Chan KCA, Tang NLS, Hui DSC, Chung GTY, Wu AKL, Chim SSC, Chiu RWK, Lee N, Choi KW, Sung YM, Chan PKS, Tong YK, Lai ST, Yu WC, Tsang O, Lo YMD. Absence of association between angiotensin converting enzyme polymorphism and development of adult respiratory distress syndrome in patients with severe acute respiratory syndrome: a case control study. BMC Infect Dis 2005; 5:26. [PMID: 15819995 PMCID: PMC1090578 DOI: 10.1186/1471-2334-5-26] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2005] [Accepted: 04/09/2005] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND It has been postulated that genetic predisposition may influence the susceptibility to SARS-coronavirus infection and disease outcomes. A recent study has suggested that the deletion allele (D allele) of the angiotensin converting enzyme (ACE) gene is associated with hypoxemia in SARS patients. Moreover, the ACE D allele has been shown to be more prevalent in patients suffering from adult respiratory distress syndrome (ARDS) in a previous study. Thus, we have investigated the association between ACE insertion/deletion (I/D) polymorphism and the progression to ARDS or requirement of intensive care in SARS patients. METHOD One hundred and forty genetically unrelated Chinese SARS patients and 326 healthy volunteers were recruited. The ACE I/D genotypes were determined by polymerase chain reaction and agarose gel electrophoresis. RESULTS There is no significant difference in the genotypic distributions and the allelic frequencies of the ACE I/D polymorphism between the SARS patients and the healthy control subjects. Moreover, there is also no evidence that ACE I/D polymorphism is associated with the progression to ARDS or the requirement of intensive care in the SARS patients. In multivariate logistic analysis, age is the only factor associated with the development of ARDS while age and male sex are independent factors associated with the requirement of intensive care. CONCLUSION The ACE I/D polymorphism is not directly related to increased susceptibility to SARS-coronavirus infection and is not associated with poor outcomes after SARS-coronavirus infection.
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Affiliation(s)
- KC Allen Chan
- The Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
| | - Nelson LS Tang
- The Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
| | - David SC Hui
- The Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
| | - Grace TY Chung
- The Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
| | - Alan KL Wu
- The Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
| | - Stephen SC Chim
- The Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
| | - Rossa WK Chiu
- The Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
| | - Nelson Lee
- The Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
| | - KW Choi
- The Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
| | - YM Sung
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
| | - Paul KS Chan
- The Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
| | - YK Tong
- The Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
| | - ST Lai
- Department of Medicine and Geriatrics, Princess Margaret Hospital, Hong Kong
| | - WC Yu
- Department of Medicine and Geriatrics, Princess Margaret Hospital, Hong Kong
| | - Owen Tsang
- Department of Medicine and Geriatrics, Princess Margaret Hospital, Hong Kong
| | - YM Dennis Lo
- The Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
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719
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Abstract
Familial aggregation of common chronic kidney diseases provides a unique opportunity to investigate the susceptibility genetic and environmental factors. In the past decade, a wealth of new data has become available concerning the genetic susceptibility leading to numerous nephropathies. Knowledge of the genetic components allows better understanding of initiation and progression of these chronic kidney diseases. In addition, one can envision that identification of genetically susceptible individuals might lead to earlier diagnosis and potential reversal of the current epidemic of end-stage renal disease. The goal of the current discussion is to review various issues pertaining to the role of genetic factors in common chronic kidney diseases, as exemplified by two leading causes of end-stage renal diseases worldwide, nephropathy of type 2 diabetes and IgA nephropathy. The genetic and environmental interplay leading to the nephropathies is highlighted.
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Affiliation(s)
- Kai Ming Chow
- Division of Nephrology, Department of Medicine and Therapeutics, Prince of Wales Hospital, Chinese University of Hong Kong, Shatin, Hong Kong, China
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720
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Gordon A. Genetic Polymorphisms in Severe Sepsis and Septic Shock. J Intensive Care Soc 2005. [DOI: 10.1177/175114370500600115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Anthony Gordon
- Clinical Research Fellow, Centre for Experimental Medicine, Nephrology and Critical Care and Institute of Cell & Molecular Science, William Harvey Research Institute, Barts and The London Queen Mary School of Medicine and Dentistry, University of London, London, UK
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721
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Nelson KB, Dambrosia JM, Iovannisci DM, Cheng S, Grether JK, Lammer E. Genetic polymorphisms and cerebral palsy in very preterm infants. Pediatr Res 2005; 57:494-9. [PMID: 15718364 DOI: 10.1203/01.pdr.0000156477.00386.e7] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In the present study, we examine whether selected genetic polymorphisms contribute to the development of cerebral palsy (CP) in very preterm infants. Subjects were 96 singleton infants with later-diagnosed CP and 119 control children, white non-Hispanic (n for CP=74, controls=88) or white Hispanic (CP=22, controls=31), born <32 wk gestation. Presence of CP was identified through state service agencies, with review of medical records. DNA extracted from archived neonatal blood was genotyped using multi-locus polymerase chain reaction amplification and immobilized sequence-specific oligonucleotide probes. Single nucleotide polymorphisms (SNPs) showing evidence of association with development of CP were endothelial nitric oxide synthase (eNOS) A(-922)G, factor 7 (F7) arg353gln and del(-323)10bp-ins, and lymphotoxin A (LTA) thr26asn. In white non-Hispanic children, beta-2 adrenergic receptor gln27glu was associated with CP risk; in Hispanic children, plasminogen activator inhibitor-1 (PAI-1) 4G(-675)5G and G11053T were associated with risk of CP. In a logistic regression considering these SNPs simultaneously in non-Hispanics, an association with CP was observed for heterozygotes of eNOS -922 (OR 3.0, CI 1.4-6.4), F7 (OR 2.7, CI 1.1-6.5), LTA (OR 2.1, CI 1.0-4.6), and PAI-1 (OR 3.2, CI 1.2-8.7). Factor 5, Factor 2, methylene tetrahydrofolate reductase, tumor necrosis factor-alpha, and other SNPs tested were not significantly associated with CP risk. We conclude that further study of genetic factors that may influence susceptibility to CP in very preterm infants is warranted.
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Affiliation(s)
- Karin B Nelson
- National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892-1447, and Children's Hospital and Research Center at Oakland, CA 94609-1673, USA.
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722
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The GABBR1 locus and the G1465A variant is not associated with temporal lobe epilepsy preceded by febrile seizures. BMC MEDICAL GENETICS 2005; 6:13. [PMID: 15799783 PMCID: PMC1079842 DOI: 10.1186/1471-2350-6-13] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/05/2005] [Accepted: 03/30/2005] [Indexed: 11/10/2022]
Abstract
BACKGROUND Polymorphism G1465A in the GABBR1 gene has been suggested as a risk factor for non-lesional temporal lobe epilepsy (TLE); however, this genetic association study has not been independently replicated. We attempted to replicate this study in our cohort of patients with TLE. Furthermore, we also analyzed the coding sequence of this gene and searched for disease-causing mutations. METHODS We included 120 unrelated individuals with TLE that was preceded by febrile seizures (FS) who did not have any evidence of structural lesions suggesting secondary epilepsy. 66 individuals had positive family history of TLE epilepsy and 54 were sporadic. Each patient was genotyped for the presence of G1465A polymorphism. All exons of the GABBR1 gene were screened by single strand confirmation polymorphism method. Genotypes were compared with two independent matched control groups. RESULTS We detected two A alleles of the G1465A polymorphism in one homozygous control subject (0.87% of all alleles) and one A allele in a patient with TLE (0.45%, not significant). Other detected polymorphisms in coding regions had similar frequencies in epilepsy patients and control groups. No disease causing mutations in the GABBR1 gene were detected in patients with sporadic or familial TLE. CONCLUSION Our results indicate that TLE preceded by FS is not associated with the polymorphisms or mutations in the GABBR1 gene, including the G1465A polymorphism. The proportion of TLE patients with FS in the original study, reporting this positive association, did not differ between allele A negative and positive cases. Thus, our failure to reproduce this result is likely applicable to all non-lesional TLE epilepsies.
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723
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Gordon AC, Lagan AL, Aganna E, Cheung L, Peters CJ, McDermott MF, Millo JL, Welsh KI, Holloway P, Hitman GA, Piper RD, Garrard CS, Hinds CJ. TNF and TNFR polymorphisms in severe sepsis and septic shock: a prospective multicentre study. Genes Immun 2005; 5:631-40. [PMID: 15526005 DOI: 10.1038/sj.gene.6364136] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Tumour necrosis factor (TNF) is an important pro-inflammatory cytokine produced in sepsis. Studies examining the association of individual TNF single nucleotide polymorphisms with sepsis have produced conflicting results. This study investigated whether common polymorphisms of the TNF locus and the two receptor genes, TNFRSF1A and TNFRSF1B, influence circulating levels of encoded proteins, and whether individual polymorphisms or extended haplotypes of these genes are associated with susceptibility, severity of illness or outcome in adult patients with severe sepsis or septic shock. A total of 213 Caucasian patients were recruited from eight intensive care units (ICU) in the UK and Australia. Plasma levels of TNF (P = 0.02), sTNFRSF1A (P = 0.005) and sTNFRSF1B (P = 0.01) were significantly higher in those who died on ICU compared to those who survived. There was a positive correlation between increasing soluble receptor levels and organ dysfunction (increasing SOFA score) (sTNFRSF1A R = 0.51, P < 0.001; sTNFRSF1B R = 0.53, P < 0.001), and in particular with the degree of renal dysfunction. In this study, there were no significant associations between the selected candidate TNF or TNF receptor polymorphisms, or their haplotypes, and susceptibility to sepsis, illness severity or outcome. The influence of polymorphisms of the TNF locus on susceptibility to, and outcome from sepsis remains uncertain.
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Affiliation(s)
- A C Gordon
- Institute of Cell and Molecular Science & William Harvey Research Institute, Barts and The London Queen Mary's School of Medicine and Dentistry, University of London, London, UK
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724
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Trikalinos TA, Ntzani EE, Contopoulos-Ioannidis DG, Ioannidis JPA. Establishment of genetic associations for complex diseases is independent of early study findings. Eur J Hum Genet 2005; 12:762-9. [PMID: 15213707 DOI: 10.1038/sj.ejhg.5201227] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Numerous genetic association studies for complex diseases are performed. Investigators place emphasis on formal statistical significance (P-values < 0.05), but the predictive ability of early statistically significant ('positive') findings is unclear. We scrutinized 55 cumulative meta-analyses of genetic associations (579 studies), in order to assess whether having statistical significance in the earliest (first) published study or in at least half among several (> or =3) early-published studies, or high statistical significance in early studies had any predictive ability for establishing or refuting the presence of the genetic association in subsequent research. In 35 associations, a first study was 'positive' and in 15 associations more than half of the early-published reports were 'positive'. The average publication rate of subsequent studies increased 1.71-fold with a 'positive' first report. When compared against the summary results of subsequent research, sensitivity and specificity were 0.65 and 0.38 for the first reports, and 0.40 and 0.73, respectively, when at least three early studies were considered. First studies also had poor predictive ability, when we considered the estimated attributable fraction and coverage of the 95% confidence interval thereof or higher levels of statistical significance. We conclude that although 'positive' findings in the very first reports provide strong incentive for conducting more studies on a putative genetic epidemiological association, the statistical significance or even the magnitude of the effect of early studies cannot adequately predict eventual establishment of an association. Conversely, many genuine epidemiological associations would be missed, if research were abandoned after early underpowered 'negative' studies.
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Affiliation(s)
- Thomas A Trikalinos
- Clinical and Molecular Epidemiology Unit and Clinical Trials and Evidence-Based Medicine Unit, Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece
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725
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Navis G. ACE genotype and long-term graft survival after renal transplantation. Nephrol Dial Transplant 2005; 20:1019-20. [PMID: 15769820 DOI: 10.1093/ndt/gfh743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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726
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Affiliation(s)
- Wayne D Hall
- Institute for Molecular Bioscience of the University of Queensland in St Lucia, Queensland, Australia.
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727
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Hurme M, Lehtimäki T, Jylhä M, Karhunen PJ, Hervonen A. Interleukin-6 −174G/C polymorphism and longevity: a follow-up study. Mech Ageing Dev 2005; 126:417-8. [PMID: 15664628 DOI: 10.1016/j.mad.2004.10.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2004] [Indexed: 10/26/2022]
Abstract
Increased rate of inflammation has been observed to be associated with aging. This is manifested, e.g. as increased blood levels of proinflammatory cytokines, such as interleukin-6 (IL-6). The production of IL-6 is, at least partially, genetically determined the single nucleotide polymorphism (SNP) at the promoter (-174G/C) being decisive. Consequently, some studies have demonstrated that the -174G/C genotype frequencies are different in very old persons as compared to younger ones. However, the results published this far have been conflicting. One of the main confounding factors in these kind of case/control association studies is the undetected difference in the population structure. To avoid this, we now have collected the mortality data of our cohort of 285 nonagenarians (representing mortality between 90 and 95 years of age) and correlated these to the IL-6 genotype. The frequency of -174 allele G was clearly higher in the survivors (n = 114) than in the non-survivors (n = 171).
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Affiliation(s)
- M Hurme
- Department of Microbiology and Immunology, University of Tampere Medical School, Tampere University Hospital, FIN-33014, Tampere, Finland.
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728
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Maier LM, Chapman J, Howson JMM, Clayton DG, Pask R, Strachan DP, McArdle WL, Twells RCJ, Todd JA. No evidence of association or interaction between the IL4RA, IL4, and IL13 genes in type 1 diabetes. Am J Hum Genet 2005; 76:517-21. [PMID: 15660293 PMCID: PMC1196402 DOI: 10.1086/428387] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2004] [Accepted: 12/22/2004] [Indexed: 02/03/2023] Open
Abstract
Attempts to identify susceptibility loci that, on their own, have marginal main effects by use of gene-gene interaction tests have increased in popularity. The results obtained from analyses of epistasis are, however, difficult to interpret. Gene-gene interaction, albeit only marginally significant, has recently been reported for the interleukin-4 and interleukin-13 genes (IL4 and IL13) with the interleukin-4 receptor A gene (IL4RA), contributing to the susceptibility of type 1 diabetes (T1D). We aimed to replicate these findings by genotyping both large family and case-control data sets and by using previously published data. Gene-gene interaction tests were performed using linear regression models in cases only. We did not find any single-locus associations with T1D and did not obtain evidence of gene-gene interaction. Additional support from independent samples will be even more important in the study of gene-gene interactions and other subgroup analyses.
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Affiliation(s)
- Lisa M Maier
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.
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729
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Ogimoto A, Higaki J. [Genome-wide analysis of single nucleotide polymorphisms]. Nihon Yakurigaku Zasshi 2005; 125:148-52. [PMID: 15855733 DOI: 10.1254/fpj.125.148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
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730
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Thomas DC. The Need for a Systematic Approach to Complex Pathways in Molecular Epidemiology. Cancer Epidemiol Biomarkers Prev 2005; 14:557-9. [PMID: 15767327 DOI: 10.1158/1055-9965.epi-14-3-edb] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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731
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Shen H, Liu Y, Liu P, Recker RR, Deng HW. Nonreplication in genetic studies of complex diseases--lessons learned from studies of osteoporosis and tentative remedies. J Bone Miner Res 2005; 20:365-76. [PMID: 15746981 DOI: 10.1359/jbmr.041129] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2004] [Revised: 08/29/2004] [Accepted: 10/15/2004] [Indexed: 12/17/2022]
Abstract
Inconsistent results have accumulated in genetic studies of complex diseases/traits over the past decade. Using osteoporosis as an example, we address major potential factors for the nonreplication results and propose some potential remedies. Over the past decade, numerous linkage and association studies have been performed to search for genes predisposing to complex human diseases. However, relatively little success has been achieved, and inconsistent results have accumulated. We argue that those nonreplication results are not unexpected, given the complicated nature of complex diseases and a number of confounding factors. In this article, based on our experience in genetic studies of osteoporosis, we discuss major potential factors for the inconsistent results and propose some potential remedies. We believe that one of the main reasons for this lack of reproducibility is overinterpretation of nominally significant results from studies with insufficient statistical power. We indicate that the power of a study is not only influenced by the sample size, but also by genetic heterogeneity, the extent and degree of linkage disequilibrium (LD) between the markers tested and the causal variants, and the allele frequency differences between them. We also discuss the effects of other confounding factors, including population stratification, phenotype difference, genotype and phenotype quality control, multiple testing, and genuine biological differences. In addition, we note that with low statistical power, even a "replicated" finding is still likely to be a false positive. We believe that with rigorous control of study design and interpretation of different outcomes, inconsistency will be largely reduced, and the chances of successfully revealing genetic components of complex diseases will be greatly improved.
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Affiliation(s)
- Hui Shen
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
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732
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Gouni-Berthold I, Giannakidou E, Müller-Wieland D, Faust M, Kotzka J, Berthold HK, Krone W. The Pro387Leu variant of protein tyrosine phosphatase-1B is not associated with diabetes mellitus type 2 in a German population. J Intern Med 2005; 257:272-80. [PMID: 15715684 DOI: 10.1111/j.1365-2796.2004.01446.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
OBJECTIVES Diabetes mellitus type 2 (DM-2) is a complex disorder with a strong genetic background. Protein tyrosine phosphatase-1B (PTP-1B) dephosphorylates various receptor protein kinases in vitro, including the beta subunit of the insulin receptor, therefore representing a potential candidate to be involved in the polygenic pathogenesis of DM-2. Recently a Pro387Leu variant of the PTP-1B gene has been associated with an increased risk of DM-2 in a Danish population. Reports from China and Finland failed to confirm this association. DESIGN, SETTING AND SUBJECTS The purpose of the present study was to examine the possible association between the presence of DM-2 and the Pro387Leu polymorphism in a German Caucasian population. A total of 836 subjects (age 20-92 years) participated in the study. The presence of the Pro387Leu variant of the PTP-1B gene was investigated using polymerase chain reaction (PCR) restriction fragment-length polymorphism in 402 subjects with DM-2 (231 men, 171 women, age 63.1 +/- 10.8 years, BMI 28.7 +/- 5.1 kg m(-2)) and in 434 normoglycemic age- and sex-matched control subjects (248 men, 186 women, age 64.4 +/- 6.5 years, BMI 26.5 +/- 3.7 kg m(-2)). RESULTS Nine subjects in the control group and nine in the diabetic group (allelic frequency 0.99% in both groups) carried the Pro387Leu polymorphism. A meta-analysis on published data of >3000 subjects including our own data did not find an association between the polymorphism and DM-2. In addition, the polymorphism had no significant influence on the presence of atherosclerotic disease, whilst the influence of other known cardiovascular risk factors was confirmed. Furthermore, the impact of the mutation on metabolic and anthropometric parameters in both groups was examined. Amongst the controls there were no significant differences in BMI, HDL and LDL cholesterol or blood pressure between the two groups with or without the Pro387Leu polymorphism. The same was true for the diabetic group. Interestingly, in both diabetics and controls, Pro387Leu carriers had significantly higher triglycerides. In a logistic regression model only BMI and family history but not polymorphism were predictors of DM-2. CONCLUSIONS In conclusion, the present data suggest that in a German Caucasian population the Pro387Leu polymorphism of the PTP-1B gene is not associated with DM-2 but may play a role in other metabolic phenotypes.
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Affiliation(s)
- I Gouni-Berthold
- Department of Internal Medicine II, University of Cologne and Center of Molecular Medicine Cologne (CMMC), Cologne, Germany.
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733
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Abstract
Asthma is a complex genetic disorder. Significant progress has been made in identifying genes that convey risk of development and expression of the asthma phenotype. This review critically examines the approaches that have been used, the successes achieved and the difficulties that have been encountered. The multi-factorial nature of the disease and the complex interplay of the various risk factors with one another have highlighted the importance of adequate power and study design in pinpointing genes of real interest.
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Affiliation(s)
- Will Carroll
- Academic Department of Paediatrics, University Hospital of North Staffordshire, Newcastle, Stoke-on-Trent ST4 6QG, UK.
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734
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Heidinger K, König IR, Bohnert A, Kleinsteiber A, Hilgendorff A, Gortner L, Ziegler A, Chakraborty T, Bein G. Polymorphisms in the human surfactant protein-D (SFTPD) gene: strong evidence that serum levels of surfactant protein-D (SP-D) are genetically influenced. Immunogenetics 2005; 57:1-7. [PMID: 15700120 PMCID: PMC7100655 DOI: 10.1007/s00251-005-0775-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2004] [Revised: 12/23/2004] [Indexed: 11/30/2022]
Abstract
The collectin surfactant protein-D (SP-D) plays a significant role in innate immunity. Epidemiological studies described associations between single nucleotide polymorphisms (SNPs) of the human gene coding surfactant protein-D (SFTPD) and infectious pulmonary diseases. Studies on twins indicated very strong genetic dependence for serum levels of SP-D. The aim of this study was to determine the genetic influence of sequence variations within the SFTPD gene on the constitutional serum SP-D levels. We sequenced the 5′ untranslated region (5′UTR), the coding region and the 3′ region of the SFTPD gene of 32 randomly selected blood donors. Six validated SNPs were genotyped with sequence-specific probes (TaqMan 7000) in 290 German blood donors. Serum SP-D levels were analysed by ELISA, and the association of SFTPD haplotype estimates with the quantitative phenotype serum SP-D level was determined. One single SFTPD haplotype (allele frequency 13.53%) revealed a negative association with serum SP-D levels (P<0.0001). This was confirmed in a second prospectively collected group of blood donors (n=160, P=0.0034). The discovery of a frequent negative variant of the SFTPD gene provides a basis for genetic analysis of the function of SP-D in the resistance against pulmonary infections and inflammatory disorders in humans.
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Affiliation(s)
- Kathrin Heidinger
- Institute of Clinical Immunology and Transfusion Medicine, University of Giessen, Langhansstrasse 7, 35392, Giessen, Germany.
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735
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Bleumink GS, Schut AFC, Sturkenboom MCJM, Deckers JW, van Duijn CM, Stricker BHC. Genetic polymorphisms and heart failure. Genet Med 2005; 6:465-74. [PMID: 15545741 DOI: 10.1097/01.gim.0000144061.70494.95] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Heart failure is a complex clinical syndrome. There is evidence for a genetic contribution to the pathophysiology of heart failure. Considering the fundamental role of neurohormonal factors in the pathophysiology and progression of cardiac dysfunction and hypertrophy, variants of genes involved in this system are logical candidate genes in heart failure. In this report, genetic polymorphisms of the major neurohormonal systems in heart failure will be discussed. Studies on polymorphisms of the renin-angiotensin-aldosterone system (RAAS), adrenergic receptor polymorphisms, endothelin (receptor) polymorphisms, and a group of miscellaneous polymorphisms that may be involved in the development or phenotypic expression of heart failure will be reviewed. Research on left ventricular hypertrophy is also included. The majority of genetic association studies focused on the ACE I/D polymorphism. Initial genetic associations have often been difficult to replicate, mainly due to problems in study design and lack of power. Promising results have been obtained with genetic polymorphisms of the RAAS and sympathetic system. Considering the evidence so far, a modifying role for these polymorphisms seems more likely than a role of these variants as susceptibility genes. Besides the need for larger studies to examine the effects of single nucleotide polymorphisms and haplotypes, future studies also need to focus on the complexity of these systems and study gene-gene interactions and gene-environment interactions.
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Affiliation(s)
- Gysèle S Bleumink
- Department of Epidemiology and Biostatistics, Erasmus Medical Center, Rotterdam, The Netherlands
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736
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Lee YH, Harley JB, Nath SK. CTLA-4 polymorphisms and systemic lupus erythematosus (SLE): a meta-analysis. Hum Genet 2005; 116:361-7. [PMID: 15688186 DOI: 10.1007/s00439-004-1244-1] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2004] [Accepted: 12/05/2004] [Indexed: 12/01/2022]
Abstract
Several reports demonstrate association between variants of the cytotoxic T lymphocyte antigen-4 (CTLA-4) and autoimmune diseases. CTLA-4 may generate autoimmunity by immune dysregulation, making CTLA-4 an attractive candidate gene for systemic lupus erythematosus (SLE) susceptibility. Previous CTLA-4 association studies with SLE, however, have produced inconsistent results. We have performed a meta-analysis to better assess the purported associations. A total of 14 independent studies (to July 2004) testing association between one or more CTLA-4 polymorphisms and SLE were used in this analysis. We have compared allele and genotype frequencies at four polymorphic sites found in exon-1 (at +49), the promoter region (at -318 and -1722), and the 3' untranslated region (3'UTR) (dinucleotide repeat). We have evaluated both fixed and random effect models, depending on the presence of between-study heterogeneity. The data demonstrate that the exon-1 +49 polymorphism is significantly associated with SLE susceptibility. The overall risk, measured by odds ratio (OR), for exon-1 +49 GG genotype is 1.287 [95% confidence interval (CI)=1.031-1.562, P=0.011]. Stratification by ethnicity indicates the exon-1 +49 GG genotype is associated with SLE, at least in Asians (OR=1.293, 95% CI=1.031-1.620, P=0.026). European-derived populations have an effect of similar magnitude (OR=1.268, 95% CI=0.860-1.870, P=0.230), though not significant. Similar trends are found in allele-specific risk estimates and disease association. The OR for the exon-1 +49 risk allele (G) in Asians is 1.246 (95% CI=1.057-1.469, P=0.009), while Europeans have no evidence of allelic association (OR=0.978, 95% CI=0.833-1.148, P=0.780). In conclusion, this meta-analysis supports the CTLA-4 exon-1 +49 (A/G) polymorphism influencing the risk for developing SLE, especially in Asians.
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Affiliation(s)
- Young Ho Lee
- Arthritis and Immunology Research Program, Oklahoma Medical Research Foundation, 825 N.E. 13th Street, Oklahoma City, OK 73104, USA
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737
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Franjkovic I, Gessner A, König I, Kissel K, Bohnert A, Hartung A, Ohly A, Ziegler A, Hackstein H, Bein G. Effects of common atopy-associated amino acid substitutions in the IL-4 receptor alpha chain on IL-4 induced phenotypes. Immunogenetics 2005; 56:808-17. [PMID: 15712015 DOI: 10.1007/s00251-004-0763-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2004] [Revised: 12/07/2004] [Indexed: 01/25/2023]
Abstract
The human IL-4 receptor alpha chain gene (IL4R) is highly polymorphic and controversial reports have been published with respect to the association of different single nucleotide polymorphisms (SNPs) with atopy markers. Here we analyzed the functional and associational relevance of common IL4R coding SNPs. Transfection of B cell lines expressing the IL-4R variant V75+R576 did not result in enhanced IL-4 induced CD23 expression compared to cell lines expressing the wild type IL-4R alpha chain. Transfection of the IL-4R variant P503 into a murine T cell line did not influence IL-4 induced T-cell proliferation compared to wild type constructs. Analysis of six IL4R coding SNPs (I75V, E400A, C431R, S436L, S503P, Q576R) and common haplotypes (frequency >/=0.05%) in blood donors (n=300) did not indicate a significant association with elevated serum IgE level. Moreover, the most informative IL4R coding SNPs (I75V, C431R, Q576R) and related two- and three-point haplotypes (frequency >/=0.05%) were analyzed in a second, extended group of blood donors (n=689). Again, no significant association with elevated serum IgE was detectable. We conclude that common coding SNPs in the IL4R gene are unlikely to contribute significantly to increased IgE levels and variations outside the coding region may influence atopy susceptibility.
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Affiliation(s)
- Izolda Franjkovic
- Institute of Clinical Immunology and Transfusion Medicine, Justus Liebig University, Langhansstrasse 7, 35392 Giessen, Germany,
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738
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Halliday JL, Collins VR, Aitken MA, Richards MPM, Olsson CA. Genetics and public health--evolution, or revolution? J Epidemiol Community Health 2005; 58:894-9. [PMID: 15483303 PMCID: PMC1732597 DOI: 10.1136/jech.2003.018515] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
During the 19th and early 20th century, public health and genetics shared common ground through similar approaches to health promotion in the population. By the mid-20th century there was a division between public health and genetics, with eugenicists estranged and clinical genetics focused on single gene disorders, usually only relevant to small numbers of people. Now through a common interest in the aetiology of complex diseases such as heart disease and cancer, there is a need for people working in public health and genetics to collaborate. This is not a comfortable convergence for many, particularly those in public health. Nine main concerns are reviewed: fear of eugenics; genetic reductionism; predictive power of genes; non-modifiable risk factors; rights of individuals compared with populations; resource allocation; commercial imperative; discrimination; and understanding and education. This paper aims to contribute to the thinking and discussion about an evolutionary, multidisciplinary approach to understanding, preventing, and treating complex diseases.
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Affiliation(s)
- Jane L Halliday
- Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia.
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739
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Janssen R, Grutters JC, Ruven HJT, Zanen P, Sato H, Welsh KI, du Bois RM, van den Bosch JMM. No association between interleukin-18 gene polymorphisms and haplotypes in Dutch sarcoidosis patients. ACTA ACUST UNITED AC 2005; 63:578-83. [PMID: 15140035 DOI: 10.1111/j.0001-2815.2004.00184.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Previously, an association between susceptibility to sarcoidosis and a polymorphism in the interleukin (IL-18) gene (IL-18 -607A/C) has been reported in Japanese. The aim of the present study was to validate this association in a clinically well-characterized population of Dutch Caucasians. Three other polymorphisms at positions -656, -137, and 1248 were included in order to extend the mapping of the IL-18 gene and to enable the construction of haplotypes. Polymorphisms were determined using sequence-specific primers (SSPs) and polymerase chain reaction (PCR). A total of 236 individuals was studied (133 patients and 103 controls). No significant differences were observed in the distribution of the -607 and the other polymorphisms between Dutch sarcoidosis patients and controls. However, significant differences in IL-18 -607 genotype and allele frequency distributions were found between the Dutch and the Japanese. From the investigated IL-18-promoter polymorphisms, we were able to deduce four haplotypes. No differences were observed in haplotype frequencies between Dutch sarcoidosis patients and controls. In conclusion, IL-18 polymorphisms do not appear to influence the susceptibility to sarcoidosis in Dutch Caucasians. Important differences in allele frequencies were observed between Japanese and Dutch sarcoidosis patients and controls.
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Affiliation(s)
- R Janssen
- Heart Lung Center Utrecht, Department of Pulmonology, St. Antonius Hospital, Nieuwegein, The Netherlands
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740
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Benusiglio PR, Lesueur F, Luccarini C, Conroy DM, Shah M, Easton DF, Day NE, Dunning AM, Pharoah PD, Ponder BAJ. Common ERBB2 polymorphisms and risk of breast cancer in a white British population: a case-control study. Breast Cancer Res 2005; 7:R204-9. [PMID: 15743501 PMCID: PMC1064135 DOI: 10.1186/bcr982] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2004] [Revised: 11/29/2004] [Accepted: 12/01/2004] [Indexed: 01/21/2023] Open
Abstract
Introduction About two-thirds of the excess familial risk associated with breast cancer is still unaccounted for and may be explained by multiple weakly predisposing alleles. A gene thought to be involved in low-level predisposition to the disease is ERBB2 (HER2). This gene is involved in cell division, differentiation, and apoptosis and is frequently amplified in breast tumours. Its amplification correlates with poor prognosis. Moreover, the coding polymorphism I655V has previously been associated with an increased risk of breast cancer. Methods We aimed to determine if common polymorphisms (frequency ≥ 5%) in ERBB2 were associated with breast cancer risk in a white British population. Five single-nucleotide polymorphisms (SNPs) were selected for study: SNP 1 near the promoter, SNP 2 in intron 1, SNP 3 in intron 4, SNP 4 in exon 17 (I655V), and SNP 5 in exon 27 (A1170P). We tested their association with breast cancer in a large case–control study (n = 2192 cases and 2257 controls). Results There were no differences in genotype frequencies between cases and controls for any of the SNPs examined. To investigate the possibility that a common polymorphism not included in our study might be involved in breast cancer predisposition, we also constructed multilocus haplotypes. Our set of SNPs generated all existing (n = 6) common haplotypes and no differences were seen in haplotype frequencies between cases and controls (P = 0.44). Conclusions In our population, common ERBB2 polymorphisms are not involved in predisposition to breast cancer.
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Affiliation(s)
- Patrick R Benusiglio
- Department of Oncology, University of Cambridge, Strangeways Research Laboratories, Cambridge, UK
| | - Fabienne Lesueur
- Department of Oncology, University of Cambridge, Strangeways Research Laboratories, Cambridge, UK
| | - Craig Luccarini
- Department of Oncology, University of Cambridge, Strangeways Research Laboratories, Cambridge, UK
| | - Donald M Conroy
- Department of Oncology, University of Cambridge, Strangeways Research Laboratories, Cambridge, UK
| | - Mitul Shah
- Department of Oncology, University of Cambridge, Strangeways Research Laboratories, Cambridge, UK
| | - Douglas F Easton
- Department of Genetic Epidemiology, University of Cambridge, Strangeways Research Laboratories, Cambridge, UK
| | - Nick E Day
- EPIC, University of Cambridge, Strangeways Research Laboratories, Cambridge, UK
| | - Alison M Dunning
- Department of Oncology, University of Cambridge, Strangeways Research Laboratories, Cambridge, UK
| | - Paul D Pharoah
- Department of Oncology, University of Cambridge, Strangeways Research Laboratories, Cambridge, UK
| | - Bruce AJ Ponder
- Department of Oncology, University of Cambridge, Strangeways Research Laboratories, Cambridge, UK
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741
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Zoodsma M, Nolte IM, Schipper M, Oosterom E, van der Steege G, de Vries EGE, te Meerman GJ, van der Zee AGJ. Methylenetetrahydrofolate reductase (MTHFR) and susceptibility for (pre)neoplastic cervical disease. Hum Genet 2005; 116:247-54. [PMID: 15635481 DOI: 10.1007/s00439-004-1233-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2004] [Accepted: 11/14/2004] [Indexed: 10/26/2022]
Abstract
Methylenetetrahydrofolate reductase (MTHFR) is a critical enzyme regulating the metabolism of folate and methionine. The potential influence of MTHFR activity on DNA methylation and on the availability of uridylates and thymidylates for DNA synthesis and repair presents MTHFR as a candidate for being a cancer-predisposing gene. In the present study, we have examined a large study population to determine whether the C677T polymorphism at the MTHFR locus affects susceptibility for cervical cancer or its precursor, cervical intraepithelial neoplasia (CIN). In addition, we have investigated whether this polymorphism is causal, and not merely associated, by typing microsatellite markers in the region surrounding the MTHFR gene. A total of 311 CIN and 695 cervical cancer patients and 115 family-based and 586 unrelated controls was analysed. Association analysis showed a decreased cervical cancer risk for individuals heterozygous or homozygous for the T-allele, both for squamous cell carcinoma (heterozygous odds ration [OR] 0.66 [0.51-0.86]; homozygous OR 0.76 [0.49-1.16]) and adenocarcinoma (heterozygous OR 0.71 [0.49-1.03]; homozygous OR 0.34 [0.14-0.81]). No difference was found for high grade CIN (heterozygous OR 1.03 [0.76-1.40]; homozygous OR 0.91 [0.54-1.55]). A microsatellite haplotype containing the C allele was associated with an increased risk for cervical cancer and CIN (both among squamous cell carcinomas, adenocarcinomas and CIN II-III; OR = 2.61 [1.59-4.27]). Our study thus lends further support to the hypothesis that the MTHFR C677T polymorphism is involved in susceptibility cervical cancer but also illustrates that, despite the large sample size analysed, still larger studies are needed to establish fully the nature of this association.
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Affiliation(s)
- Margreet Zoodsma
- Department of Gynecology, University Medical Center Groningen, Hanzeplein 1, 30.001, 9700 RB, Groningen, The Netherlands
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742
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Rodríguez de Castro F, Solé-Violán J, Rodríguez-Gallego JC. Variabilidad genética en la susceptibilidad y en la gravedad de la neumonía. Arch Bronconeumol 2005; 41 Suppl 5:21-9. [PMID: 17125703 DOI: 10.1016/s0300-2896(05)70764-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- F Rodríguez de Castro
- Servicio de Neumología, Hospital Universitario de Gran Canaria Dr. Negrín, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Las Palmas, España.
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743
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Abstract
The epidemiologic approach enables the systematic evaluation of potential improvements in the safety and efficacy of drug treatment which might result from targeting treatment on the basis of genomic information. The main epidemiologic designs are the randomized control trial, the cohort study, and the case-control study, and derivatives of these proposed for investigating gene-environment interactions. However, no one design is ideal for every situation, and methodological issues, notably selection bias, information bias, confounding and chance, all play a part in determining which study design is best for a given situation. There is also a need to employ a range of different designs to establish a portfolio of evidence about specific gene-drug interactions. In view of the complexity of gene-drug interactions, pooling of data across studies is likely to be needed in order to have adequate statistical power to test hypotheses. We suggest that there may be opportunities (i) to exploit samples from trials already completed to investigate possible gene-drug interactions; (ii) to consider the use of the case-only design nested within randomized controlled trials as a possible means of reducing genotyping costs when dichotomous outcomes are being investigated; and (iii) to make use of population-based disease registries that can be linked with tissue samples, treatment information and death records, to investigate gene-treatment interactions in survival.
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Affiliation(s)
- Julian Little
- Department of Epidemiology and Community Medicine, University of Ottawa, 451 Smyth Rd, Ottawa, Ontario K1H 8M5, Canada.
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744
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Carreira PE, Gonzalez-Crespo MR, Ciruelo E, Pablos JL, Santiago B, Gomez-Camara A, Gomez-Reino JJ. Polymorphism of the interleukin-1 receptor antagonist gene: A factor in susceptibility to rheumatoid arthritis in a Spanish population. ACTA ACUST UNITED AC 2005; 52:3015-9. [PMID: 16200608 DOI: 10.1002/art.21287] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
OBJECTIVE To assess whether an interleukin-1 receptor antagonist gene (IL1RN) polymorphism is associated with disease susceptibility and/or severity in a Spanish population of patients with rheumatoid arthritis (RA). METHODS An 86-bp variable-number tandem repeat polymorphism within IL1RN intron 2 was analyzed by polymerase chain reaction in genomic DNA obtained from 247 unrelated patients with RA (group A) and 287 healthy control subjects. The polymorphism analysis was repeated in a second group of 194 patients with RA (group B). Clinical information from patients in group A was used to compare activity and severity data in patients stratified according to the different alleles or genotypes. Odds ratios (ORs) with 95% confidence intervals (95% CIs) were used to determine the strength of the association of the different alleles or genotypes with RA activity or severity. RESULTS In the control group, the allelic frequencies were 76% for IL1RN*1 (4 repeats), 21% for IL1RN*2 (2 repeats), 3% for IL1RN*3 (5 repeats), and 0.3% for IL1RN*4 (3 repeats). In group A patients with RA, both the frequency (OR 1.47, 95% CI 1.1-1.96, P = 0.007) and carriage rate (OR 1.6, 95% CI 1.1-2.2, P = 0.01) of allele IL1RN*2 were significantly increased. The increased frequency of IL1RN*2 was confirmed in group B patients with RA (OR 1.44, 95% CI 1.1-1.97, P = 0.01). In patients with RA, homozygosity for IL1RN*2 was associated with an increased number of affected articular areas during the first year of followup but not with other parameters of disease activity or severity. CONCLUSION Our results suggest that IL1RN has a role in determining susceptibility to RA in the Spanish population.
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745
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Meenagh GK, McGibbon D, Nixon J, Wright GD, Doherty M, Hughes AE. Lack of support for the presence of an osteoarthritis susceptibility locus on chromosome 6p. ACTA ACUST UNITED AC 2005; 52:2040-3. [PMID: 15986344 DOI: 10.1002/art.21120] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
OBJECTIVE To replicate, in a Northern Irish population, the previously reported association between a locus on chromosome 6 and hip osteoarthritis (OA). METHODS Patients with hip OA were identified from a registry of patients who had undergone total hip replacement surgery over an 8-year period at a single large orthopedic unit in Northern Ireland. Patients identified as index cases were contacted by mail and asked to reply only if another family member also had undergone total hip replacement surgery. Using this approach, we identified 288 sibling pairs concordant for primary hip OA. DNA was extracted from peripheral blood, and microsatellite markers were amplified by polymerase chain reaction and subsequently genotyped. RESULTS No evidence of linkage to this region was demonstrated by either 2-point analysis or multipoint analysis of 17 microsatellites. CONCLUSION The reported association between a locus on chromosome 6 and hip OA could not be confirmed in this population. Different methods of ascertainment and phenotyping of OA may contribute to the current inability to replicate genetic associations for hip OA.
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Affiliation(s)
- Gary K Meenagh
- Department of Rheumatology, Musgrave Park Hospital, Belfast, UK.
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746
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Ikari K, Kuwahara M, Nakamura T, Momohara S, Hara M, Yamanaka H, Tomatsu T, Kamatani N. Association betweenPADI4 and rheumatoid arthritis: A replication study. ACTA ACUST UNITED AC 2005; 52:3054-7. [PMID: 16200584 DOI: 10.1002/art.21309] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
OBJECTIVE The peptidylarginine deiminase type 4 gene (PADI4) was recently reported to be associated with rheumatoid arthritis (RA) in a Japanese population. The presence of a single-nucleotide polymorphism (SNP) located in intron 3 of PADI4 provided the strongest evidence of this association. Moreover, functional haplotypes that affect stability of transcripts were identified. However, subsequent research failed to confirm the observed association in a UK population. The present study was undertaken to further investigate the association of PADI4 with RA, using a series of population-based samples from subjects with the same ethnic background as the subjects in the original study. METHODS DNA samples were obtained from 1,230 Japanese RA patients and 948 ethnically matched controls. Genotyping was performed using 5' allele discrimination assays. All samples were genotyped for 3 SNPs on PADI4 (padi4_94, padi4_104, and padi4_102), which comprised the reported haplotypes. Chi-square testing was performed for a case-control study and the PENHAPLO program was used for haplotype estimation. RESULTS All tested SNPs were found to show significant differences in frequency between cases and controls (P = 0.010-0.0008), which confirmed the association observed in the original study. Odds ratios calculated for allele frequencies were 1.23, 1.21, and 1.36 in padi4_94, padi4_104, and padi4_102 respectively. CONCLUSION Replication of association in individual samples strongly suggests that PADI4 is a true susceptibility gene for RA.
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Affiliation(s)
- Katsunori Ikari
- Institute of Rheumatology, Tokyo Women's Medical University, Kwada, Tokyo, Japan.
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747
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Kang CP, Lee HS, Ju H, Cho H, Kang C, Bae SC. A functional haplotype of thePADI4 gene associated with increased rheumatoid arthritis susceptibility in Koreans. ACTA ACUST UNITED AC 2005; 54:90-6. [PMID: 16385500 DOI: 10.1002/art.21536] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
OBJECTIVE Anticitrullinating autoantibodies are specific markers for rheumatoid arthritis (RA). A functional haplotype of 4 exonic single-nucleotide polymorphisms (SNPs) in a citrullinating enzyme, peptidylarginine deiminase 4 (PADI4), was shown to be associated with susceptibility to RA in a Japanese population and was shown to increase the stability of PADI4 messenger RNA. However, the association was not confirmed in 4 subsequent studies involving Caucasian RA patients living in the UK, a French Caucasian population, and a Spanish population. The aim of the current study was to investigate the association of SNPs in the PADI4 gene with RA in a Korean population. METHODS Four exonic SNPs of the PADI4 gene (padi4_89, padi4_90, padi4_92, and padi4_104) were genotyped in 545 unrelated patients with RA and 392 controls, using the MassArray SNP genotyping system. Allelic, genotypic, and haplotypic associations of the SNPs with RA susceptibility were examined using the chi-square test and multivariate logistic regression analyses. RESULTS Increased RA susceptibility was significantly associated with the minor alleles of padi4_89 (P = 2.3 x 10(-5)), padi4_90 (P = 2.3 x 10(-5)), padi4_92 (P = 2.1 x 10(-5)), and padi4_104 (P = 1.1 x 10(-3)) and the haplotype carrying the 4 minor alleles (P = 1.0 x 10(-4)). Genotypes carrying the minor alleles and HLA-DRB1 shared epitope (SE) alleles (P = 9.4 x 10(-21)) were also associated with increased RA susceptibility. The genotypic associations were sustained among individuals who did not carry any SE alleles, except in the case of padi4_104. Individuals carrying the risk SNPs and/or SE alleles were more susceptible to RA than were individuals carrying neither risk SNPs nor SE alleles. CONCLUSION The PADI4 SNPs and haplotypes are associated with RA susceptibility in Koreans. Thus, the association of PADI4 with RA may depend on genetic heterogeneity between Asians and Europeans.
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Affiliation(s)
- Changsoo Paul Kang
- Dept. of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701, Korea.
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748
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Tomer Y, Greenberg D. The thyroglobulin gene as the first thyroid-specific susceptibility gene for autoimmune thyroid disease. Trends Mol Med 2004; 10:306-8. [PMID: 15242677 DOI: 10.1016/j.molmed.2004.05.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Recent linkage and association studies provide evidence for thyroglobulin (Tg) being an autoimmune thyroid disease (AITD) susceptibility gene. The Tg locus has been reported to be linked with AITD in two independent studies, and further analysis demonstrated that markers within the Tg gene were associated with AITD. Furthermore, missense single-nucleotide polymorphisms (SNPs) in the Tg gene were shown to be associated with autoimmune thyroiditis in both mice and humans. If Tg is confirmed as a susceptibility gene for AITD, it could provide a novel therapeutic target.
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Affiliation(s)
- Yaron Tomer
- Division of Endocrinology, Department of Medicine, Mount Sinai School of Medicine, New York, NY 10029, USA.
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749
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Martin RJL, Savage DA, Carson DJ, Maxwell AP, Patterson CC. Interleukin 18 promoter polymorphisms are not strongly associated with type I diabetes in a UK population. Genes Immun 2004; 6:171-4. [PMID: 15674367 DOI: 10.1038/sj.gene.6364161] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Interleukin 18 (IL18) is a proinflammatory cytokine whose levels are increased in the subclinical stage of insulin-dependent (type I) diabetes mellitus. Previous case-control studies have reported associations between IL18 -607C>A and -137G>C promoter polymorphisms and type I diabetes. We performed case-control and family-based association studies employing Pyrosequencing to assess if these IL18 polymorphisms are also associated with the development of type I diabetes in the Northern Ireland population. The chi2 analysis of genotype and allele frequencies for the IL18 polymorphisms in cases (n=433) vs controls (n=426) revealed no significant differences (P>0.05). Assessment of allele transmission distortion from informative parents to affected offspring also failed to confirm previously reported associations. Stratification of these analyses for age-at-onset and HLA-DR type did not reveal any significance associations. In conclusion, our data do not support the strong positive associations of IL18 promoter polymorphisms with type I diabetes reported in previous smaller studies.
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Affiliation(s)
- R J L Martin
- Department of Medical Genetics, The Queen's University of Belfast, Belfast City Hospital, Belfast, Northern Ireland.
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750
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Chae SC, Park YR, Oh GJ, Lee JH, Chung HT. The suggestive association of eotaxin-2 and eotaxin-3 gene polymorphisms in Korean population with allergic rhinitis. Immunogenetics 2004; 56:760-4. [PMID: 15580493 DOI: 10.1007/s00251-004-0746-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2004] [Revised: 10/28/2004] [Indexed: 11/25/2022]
Abstract
The eotaxin gene family (eotaxin, eotaxin-2 and eotaxin-3) has been implicated in the recruitment of eosinophils, basophiles and Th2 lymphocytes that are central aspects of allergic diseases. To determine whether single-nucleotide polymorphisms (SNPs) of the eotaxin-2 and eotaxin-3 genes are associated with susceptibility to allergic rhinitis, we scanned 178 allergic rhinitis patients and 281 controls without allergic rhinitis using the direct sequencing and single-base extension (SBE) methods. We also calculated the haplotype frequencies between +179T>C and +275C>T of eotaxin-2 and +2497T>G of eotaxin-3 in both controls and allergic rhinitis patients. The haplotype frequency between controls and allergic rhinitis patients was suggestively associated (P=0.0001). The genotype frequencies of eotaxin-3 +2497T>G in allergic rhinitis patients were suggestively different from those in non-allergic rhinitis controls (P=<0.0007). Our results strongly suggest that the SNP of eotaxin-3 might be associated with susceptibility to allergic rhinitis.
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Affiliation(s)
- Soo-Cheon Chae
- Genome Research Center for Immune Disorders, Wonkwang University School of Medicine, Iksan, Chonbuk, 570-749, Korea
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