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Sebastiani P, Timofeev N, Dworkis DA, Perls TT, Steinberg MH. Genome-wide association studies and the genetic dissection of complex traits. Am J Hematol 2009; 84:504-15. [PMID: 19569043 PMCID: PMC2895326 DOI: 10.1002/ajh.21440] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The availability of affordable high throughput technology for parallel genotyping has opened the field of genetics to genome-wide association studies (GWAS), and in the last few years hundreds of articles reporting results of GWAS for a variety of heritable traits have been published. What do these results tell us? Although GWAS have discovered a few hundred reproducible associations, this number is underwhelming in relation to the huge amount of data produced, and challenges the conjecture that common variants may be the genetic causes of common diseases. We argue that the massive amount of genetic data that result from these studies remains largely unexplored and unexploited because of the challenge of mining and modeling enormous data sets, the difficulty of using nontraditional computational techniques and the focus of accepted statistical analyses on controlling the false positive rate rather than limiting the false negative rate. In this article, we will review the common approach to analysis of GWAS data and then discuss options to learn more from these data. We will use examples from our ongoing studies of sickle cell anemia and also GWAS in multigenic traits.
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Affiliation(s)
- Paola Sebastiani
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts 02118, USA.
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302
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O’Neill SK, Liu E, Cambier JC. Change you can B(cell)eive in: recent progress confirms a critical role for B cells in type 1 diabetes. Curr Opin Endocrinol Diabetes Obes 2009; 16:293-8. [PMID: 19502979 PMCID: PMC2968699 DOI: 10.1097/med.0b013e32832e06a7] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
PURPOSE OF REVIEW Here we review extant recent findings regarding the multiple roles of B cells in type 1 diabetes (T1D) and discuss how autoreactive B cells may become activated by a breach in B cell tolerance, and thereby initiate disease. Finally, we discuss the use of B cell-targeted therapies for treatment of autoimmunity. RECENT FINDINGS Anti-CD20-specific depletion of B cells prevents and reverses diabetes in human CD20/non-obese diabetic (NOD) mice. Correspondingly, in nontransgenic NOD mice, B cells are effectively depleted with high dose antimouse CD20 mAbs of varying isotypes, and this also prevents diabetes in more than 60% of the mice when administered early, and significantly delays disease in 15-week-old animals. A separate study revealed that targeting B cells with anti-CD22/cal monoclonal antibody therapy delays diabetes onset in prediabetic NOD mice and restores normoglycemia in new-onset hyperglycemic NOD mice. In humans, a clinical trial of rituximab in new onset type 1 diabetics has yielded promising preliminary findings. SUMMARY B cells are major players in T1D in humans, and clearly essential for disease development in the NOD mouse model of T1D. In this review, we discuss the silencing of autoreactive B cells and how failure of this process may contribute to autoimmunity. Further, we describe the most recent advances in studies of therapeutic effects of B cell depletion in T1D, and provide recent data indicating the diverse functions by which B cells may mediate disease.
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Affiliation(s)
- Shannon K. O’Neill
- University of Colorado Denver and National Jewish Health, 1400 Jackson Street, Denver, Colorado
| | - Edwin Liu
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Aurora, Colorado, USA
| | - John C. Cambier
- University of Colorado Denver and National Jewish Health, 1400 Jackson Street, Denver, Colorado
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303
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Bergholdt R, Brorsson C, Lage K, Nielsen JH, Brunak S, Pociot F. Expression profiling of human genetic and protein interaction networks in type 1 diabetes. PLoS One 2009; 4:e6250. [PMID: 19609442 PMCID: PMC2707614 DOI: 10.1371/journal.pone.0006250] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2009] [Accepted: 06/17/2009] [Indexed: 01/07/2023] Open
Abstract
Proteins contributing to a complex disease are often members of the same functional pathways. Elucidation of such pathways may provide increased knowledge about functional mechanisms underlying disease. By combining genetic interactions in Type 1 Diabetes (T1D) with protein interaction data we have previously identified sets of genes, likely to represent distinct cellular pathways involved in T1D risk. Here we evaluate the candidate genes involved in these putative interaction networks not only at the single gene level, but also in the context of the networks of which they form an integral part. mRNA expression levels for each gene were evaluated and profiling was performed by measuring and comparing constitutive expression in human islets versus cytokine-stimulated expression levels, and for lymphocytes by comparing expression levels among controls and T1D individuals. We identified differential regulation of several genes. In one of the networks four out of nine genes showed significant down regulation in human pancreatic islets after cytokine exposure supporting our prediction that the interaction network as a whole is a risk factor. In addition, we measured the enrichment of T1D associated SNPs in each of the four interaction networks to evaluate evidence of significant association at network level. This method provided additional support, in an independent data set, that two of the interaction networks could be involved in T1D and highlights the following processes as risk factors: oxidative stress, regulation of transcription and apoptosis. To understand biological systems, integration of genetic and functional information is necessary, and the current study has used this approach to improve understanding of T1D and the underlying biological mechanisms.
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Affiliation(s)
- Regine Bergholdt
- Hagedorn Research Institute and Steno Diabetes Center, Gentofte, Denmark.
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304
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Jacob K, Albrecht S, Sollier C, Faury D, Sader E, Montpetit A, Serre D, Hauser P, Garami M, Bognar L, Hanzely Z, Montes JL, Atkinson J, Farmer JP, Bouffet E, Hawkins C, Tabori U, Jabado N. Duplication of 7q34 is specific to juvenile pilocytic astrocytomas and a hallmark of cerebellar and optic pathway tumours. Br J Cancer 2009; 101:722-33. [PMID: 19603027 PMCID: PMC2736806 DOI: 10.1038/sj.bjc.6605179] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background: Juvenile pilocytic astrocytomas (JPA), a subgroup of low-grade astrocytomas (LGA), are common, heterogeneous and poorly understood subset of brain tumours in children. Chromosomal 7q34 duplication leading to fusion genes formed between KIAA1549 and BRAF and subsequent constitutive activation of BRAF was recently identified in a proportion of LGA, and may be involved in their pathogenesis. Our aim was to investigate additional chromosomal unbalances in LGA and whether incidence of 7q34 duplication is associated with tumour type or location. Methods and results: Using Illumina-Human-Hap300-Duo and 610-Quad high-resolution-SNP-based arrays and quantitative PCR on genes of interest, we investigated 84 paediatric LGA. We demonstrate that 7q34 duplication is specific to sporadic JPA (35 of 53 – 66%) and does not occur in other LGA subtypes (0 of 27) or NF1-associated-JPA (0 of 4). We also establish that it is site specific as it occurs in the majority of cerebellar JPA (24 of 30 – 80%) followed by brainstem, hypothalamic/optic pathway JPA (10 of 16 – 62.5%) and is rare in hemispheric JPA (1 of 7 – 14%). The MAP-kinase pathway, assessed through ERK phosphorylation, was active in all tumours regardless of 7q34 duplication. Gain of function studies performed on hTERT-immortalised astrocytes show that overexpression of wild-type BRAF does not increase cell proliferation or baseline MAPK signalling even if it sensitises cells to EGFR stimulation. Conclusions and interpretation: Our results suggest that variants of JPA might arise from a unique site-restricted progenitor cell where 7q34 duplication, a hallmark of this tumour-type in association to MAPK-kinase pathway activation, potentially plays a site-specific role in their pathogenesis. Importantly, gain of function abnormalities in components of MAP-Kinase signalling are potentially present in all JPA making this tumour amenable to therapeutic targeting of this pathway.
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Affiliation(s)
- K Jacob
- Department of Pediatrics and Human Genetics, Montreal Children's Hospital, McGill University Health Center, Montreal H3Z 2Z3, Canada.
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305
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Sleiman PM, Hakonarson H. Pharmacogenetics and functional genomics in asthma. Per Med 2009; 6:409-416. [PMID: 29783539 DOI: 10.2217/pme.09.30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Asthma is a complex phenotype caused by a combination of genetic and environmental factors that remain poorly understood. The common variants involved in the pathogenesis of asthma have proved difficult to identify by candidate gene association studies. As a result, few genetic variants influencing clinical response to asthma and allergy medications have been uncovered. Recently, genome-wide association, which is more robust in identifying common predisposition variants, has been applied to disorders such as asthma. As genome-wide associations are hypothesis-free, they raise the possibility of identifying novel biological pathways that could be translated to the future benefit of patients through improved diagnostic and therapeutic measures in the form of personalized medicine. This review addresses both recent advances in the genetics of asthma and their potential in transforming the treatment of the disorder into more individualized care in the near future.
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Affiliation(s)
- Patrick Ma Sleiman
- Center for Applied Genomics, 1216E Abramson Research Center, 3615 Civic Center Blvd., Philadelphia, PA 19104-4318, USA.
| | - Hakon Hakonarson
- Center for Applied Genomics, 1216E Abramson Research Center, 3615 Civic Center Blvd., Philadelphia, PA 19104-4318, USA.
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306
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Wu X, Zhu X, Wang X, Ma J, Zhu S, Li J, Liu Y. Intron polymorphism in the KIAA0350 gene is reproducibly associated with susceptibility to type 1 diabetes (T1D) in the Han Chinese population. Clin Endocrinol (Oxf) 2009; 71:46-9. [PMID: 19178520 DOI: 10.1111/j.1365-2265.2008.03437.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Three independent genome-wide association studies in white populations have reported that single nucleotide polymorphisms (SNPs) in the KIAA0350 gene are associated with susceptibility to type 1 diabetes (T1D). The gene product of KIAA0350 is predicted to be a sugar binding C-type lectin. In the present study, we investigated whether SNPs in this gene were associated with T1D in the Han Chinese population. DESIGN AND METHODS In this case-controlled association study, a total of 205 T1D patients and 422 non-diabetic subjects of the Han Chinese population were enrolled. Two SNPs, namely, rs17802927 and rs725613, in the KIAA0350 gene were genotyped using a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) protocol. RESULTS The intron SNP rs725613 was strongly associated with T1D in the Han Chinese population [P = 0.00007, odds ratio (OR) = 0.527, 95% confidence interval (CI) = 0.383-0.726], and the frequencies of its genotypes in the T1D group significantly differed from those in the control group (P = 0.0001). CONCLUSION The intron polymorphism rs725613 in the KIAA0350 gene is associated with susceptibility to T1D, and this association is not race specific.
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Affiliation(s)
- Xiaopan Wu
- National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
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307
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Grant SF, Bradfield JP, Zhang H, Wang K, Kim CE, Annaiah K, Santa E, Glessner JT, Thomas K, Garris M, Frackelton EC, Otieno FG, Shaner JL, Smith RM, Imielinski M, Chiavacci RM, Li M, Berkowitz RI, Hakonarson H. Investigation of the locus near MC4R with childhood obesity in Americans of European and African ancestry. Obesity (Silver Spring) 2009; 17:1461-5. [PMID: 19265794 PMCID: PMC2860794 DOI: 10.1038/oby.2009.53] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Recently a modest, but consistently, replicated association was demonstrated between obesity and the single-nucleotide polymorphism (SNP), rs17782313, 3' of the MC4R locus as a consequence of a meta-analysis of genome-wide association (GWA) studies of the disease in white populations. We investigated the association in the context of the childhood form of the disease utilizing data from our ongoing GWA study in a cohort of 728 European-American (EA) obese children (BMI > or =95th percentile) and 3,960 EA controls (BMI <95th percentile), as well as 1,008 African-American (AA) obese children and 2,715 AA controls. rs571312, rs10871777, and rs476828 (perfect surrogates for rs17782313) yielded odds ratios in the EA cohort of 1.142 (P = 0.045), 1.137 (P = 0.054), and 1.145 (P = 0.042); however, there was no significant association with these SNPs in the AA cohort. When investigating all 30 SNPs present on the Illumina BeadChip at this locus, again there was no evidence for association in AA cases when correcting for the number of tests employed. As such, variants 3' to the MC4R locus present on the genotyping platform utilized confer a similar magnitude of risk of obesity in white children as to their adult white counterparts but this observation did not extend to AAs.
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Affiliation(s)
- Struan F.A. Grant
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Department of Pediatrics and Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
- To whom correspondence should be addressed. or
| | - Jonathan P. Bradfield
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Haitao Zhang
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Kai Wang
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Cecilia E. Kim
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Kiran Annaiah
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Erin Santa
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Joseph T. Glessner
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Kelly Thomas
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Maria Garris
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Edward C. Frackelton
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - F. George Otieno
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Julie L. Shaner
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Ryan M. Smith
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Marcin Imielinski
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Rosetta M. Chiavacci
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Mingyao Li
- Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Robert I. Berkowitz
- Behavioral Health Center and Department of Child and Adolescent Psychiatry, The Children's Hospital of Philadelphia, Philadelphia PA 19104, USA
- Center for Weight and Eating Disorders, Department of Psychiatry, University of Pennsylvania, Philadelphia PA 19104, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Department of Pediatrics and Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
- To whom correspondence should be addressed. or
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308
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Dieguez-Gonzalez R, Akar S, Calaza M, Gonzalez-Alvaro I, Fernandez-Gutierrez B, Lamas JR, de la Serna AR, Caliz R, Blanco FJ, Pascual-Salcedo D, Velloso ML, Perez-Pampin E, Pablos JL, Navarro F, Narvaez J, Lopez-Longo FJ, Herrero-Beaumont G, Gomez-Reino JJ, Gonzalez A. Lack of association with rheumatoid arthritis of selected polymorphisms in 4 candidate genes: CFH, CD209, eotaxin-3, and MHC2TA. J Rheumatol 2009; 36:1590-5. [PMID: 19567623 DOI: 10.3899/jrheum.090022] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
OBJECTIVE To investigate associations with rheumatoid arthritis (RA) of single-nucleotide polymorphisms (SNP) in 4 candidate genes, complement factor H (CFH), CD209 or DC-SIGN, eotaxin-3, and the MHC class II Transactivator (MHC2TA) genes. These SNP have been reported as important for RA (eotaxin-3 and MHC2TA) or for other immune-mediated diseases (CFH and CD209). METHODS Genotypes for the 7 selected SNP were obtained from 1587 patients with RA and 1570 controls of Spanish ancestry. Analyses were carried out after stratification for sex, erosions, rheumatoid factor, shared epitope, anti-cyclic citrullinated peptide antibodies, and the R620W PTPN22 SNP. RESULTS None of the comparisons between patients with RA and controls or between the different strata of patients according to disease features was significant. CONCLUSION None of the SNP in CFH and CD209 showed evidence of association with RA. We did not replicate the association of eotaxin-3 with RA described in Koreans, or that of the MHC2T SNP.
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Affiliation(s)
- Rebeca Dieguez-Gonzalez
- Laboratorio de Investigacion 10, Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain
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309
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Pearce SHS, Merriman TR. Genetics of type 1 diabetes and autoimmune thyroid disease. Endocrinol Metab Clin North Am 2009; 38:289-301, vii-viii. [PMID: 19328412 DOI: 10.1016/j.ecl.2009.01.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The search for the susceptibility alleles for the complex genetic conditions of type 1 diabetes and autoimmune thyroid diseases has gained momentum in recent years. Studies have revealed several novel disease susceptibility alleles of relevance to both conditions, which brings the total number of genetic variants contributing to type 1 diabetes to ten. Additional genetic loci remain to be discovered, particularly in the autoimmune thyroid diseases. In the future, the density and coverage of single nucleotide polymorphisms available for high throughput genotyping will improve, and detailed analysis of the role of copy number variants in these diseases will shed new light on the pathogenesis of these common endocrinopathies.
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Affiliation(s)
- Simon H S Pearce
- Institute of Human Genetics, University of Newcastle, International Centre for Life, Newcastle upon Tyne, UK.
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310
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Barrett JC, Clayton D, Concannon P, Akolkar B, Cooper JD, Erlich HA, Julier C, Morahan G, Nerup J, Nierras C, Plagnol V, Pociot F, Schuilenburg H, Smyth DJ, Stevens H, Todd JA, Walker NM, Rich SS. Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes. Nat Genet 2009; 41:703-7. [PMID: 19430480 PMCID: PMC2889014 DOI: 10.1038/ng.381] [Citation(s) in RCA: 1309] [Impact Index Per Article: 87.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2008] [Accepted: 04/15/2009] [Indexed: 02/07/2023]
Abstract
Type 1 diabetes (T1D) is a common autoimmune disorder that arises from the action of multiple genetic and environmental risk factors. We report the findings of a genome-wide association study of T1D, combined in a meta-analysis with two previously published studies. The total sample set included 7,514 cases and 9,045 reference samples. Forty-one distinct genomic locations provided evidence for association with T1D in the meta-analysis (P < 10(-6)). After excluding previously reported associations, we further tested 27 regions in an independent set of 4,267 cases, 4,463 controls and 2,319 affected sib-pair (ASP) families. Of these, 18 regions were replicated (P < 0.01; overall P < 5 × 10(-8)) and 4 additional regions provided nominal evidence of replication (P < 0.05). The many new candidate genes suggested by these results include IL10, IL19, IL20, GLIS3, CD69 and IL27.
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MESH Headings
- Algorithms
- Antigens, CD/genetics
- CTLA-4 Antigen
- Chromosome Mapping/methods
- Chromosomes, Human, Pair 1/genetics
- Chromosomes, Human, Pair 17/genetics
- Chromosomes, Human, Pair 2/genetics
- DEAD-box RNA Helicases/genetics
- DNA/genetics
- Diabetes Mellitus, Type 1/epidemiology
- Diabetes Mellitus, Type 1/genetics
- Diabetes Mellitus, Type 1/immunology
- Family
- Female
- Genome-Wide Association Study
- Genotype
- HLA Antigens/genetics
- Humans
- Interferon-Induced Helicase, IFIH1
- Male
- Meta-Analysis as Topic
- Polymorphism, Single Nucleotide/genetics
- Protein Tyrosine Phosphatase, Non-Receptor Type 22/genetics
- Risk Assessment
- Siblings
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Affiliation(s)
- Jeffrey C. Barrett
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 0XY, UK
| | - David Clayton
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 0XY, UK
| | - Patrick Concannon
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Beena Akolkar
- Division of Diabetes, Endocrinology, and Metabolic Diseases, The National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD, USA
| | - Jason D. Cooper
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 0XY, UK
| | | | - Cécile Julier
- Inserm U730, Centre National de Génotypage, Evry, FR
| | - Grant Morahan
- Centre for Diabetes Research, The Western Australian Institute for Medical Research, and Centre for Medical Research, University of Western Australia, Perth, WA, AUSTRALIA
| | | | | | - Vincent Plagnol
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 0XY, UK
| | | | - Helen Schuilenburg
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 0XY, UK
| | - Deborah J. Smyth
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 0XY, UK
| | - Helen Stevens
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 0XY, UK
| | - John A. Todd
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 0XY, UK
| | - Neil M. Walker
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 0XY, UK
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, Division of Biostatistics and Epidemiology, University of Virginia, Charlottesville, VA, USA
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311
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Dema B, Martínez A, Fernández-Arquero M, Maluenda C, Polanco I, Angeles Figueredo M, de la Concha EG, Urcelay E, Núñez C. Autoimmune disease association signals in CIITA and KIAA0350 are not involved in celiac disease susceptibility. ACTA ACUST UNITED AC 2009; 73:326-9. [PMID: 19317741 DOI: 10.1111/j.1399-0039.2009.01216.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Celiac disease (CD) is a multifactorial disease characterized by intestinal inflammation after gluten exposure in genetically susceptible individuals. A strong influence of certain human leukocyte antigen (HLA) alleles (those coding the HLA-DQ2 and DQ8 heterodimers) is well established, but they cannot explain the overall genetic risk. CIITA could be a good candidate gene for CD because it is mainly transcriptionally regulated, and it encodes the master regulator of major histocompatibilty complex class II gene transcription. CIITA is located in 16p13, a region also containing KIAA0350 (CLEC16A), associated with two autoimmune diseases in genome-wide association studies. We aimed at studying the involvement of polymorphisms in CIITA and KIAA0350 in CD susceptibility, with special attention to evaluate the possible presence of more than one risk factor in the region. We performed a case-control study with 607 CD patients and up to 794 healthy controls, all Spaniards. All samples were genotyped for five single nucleotide polymorphisms: rs3087456 (-168A/G) and rs4774 in CIITA and rs7203459, rs6498169 and rs2903692 in KIAA0350. No significant results were obtained when comparing genotypic, allelic or haplotypic frequencies between patients and controls. Our results seem to discard the influence in CD susceptibility of CIITA and KIAA0350 markers previously associated with other autoimmune diseases.
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Affiliation(s)
- B Dema
- Servicio de Inmunología Clínica, Hospital Clínico San Carlos, Madrid, Spain
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312
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Silva AM, Bettencourt A, Pereira C, Santos E, Carvalho C, Mendonça D, Costa PP, Monteiro L, Martins B. Protective role of the HLA–A*02 allele in Portuguese patients with multiple sclerosis. Mult Scler 2009; 15:771-4. [DOI: 10.1177/1352458509104588] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background Multiple sclerosis (MS) is associated with human leukocyte antigen (HLA) HLA–DRB1*15. Recent evidence that CD8 T cells are implicated in MS suggests that HLA class I may also contribute. An association of HLA–A*02 and A*03 alleles has been described. Objectives We examined the influence of HLA–A*02 and HLA–A*03 in Portuguese patients with MS, independently of HLA–DRB1*15 using a logistic regression model. Conclusions DRB1*15 increased the risk of developing MS and HLA–A*02 decreased the risk. A*03 had no effect. To analyze if HLA–A*02 association was independent from DRB1*15, an interaction between these two alleles was introduced in the model; no significant interaction was found.
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Affiliation(s)
- AM Silva
- Departamento de Neurologia, Centro Hospitalar do Porto – Hospital de Santo António, Porto, Portugal
| | - A Bettencourt
- UMIB – Instituto de Ciências Biomédicas Abel Salazar (ICBAS-UP), Porto, Portugal
| | - C Pereira
- UMIB – Instituto de Ciências Biomédicas Abel Salazar (ICBAS-UP), Porto, Portugal
| | - E Santos
- Departamento de Neurologia, Centro Hospitalar do Porto – Hospital de Santo António, Porto, Portugal
| | - C Carvalho
- Unidade de Investigação, Centro de Genética Médica Jacinto de Magalhães, Porto, Portugal
| | - D Mendonça
- Departamento do estudo de populações, Instituto de Ciências Biomédicas Abel Salazar (ICBAS-UP), Porto, Portugal
| | - PP Costa
- UMIB – Instituto de Ciências Biomédicas Abel Salazar (ICBAS-UP), Porto, Portugal; Unidade de Investigação, Centro de Genética Médica Jacinto de Magalhães, Porto, Portugal
| | - L Monteiro
- Departamento de Neurologia, Centro Hospitalar do Porto – Hospital de Santo António, Porto, Portugal
| | - B Martins
- UMIB – Instituto de Ciências Biomédicas Abel Salazar (ICBAS-UP), Porto, Portugal; Unidade de Investigação, Centro de Genética Médica Jacinto de Magalhães, Porto, Portugal
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313
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Qu HQ, Grant SFA, Bradfield JP, Kim C, Frackelton E, Hakonarson H, Polychronakos C. Association of RASGRP1 with type 1 diabetes is revealed by combined follow-up of two genome-wide studies. J Med Genet 2009; 46:553-4. [PMID: 19465406 DOI: 10.1136/jmg.2009.067140] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
BACKGROUND The two genome-wide association studies published by us and by the Wellcome Trust Case-Control Consortium (WTCCC) revealed a number of novel loci, but neither had the statistical power to elucidate all of the genetic components of type 1 diabetes risk, a task for which larger effective sample sizes are needed. METHODS We analysed data from two sources: (1) The previously published second stage of our study, with a total sample size of the two stages consisting of 1046 Canadian case-parent trios and 538 multiplex families with 929 affected offspring from the Type 1 Diabetes Genetics Consortium (T1DGC); (2) the Rapid Response 2 (RR2) project of the T1DGC, which genotyped 4417 individuals from 1062 non-overlapping families, including 2059 affected individuals (mostly sibling pairs) for the 1536 markers with the highest statistical significance for type 1 diabetes in the WTCCC results. RESULTS One locus, mapping to a linkage disequilibrium (LD) block at chr15q14, reached statistical significance by combining results from two markers (rs17574546 and rs7171171) in perfect LD with each other (r2 = 1). We obtained a joint p value of 1.3 x 10(-6), which exceeds by an order of magnitude the conservative threshold of 3.26 x 10(-5) obtained by correcting for the 1536 single nucleotide polymorphisms (SNPs) tested in our study. Meta-analysis with the original WTCCC genome-wide data produced a p value of 5.83 x 10(-9). CONCLUSIONS A novel type 1 diabetes locus was discovered. It involves RASGRP1, a gene known to play a crucial role in thymocyte differentiation and T cell receptor (TCR) signalling by activating the Ras signalling pathway.
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314
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Liao KP, Gunnarsson M, Källberg H, Ding B, Plenge RM, Padyukov L, Karlson EW, Klareskog L, Askling J, Alfredsson L. Specific association of type 1 diabetes mellitus with anti-cyclic citrullinated peptide-positive rheumatoid arthritis. ACTA ACUST UNITED AC 2009; 60:653-60. [PMID: 19248096 DOI: 10.1002/art.24362] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
OBJECTIVE The co-occurrence of autoimmune diseases such as rheumatoid arthritis (RA) and type 1 diabetes mellitus (DM) has been reported in individuals and families. In this study, the strength and nature of this association were investigated at the population level in a Swedish case-control cohort. METHODS For this case-control study, 1,419 patients with incident RA diagnosed between 1996 and 2003 were recruited from university, public, and private rheumatology units throughout Sweden; 1,674 matched control subjects were recruited from the Swedish national population registry. Sera from the subjects were tested for the presence of antibodies to cyclic citrullinated peptide (anti-CCP), rheumatoid factor (RF), and the 620W PTPN22 allele. Information on a history of diabetes was obtained by questionnaire, telephone interview, and/or medical record review. The prevalence of type 1 DM and type 2 DM was compared between patients with incident RA and control subjects and further stratified for the presence of anti-CCP, RF, and the PTPN22 risk allele. RESULTS Type 1 DM was associated with an increased risk of RA (odds ratio [OR] 4.9, 95% confidence interval [95% CI] 1.8-13.1), and this association was specific for anti-CCP-positive RA (OR 7.3, 95% CI 2.7-20.0), but not anti-CCP-negative RA. Further adjustment for the presence of PTPN22 attenuated the risk of anti-CCP-positive RA in patients with type 1 DM to an OR of 5.3 (95% CI 1.5-18.7). No association between RA and type 2 DM was observed. CONCLUSION The association between type 1 DM and RA is specific for a particular RA subset, anti-CCP-positive RA. The risk of developing RA later in life in patients with type 1 DM may be attributed, in part, to the presence of the 620W PTPN22 allele, suggesting that this risk factor may represent a common pathway for the pathogenesis of these 2 diseases.
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Affiliation(s)
- Katherine P Liao
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Boston, MA 02114, USA.
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315
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Affiliation(s)
- Patrick Concannon
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA.
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316
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Abstract
Type 1 diabetes (T1D) is a chronic disease that typically manifests itself in childhood through the autoimmune destruction of pancreatic beta cells, resulting in a lack of production of insulin. T1D is a multifactorial disease with a strong genetic component that is thought to interact with specific environmental triggers. Several genetic determinants of T1D were already established before the era of genome-wide association studies, primarily with the HLA class II genes, encoding highly polymorphic antigen-presenting proteins that account for almost 50% of the genetic risk for T1D. The recent development of high-throughput single nucleotide polymorphism genotyping array technologies has enabled investigators to perform high-density genome-wide association studies in search of the remaining T1D loci. Combined with the well-established genes known for many years, 16 loci have now been uncovered to date as being robustly associated with the pathogenesis of this phenotype.
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Affiliation(s)
- Struan F A Grant
- Center for Applied Genomics, 1216E Abramson Research Center, 3615 Civic Center Boulevard, Philadelphia, PA 19104-4318, USA
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317
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Márquez A, Varadé J, Robledo G, Martínez A, Mendoza JL, Taxonera C, Fernández-Arquero M, Díaz-Rubio M, Gómez-García M, López-Nevot MA, de la Concha EG, Martín J, Urcelay E. Specific association of a CLEC16A/KIAA0350 polymorphism with NOD2/CARD15(-) Crohn's disease patients. Eur J Hum Genet 2009; 17:1304-8. [PMID: 19337309 DOI: 10.1038/ejhg.2009.50] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Independent genome-wide association studies highlighted the function of CLEC16A/KIAA0350 polymorphisms modifying the risk to either multiple sclerosis (rs6498169) or type 1 diabetes (rs2903692). This C-type lectin gene maps to a linkage disequilibrium block at 16p13 and a functional role of this gene could be envisaged for other immune-related conditions, such as inflammatory bowel disease (IBD). The present study, aimed at investigating the association of those two polymorphisms with IBD, included 720 IBD patients and 550 ethnically matched healthy controls. The effect of rs2903692 previously described in diabetes was observed specifically for Crohn's disease (CD) patients lacking the main susceptibility factor described to date, that is, three polymorphisms within another pattern recognition gene, NOD2/CARD15 (NOD2(-) vs NOD2(+) CD patients, G vs A: P=0.008; OR (95% CI)=1.54 (1.10-2.15); NOD2(-) CD patients vs controls: P=0.008; OR (95% CI)=1.37 (1.08-1.73)). Replication of these findings was performed in independent Spanish cohorts of 544 IBD patients and 340 controls and the combined data yielded significant differences (405 NOD2(-) vs 204 NOD2(+) CD patients, G vs A: P=0.0012; OR(M-H) (95% CI)=1.49 (1.17-1.90); NOD2(-) CD patients vs controls: P=0.0007; OR(M-H) (95% CI)=1.35 (1.13-1.60)). The pooled analysis of the ulcerative colitis patients vs controls also yielded a significant risk (P=0.0005; OR (95% CI)=1.52 (1.19-1.93)). These data would suggest that microbial recognition through different pathways seems to converge in the development of these polygenic bowel diseases.
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Affiliation(s)
- Ana Márquez
- Department of Immunology, Hospital Clínico San Carlos, Madrid, Spain
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318
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Abrahamsen B, Brixen K. Mapping the prescriptiome to fractures in men--a national analysis of prescription history and fracture risk. Osteoporos Int 2009; 20:585-97. [PMID: 18690484 DOI: 10.1007/s00198-008-0711-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2008] [Accepted: 06/11/2008] [Indexed: 12/21/2022]
Abstract
SUMMARY A nationwide case-control study was performed in 62,865 men aged 50+ using fracture data from the national hospital discharge register to screen all redeemed prescriptions in the past 5 years for significant mapping to fracture risk, employing measures to control for false discovery rate. INTRODUCTION Osteoporosis in men is frequently related to alcohol abuse, hypogonadism, hypercalciuria, or the use of glucocorticoids. Very limited information is available on the impact of other medications on fracture risk in men. METHODS We conducted a nationwide population-based case-control study collecting fracture data from the Danish National Hospital Discharge Register and prescriptions from the National Prescriptions Database (1995-2000). We included men aged 50+ years, with hospital-treated fractures in the year 2000 (n = 15,716), and age- and sex-matched controls (n = 47,149). RESULTS We identified 3.2 million redemptions of prescriptions for 1,073 different drugs. The analysis confirmed associations between fracture risk and use of sedatives, anti-epileptics, anti-psychotics, anxiolytics, SSRI, opioids and other analgesics, loop diuretics, and glucorticoids. New associations were also found. We observed an odds ratio (OR [95% CI] for any fracture) for fracture in users of dopaminergic agents (1.6 [1.3-1.9]) and iron compounds (1.2 [1.1-1.5]). The largest impact on fracture risk at population level was exerted by loop diuretics and analgesics. CONCLUSIONS An array of drugs is associated with fracture risk in men. The "prescriptiome" analysis can be used as a surveillance tool for drug-induced osteoporosis and in the planning of preventive measures.
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Affiliation(s)
- B Abrahamsen
- Department of Internal Medicine and Endocrinology, Copenhagen University Hospital Gentofte, Copenhagen, Denmark.
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319
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Wallis RH, Wang K, Marandi L, Hsieh E, Ning T, Chao GY, Sarmiento J, Paterson AD, Poussier P. Type 1 diabetes in the BB rat: a polygenic disease. Diabetes 2009; 58:1007-17. [PMID: 19168599 PMCID: PMC2661594 DOI: 10.2337/db08-1215] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
OBJECTIVE Two type 1 diabetes susceptibility genes have been identified in the spontaneously diabetic biobreeding diabetes-prone (BBDP) rat, the major histocompatibility complex (MHC) (RT1) class II u haplotype (Iddm1) and Gimap5 (Iddm2). The strong effects of these have impeded previous efforts to map additional loci. We tested the hypothesis that type 1 diabetes is a polygenic disease in the BBDP rat. RESEARCH DESIGN AND METHODS We performed the most comprehensive genome-wide linkage analysis for type 1 diabetes, age of disease onset (AOO), and insulitis subphenotypes in 574 F2 animals from a cross-intercross between BBDP and type 1 diabetes-resistant, double congenic ACI.BBDP-RT1u,Gimap5 (ACI.BB(1u.lyp)) rats, where both Iddm1 and Iddm2 were fixed as BBDP. RESULTS A total of 19% of these F2 animals developed type 1 diabetes, and eight type 1 diabetes susceptibility loci were mapped, six showing significant linkage (chromosomes 1, 3, 6 [two loci], 12, and 14) and two (chromosomes 2 and 17) suggestive linkage. The chromosomes 6, 12, and 14 intervals were also linked to the severity of islet infiltration by immunocytes, while those on chromosomes 1, 6 (two loci), 14, 17, and a type 1 diabetes-unlinked chromosome 8 interval showed significant linkage to the degree of islet atrophy. Four loci exhibited suggestive linkage to AOO on chromosomes 2 (two loci), 7, and 18 but were unlinked to type 1 diabetes. INS, PTPN22, IL2/IL21, C1QTNF6, and C12orf30, associated with human type 1 diabetes, are contained within the chromosomes 1, 2, 7, and 12 loci. CONCLUSIONS This study demonstrates that the BBDP diabetic syndrome is a complex, polygenic disease that may share additional susceptibility genes besides MHC class II with human type 1 diabetes.
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Affiliation(s)
- Robert H. Wallis
- Sunnybrook Health Sciences Centre Research Institute, Departments of Medicine and Immunology, University of Toronto, Toronto, Ontario, Canada; the
| | - KeSheng Wang
- Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada; the
- Department of Biostatistics and Epidemiology, College of Public Health, East Tennessee State University, Johnson City, Tennessee; the
| | - Leili Marandi
- Sunnybrook Health Sciences Centre Research Institute, Departments of Medicine and Immunology, University of Toronto, Toronto, Ontario, Canada; the
| | - Eugene Hsieh
- Sunnybrook Health Sciences Centre Research Institute, Departments of Medicine and Immunology, University of Toronto, Toronto, Ontario, Canada; the
- Department of Laboratory Medicine and Pathology, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada; and the
| | - Terri Ning
- Sunnybrook Health Sciences Centre Research Institute, Departments of Medicine and Immunology, University of Toronto, Toronto, Ontario, Canada; the
| | - Gary Y.C. Chao
- Sunnybrook Health Sciences Centre Research Institute, Departments of Medicine and Immunology, University of Toronto, Toronto, Ontario, Canada; the
| | - Janice Sarmiento
- Sunnybrook Health Sciences Centre Research Institute, Departments of Medicine and Immunology, University of Toronto, Toronto, Ontario, Canada; the
| | - Andrew D. Paterson
- Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada; the
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Philippe Poussier
- Sunnybrook Health Sciences Centre Research Institute, Departments of Medicine and Immunology, University of Toronto, Toronto, Ontario, Canada; the
- Corresponding author: Philippe Poussier,
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320
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Concannon P, Chen WM, Julier C, Morahan G, Akolkar B, Erlich HA, Hilner JE, Nerup J, Nierras C, Pociot F, Todd JA, Rich SS. Genome-wide scan for linkage to type 1 diabetes in 2,496 multiplex families from the Type 1 Diabetes Genetics Consortium. Diabetes 2009; 58:1018-22. [PMID: 19136655 PMCID: PMC2661598 DOI: 10.2337/db08-1551] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVE Type 1 diabetes arises from the actions of multiple genetic and environmental risk factors. Considerable success at identifying common genetic variants that contribute to type 1 diabetes risk has come from genetic association (primarily case-control) studies. However, such studies have limited power to detect genes containing multiple rare variants that contribute significantly to disease risk. RESEARCH DESIGN AND METHODS The Type 1 Diabetes Genetics Consortium (T1DGC) has assembled a collection of 2,496 multiplex type 1 diabetic families from nine geographical regions containing 2,658 affected sib-pairs (ASPs). We describe the results of a genome-wide scan for linkage to type 1 diabetes in the T1DGC family collection. RESULTS Significant evidence of linkage to type 1 diabetes was confirmed at the HLA region on chromosome 6p21.3 (logarithm of odds [LOD] = 213.2). There was further evidence of linkage to type 1 diabetes on 6q that could not be accounted for by the major linkage signal at the HLA class II loci on chromosome 6p21. Suggestive evidence of linkage (LOD > or =2.2) was observed near CTLA4 on chromosome 2q32.3 (LOD = 3.28) and near INS (LOD = 3.16) on chromosome 11p15.5. Some evidence for linkage was also detected at two regions on chromosome 19 (LOD = 2.84 and 2.54). CONCLUSIONS Five non-HLA chromosome regions showed some evidence of linkage to type 1 diabetes. A number of previously proposed type 1 diabetes susceptibility loci, based on smaller ASP numbers, showed limited or no evidence of linkage to disease. Low-frequency susceptibility variants or clusters of loci with common alleles could contribute to the linkage signals observed.
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Affiliation(s)
- Patrick Concannon
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA.
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321
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Kawasaki E, Awata T, Ikegami H, Kobayashi T, Maruyama T, Nakanishi K, Shimada A, Uga M, Kurihara S, Kawabata Y, Tanaka S, Kanazawa Y, Eguchi K. Genetic association between the interleukin-2 receptor-alpha gene and mode of onset of type 1 diabetes in the Japanese population. J Clin Endocrinol Metab 2009; 94:947-52. [PMID: 19106270 DOI: 10.1210/jc.2008-1596] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
CONTEXT/OBJECTIVE The IL-2 receptor-alpha (IL2RA), also known as CD25, is expressed on the regulatory T cells, which play an important role in the control of immune responses and the maintenance of immune homeostasis. Our objective was to determine whether variants in the IL2RA gene are associated with type 1 diabetes in the Japanese population. DESIGN/PATIENTS We genotyped the four single-nucleotide polymorphisms (rs706778, rs3118470, ss52580101, and rs11594656) of the IL2RA in 885 patients with type 1 diabetes and 606 control subjects of Japanese origin. The allele and genotype frequencies were examined in the patient groups stratified by their mode of onset in a case-control study. RESULTS We found evidence of association with acute-onset, but not slow-onset and fulminant, type 1 diabetes for two of the four single-nucleotide polymorphisms genotyped (rs706778 and rs3118470). The rs706778 A allele and the rs3118470 G allele were associated with an increased disease risk [odds ratio (OR) for rs706778 AA genotype 1.54, P = 4.2 x 10(-4) and OR for rs3118470 GG genotype 1.50, P = 0.0019, respectively]. Furthermore, the A-G haplotype was associated with increased type 1 diabetes risk in the acute-onset form (OR 1.30, P = 0.002). CONCLUSIONS The present data confirm the type 1 diabetes association with IL2RA and provide evidence that the different contributions of the IL2RA in the susceptibility to acute-onset and other forms of type 1 diabetes in the Japanese population.
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Affiliation(s)
- Eiji Kawasaki
- Department of Metabolism/Diabetes and Clinical Nutrition, Nagasaki University Hospital of Medicine and Dentistry, 1-7-1 Sakamoto, Nagasaki 852-8501, Japan.
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322
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Gylvin T, Ek J, Nolsøe R, Albrechtsen A, Andersen G, Bergholdt R, Brorsson C, Bang-Berthelsen CH, Hansen T, Karlsen AE, Billestrup N, Borch-Johnsen K, Jørgensen T, Pedersen O, Mandrup-Poulsen T, Nerup J, Pociot F. Functional SOCS1 polymorphisms are associated with variation in obesity in whites. Diabetes Obes Metab 2009; 11:196-203. [PMID: 19215277 DOI: 10.1111/j.1463-1326.2008.00900.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
AIMS/HYPOTHESIS The suppressor of cytokine signalling 1 (SOCS1) is a natural inhibitor of cytokine and insulin signalling pathways and may also play a role in obesity. In addition, SOCS1 is considered a candidate gene in the pathogenesis of both type 1 diabetes (T1D) and type 2 diabetes (T2D). The objective was to perform mutation analysis of SOCS1 and to test the identified variations for association to T2D-related quantitative traits, T2D or T1D. METHODS Mutation scanning was performed by direct sequencing in 27 white Danish subjects. Genotyping was carried out by TaqMan allelic discrimination. A total of more than 8100 individuals were genotyped. RESULTS Eight variations were identified in the 5' untranslated region (UTR) region. Two of these had allele frequencies below 1% and were not further examined. The six other variants were analysed in groups of T1D families (n = 1461 subjects) and T2D patients (n = 1430), glucose tolerant first-degree relatives of T2D patients (n = 212) and normal glucose tolerant (NGT) subjects. The rs33977706 polymorphism (-820G > T) was associated with a lower body mass index (BMI) (p = 0.004). In a second study (n = 4625 NGT subjects), significant associations of both the rs33977706 and the rs243330 (-1656G > A) variants to obesity were found (p = 0.047 and p = 0.015) respectively. The rs33977706 affected both binding of a nuclear protein to and the transcriptional activity of the SOCS1 promoter, indicating a relationship between this polymorphism and gene regulation. CONCLUSIONS/INTERPRETATION This study demonstrates that functional variations in the SOCS1 promoter may associate with alterations in BMI in the general white population.
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Affiliation(s)
- T Gylvin
- Steno Diabetes Center, Gentofte, Denmark
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323
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Chien JW, Zhao LP, Storer B, Martin PJ, Boeckh M, Warren EH, Hansen JA. Improving hematopoietic cell transplant outcomes in a new era of genomic research. Biol Blood Marrow Transplant 2009; 15:42-5. [PMID: 19147077 DOI: 10.1016/j.bbmt.2008.11.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Jason W Chien
- Clinical Research Division and Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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324
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Joint analysis of tightly linked SNPs in screening step of genome-wide association studies leads to increased power. Eur J Hum Genet 2009; 17:1043-9. [PMID: 19223937 DOI: 10.1038/ejhg.2009.7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Recent developments in genome-wide association studies (GWAS) have lead to the localization of disease genes for many complex diseases. The scrutiny of the respective publications reveals, first, that statistical analysis is restricted typically to single-marker analysis in the first step, and that, second, the presence of multiple, independently associated SNPs within the same linkage disequilibrium (LD) region is a common phenomenon. Motivated by this observation, we show through a power simulation study that a simultaneous analysis of tightly linked SNPs in the initial GWAS analysis step would lead to increased power, when compared with that in single-marker analysis. This is true for all the three approaches we considered (implementations in BEAGLE, FAMHAP and UNPHASED). The best performance was obtained using a two-marker haplotype analysis. In conclusion, we would expect additional gene findings for re-analyzing successful GWAS with a multi-marker approach.
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325
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Yang S, Wang K, Gregory B, Berrettini W, Wang LS, Hakonarson H, Bucan M. Genomic landscape of a three-generation pedigree segregating affective disorder. PLoS One 2009; 4:e4474. [PMID: 19214233 PMCID: PMC2637422 DOI: 10.1371/journal.pone.0004474] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2008] [Accepted: 12/30/2008] [Indexed: 11/18/2022] Open
Abstract
Bipolar disorder (BPD) is a common psychiatric illness with a complex mode of inheritance. Besides traditional linkage and association studies, which require large sample sizes, analysis of common and rare chromosomal copy number variants (CNVs) in extended families may provide novel insights into the genetic susceptibility of complex disorders. Using the Illumina HumanHap550 BeadChip with over 550,000 SNP markers, we genotyped 46 individuals in a three-generation Old Order Amish pedigree with 19 affected (16 BPD and three major depression) and 27 unaffected subjects. Using the PennCNV algorithm, we identified 50 CNV regions that ranged in size from 12 to 885 kb and encompassed at least 10 single nucleotide polymorphisms (SNPs). Of 19 well characterized CNV regions that were available for combined genotype-expression analysis 11 (58%) were associated with expression changes of genes within, partially within or near these CNV regions in fibroblasts or lymphoblastoid cell lines at a nominal P value <0.05. To further investigate the mode of inheritance of CNVs in the large pedigree, we analyzed a set of four CNVs, located at 6q27, 9q21.11, 12p13.31 and 15q11, all of which were enriched in subjects with affective disorders. We additionally show that these variants affect the expression of neuronal genes within or near the rearrangement. Our analysis suggests that family based studies of the combined effect of common and rare CNVs at many loci may represent a useful approach in the genetic analysis of disease susceptibility of mental disorders.
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Affiliation(s)
- Shuzhang Yang
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Kai Wang
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Brittany Gregory
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Wade Berrettini
- Department of Psychiatry, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Li-San Wang
- Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Division of Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Maja Bucan
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
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326
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Hunter KW, Crawford NPS. The future of mouse QTL mapping to diagnose disease in mice in the age of whole-genome association studies. Annu Rev Genet 2009; 42:131-41. [PMID: 18759635 DOI: 10.1146/annurev.genet.42.110807.091659] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genome-wide association analysis is emerging as a powerful tool to define novel genes and molecular pathways involved in susceptibility to human complex disorders. However, in spite of recent successes, this approach is not without its limitations, the most notable of which is inconsistent phenotype penetrance due to varied environmental exposures. Mouse models do, however, circumvent some of these drawbacks by allowing for a much higher degree of control over genetic variation and environmental exposure, and although their application to human complex genetics is not always straightforward, they do serve as a powerful means of complementing observations in human populations. Mouse quantitative trait locus mapping has proven a successful, yet technically demanding method for defining trait susceptibility. In this review, we focus upon recent advances that are both reducing the technical burden traditionally associated with quantitative trait locus mapping, and enhancing the applicability of these approaches to human disease.
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Affiliation(s)
- Kent W Hunter
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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327
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Benyamin B, Visscher PM, McRae AF. Family-based genome-wide association studies. Pharmacogenomics 2009; 10:181-90. [DOI: 10.2217/14622416.10.2.181] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In the last 2 years, the effort to identify genes affecting common diseases and complex traits has been accelerated through the use of genome-wide association studies (GWAS). The availability of existing large collections of linkage data paved the way for the use of family-based GWAS. Although most published GWAS used population-based designs, family-based designs have played an important role, particularly in replication stages. Family-based designs offer advantages in terms of quality control, the robustness to population stratification and the ability to perform genetic analyses that cannot be achieved using a sample of unrelated individuals, such as testing for the effect of imprinted genes on phenotypes, testing whether a genetic variant is inherited or de novo and combined linkage and association analysis.
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Affiliation(s)
- Beben Benyamin
- Queensland Statistical Genetics Laboratory, Queensland Institute of Medical Research, 300 Herston Road, Brisbane, QLD 4029, Australia
| | - Peter M Visscher
- Queensland Statistical Genetics Laboratory, Queensland Institute of Medical Research, 300 Herston Road, Brisbane, QLD 4029, Australia
| | - Allan F McRae
- Queensland Statistical Genetics Laboratory, Queensland Institute of Medical Research, 300 Herston Road, Brisbane, QLD 4029, Australia
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328
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Bisgaard H, Bønnelykke K, Sleiman PMA, Brasholt M, Chawes B, Kreiner-Møller E, Stage M, Kim C, Tavendale R, Baty F, Pipper CB, Palmer CNA, Hakonarsson H. Chromosome 17q21 Gene Variants Are Associated with Asthma and Exacerbations but Not Atopy in Early Childhood. Am J Respir Crit Care Med 2009; 179:179-85. [DOI: 10.1164/rccm.200809-1436oc] [Citation(s) in RCA: 164] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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329
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Detecting shared pathogenesis from the shared genetics of immune-related diseases. Nat Rev Genet 2009; 10:43-55. [PMID: 19092835 DOI: 10.1038/nrg2489] [Citation(s) in RCA: 395] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Recent genetic studies have revealed shared immunological mechanisms in several immune-related disorders that further our understanding of the development and concomitance of these diseases. Our Review focuses on these shared aspects, using the novel findings of recently performed genome-wide association studies and non-synonymous SNP scans as a starting point. We discuss how identifying new genes that are associated with more than one autoimmune or chronic inflammatory disorder could explain the genetic basis of the shared pathogenesis of immune-related diseases. This analysis helps to highlight the key molecular pathways that are involved in these disorders and the potential roles of novel genes in immune-related diseases.
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330
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Attiyeh EF, Diskin SJ, Attiyeh MA, Mossé YP, Hou C, Jackson EM, Kim C, Glessner J, Hakonarson H, Biegel JA, Maris JM. Genomic copy number determination in cancer cells from single nucleotide polymorphism microarrays based on quantitative genotyping corrected for aneuploidy. Genome Res 2009; 19:276-83. [PMID: 19141597 DOI: 10.1101/gr.075671.107] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Microarrays are frequently used to profile genome-wide copy number (CN) aberrations. While generally robust for detecting CN variants in germline DNA, the methods used to derive CN from signal intensity values have been suboptimal when applied to cancer genomes. The complexity of genomic aberrations in cancer makes it more difficult to discriminate between signal and noise, and measuring CN as a discrete variable does not account for tumor heterogeneity. Furthermore, standard normalization approaches detect CN changes relative to the overall DNA content, which is often not diploid in cancer. We propose an algorithm that uses the degree of allelic imbalance as well as probe intensity, with a correction for aneuploidy, for a quantitative CN assessment and scoring of allelic ratios. This algorithm results in a more precise definition of CN and allelic aberration in the cancer genome, which is essential for translational efforts focused on using these tools for molecular diagnostics and for the discovery of therapeutic targets.
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Affiliation(s)
- Edward F Attiyeh
- Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, and Abramson Family Cancer Research Institute, Philadelphia, Pennsylvania 19104-4318, USA.
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331
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Abstract
DNA variations have contributed enormously to the fields of medical and forensic science, especially through their use in studies on genes responsible or susceptible to various diseases and those on screening of chromosomal abnormalities in tumors. The types of genetic variations used in these studies have changed in the past 25 years and can be classified into five major classes: RFLP (restriction fragment length polymorphism), VNTR (variable number of tandem repeat), STR (short tandem repeat or microsatellite), SNP (single-nucleotide polymorphism) and CNV (copy-number variation). Genetic linkage analysis using these tools helped to map and discover genes responsible for hundreds of hereditary diseases. Furthermore, construction of the international SNP database and recent development of high-throughput SNP typing platforms enabled us to perform genome-wide association studies, which have identified genes (or genetic variations) susceptible to common diseases or those associated with drug responses. Genome-wide sequencing of individual DNAs is gaining immense scope. Here, I summarize the history of polymorphic DNA markers and their contribution to the genetic analysis of both rare hereditary diseases and common diseases, as well as recent advances in pharmacogenetics, including our contribution to these areas.
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332
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Chang MH, Lindegren ML, Butler MA, Chanock SJ, Dowling NF, Gallagher M, Moonesinghe R, Moore CA, Ned RM, Reichler MR, Sanders CL, Welch R, Yesupriya A, Khoury MJ. Prevalence in the United States of selected candidate gene variants: Third National Health and Nutrition Examination Survey, 1991-1994. Am J Epidemiol 2009; 169:54-66. [PMID: 18936436 PMCID: PMC2638878 DOI: 10.1093/aje/kwn286] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2007] [Accepted: 08/14/2008] [Indexed: 12/21/2022] Open
Abstract
Population-based allele frequencies and genotype prevalence are important for measuring the contribution of genetic variation to human disease susceptibility, progression, and outcomes. Population-based prevalence estimates also provide the basis for epidemiologic studies of gene-disease associations, for estimating population attributable risk, and for informing health policy and clinical and public health practice. However, such prevalence estimates for genotypes important to public health remain undetermined for the major racial and ethnic groups in the US population. DNA was collected from 7,159 participants aged 12 years or older in Phase 2 (1991-1994) of the Third National Health and Nutrition Examination Survey (NHANES III). Certain age and minority groups were oversampled in this weighted, population-based US survey. Estimates of allele frequency and genotype prevalence for 90 variants in 50 genes chosen for their potential public health significance were calculated by age, sex, and race/ethnicity among non-Hispanic whites, non-Hispanic blacks, and Mexican Americans. These nationally representative data on allele frequency and genotype prevalence provide a valuable resource for future epidemiologic studies in public health in the United States.
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Affiliation(s)
- Man-Huei Chang
- National Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, GA 30341, USA.
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333
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Abstract
Extraordinary technical advances in the field of human genetics over the past few years have catalyzed an explosion of new information about the genetics of human autoimmunity. In particular, the ability to scan the entire genome for common polymorphisms that associate with disease has led to the identification of numerous new risk genes involved in autoimmune phenotypes. Several themes are emerging. Autoimmune disorders have a complex genetic basis; multiple genes contribute to disease risk, each with generally modest effects independently. In addition, it is now clear that common genes underlie multiple autoimmune disorders. There is also heterogeneity among subphenotypes within a disease and across major racial groups. The current crop of genetic associations are only the start of a complete catalog of genetic factors for autoimmunity, and it remains unclear to what extent common variation versus multiple rare variants contribute to disease susceptibility. The current review focuses on recent discoveries within functionally related groups of genes that provide clues to novel pathways of pathogenesis for human autoimmunity.
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Affiliation(s)
- Peter K. Gregersen
- Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, Manhasset, New York 11030
| | - Lina M. Olsson
- Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, Manhasset, New York 11030
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334
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Gao S, Wang X. Predicting Type 1 Diabetes Candidate Genes using Human Protein-Protein Interaction Networks. ACTA ACUST UNITED AC 2009; 2:133. [PMID: 20148193 PMCID: PMC2818071 DOI: 10.4172/jcsb.1000025] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Background Proteins directly interacting with each other tend to have similar functions and be involved in the same cellular processes. Mutations in genes that code for them often lead to the same family of disease phenotypes. Efforts have been made to prioritize positional candidate genes for complex diseases utilize the protein-protein interaction (PPI) information. But such an approach is often considered too general to be practically useful for specific diseases. Results In this study we investigate the efficacy of this approach in type 1 diabetes (T1D). 266 known disease genes, and 983 positional candidate genes from the 18 established linkage loci of T1D, are compiled from the T1Dbase (http://t1dbase.org). We found that the PPI network of known T1D genes has distinct topological features from others, with significantly higher number of interactions among themselves even after adjusting for their high network degrees (p<1e-5). We then define those positional candidates that are first degree PPI neighbours of the 266 known disease genes to be new candidate disease genes. This leads to a list of 68 genes for further study. Cross validation using the known disease genes as benchmark reveals that the enrichment is ~17.1 fold over random selection, and ~4 fold better than using the linkage information alone. We find that the citations of the new candidates in T1D-related publications are significantly (p<1e-7) more than random, even after excluding the co-citation with the known disease genes; they are significantly over-represented (p<1e-10) in the top 30 GO terms shared by known disease genes. Furthermore, sequence analysis reveals that they contain significantly (p<0.0004) more protein domains that are known to be relevant to T1D. These findings provide indirect validation of the newly predicted candidates. Conclusion Our study demonstrates the potential of the PPI information in prioritizing positional candidate genes for T1D.
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Affiliation(s)
- Shouguo Gao
- Department of Physics & the Comprehensive Diabetes Center, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL 35294, USA
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335
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Grant SFA, Qu HQ, Bradfield JP, Marchand L, Kim CE, Glessner JT, Grabs R, Taback SP, Frackelton EC, Eckert AW, Annaiah K, Lawson ML, Otieno FG, Santa E, Shaner JL, Smith RM, Skraban R, Imielinski M, Chiavacci RM, Grundmeier RW, Stanley CA, Kirsch SE, Waggott D, Paterson AD, Monos DS, Polychronakos C, Hakonarson H. Follow-up analysis of genome-wide association data identifies novel loci for type 1 diabetes. Diabetes 2009; 58:290-5. [PMID: 18840781 PMCID: PMC2606889 DOI: 10.2337/db08-1022] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
OBJECTIVE Two recent genome-wide association (GWA) studies have revealed novel loci for type 1 diabetes, a common multifactorial disease with a strong genetic component. To fully utilize the GWA data that we had obtained by genotyping 563 type 1 diabetes probands and 1,146 control subjects, as well as 483 case subject-parent trios, using the Illumina HumanHap550 BeadChip, we designed a full stage 2 study to capture other possible association signals. RESEARCH DESIGN AND METHODS From our existing datasets, we selected 982 markers with P < 0.05 in both GWA cohorts. Genotyping these in an independent set of 636 nuclear families with 974 affected offspring revealed 75 markers that also had P < 0.05 in this third cohort. Among these, six single nucleotide polymorphisms in five novel loci also had P < 0.05 in the Wellcome Trust Case-Control Consortium dataset and were further tested in 1,303 type 1 diabetes probands from the Diabetes Control and Complications Trial/Epidemiology of Diabetes Interventions and Complications (DCCT/EDIC) plus 1,673 control subjects. RESULTS Two markers (rs9976767 and rs3757247) remained significant after adjusting for the number of tests in this last cohort; they reside in UBASH3A (OR 1.16; combined P = 2.33 x 10(-8)) and BACH2 (1.13; combined P = 1.25 x 10(-6)). CONCLUSIONS Evaluation of a large number of statistical GWA candidates in several independent cohorts has revealed additional loci that are associated with type 1 diabetes. The two genes at these respective loci, UBASH3A and BACH2, are both biologically relevant to autoimmunity.
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Affiliation(s)
- Struan F A Grant
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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336
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Nosikov VV, Seregin YA. Molecular genetics of type 1 diabetes mellitus: Achievements and future trends. Mol Biol 2008. [DOI: 10.1134/s0026893308050142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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337
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Variation within the CLEC16A gene shows consistent disease association with both multiple sclerosis and type 1 diabetes in Sardinia. Genes Immun 2008; 10:15-7. [PMID: 18946483 DOI: 10.1038/gene.2008.84] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Variation within intron 19 of the CLEC16A (KIAA0350) gene region was recently found to be unequivocally associated with type 1 diabetes (T1D) in genome-wide association (GWA) studies in Northern European populations. A variant in intron 22 that is nearly independent of the intron 19 variant showed suggestive evidence of association with multiple sclerosis (MS). Here, we genotyped the rs725613 polymorphism, representative of the earlier reported associations with T1D within CLEC16A, in 1037 T1D cases, 1498 MS cases and 1706 matched controls, all from the founder, autoimmunity-prone Sardinian population. In these Sardinian samples, allele A of rs725613 is positively associated not only with T1D (odds ratio=1.15, P one-tail=5.1 x 10(-3)) but also, and with a comparable effect size, with MS (odds ratio=1.21, P one-tail 6.7 x 10(-5)). Taken together these data provide evidence of joint disease association in T1D and MS within CLEC16A and underline a shared disease pathway.
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338
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Liu S, Wang H, Jin Y, Podolsky R, Reddy MVPL, Pedersen J, Bode B, Reed J, Steed D, Anderson S, Yang P, Muir A, Steed L, Hopkins D, Huang Y, Purohit S, Wang CY, Steck AK, Montemari A, Eisenbarth G, Rewers M, She JX. IFIH1 polymorphisms are significantly associated with type 1 diabetes and IFIH1 gene expression in peripheral blood mononuclear cells. Hum Mol Genet 2008; 18:358-65. [PMID: 18927125 DOI: 10.1093/hmg/ddn342] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Genome-wide association (GWA) studies revealed a number of single nucleotide polymorphisms (SNPs) significantly associated with type 1 diabetes (T1D). In an attempt to confirm some of these candidate associations, we genotyped 2046 Caucasian patients and 2417 normal controls from the United States for SNPs in five genomic regions. While no evidence was obtained for four genomic regions (rs2929366/NM_144715 on chromosome 3, rs9127/Q7Z4C4 on chromosome 5, rs1445898/CAPSL on chromosome 5 and rs2302188/NM_033543 on chromosome 19), we provide strong evidence for association between T1D and multiple SNPs in the IFIH1 linkage disequilibrium (LD) block on chromosome 2q. Among the 10 SNPs genotyped for the 2q region, four SNPs located within the IFIH1 gene or at the 5' region of IFIH1 showed significant association with T1D in the Georgia population [odds ratio (OR) = 1.7-1.9] with the best P-value found at SNP rs1990760 (P = 8 x 10(-8) and OR = 1.9). Several SNPs outside of the IFIH1 gene also showed significant but weaker associations. Furthermore, IFIH1 gene expression levels in peripheral blood mononuclear cells are significantly correlated with IFIH1 genotypes, and higher IFIH1 levels are found in individuals with the susceptible genotypes (P = 0.005). Thus, both genetic association and gene expression data suggest that IFIH1 is the most plausible candidate gene implicated in T1D in this LD block.
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Affiliation(s)
- Siyang Liu
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta, GA 30912, USA
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339
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Abstract
Autoimmune diseases occur when an individual's own immune system attacks and destroys his or her healthy cells and tissues. Although it is clear that environmental stimuli can predispose someone to develop autoimmune diseases, twin- and family-based studies have shown that genetic factors also play an important role in modifying disease risk. Because many of these diseases are relatively common (prevalence in European-derived populations: 0.01-1%) and exhibit a complex mode of inheritance, many DNA sequence variants with modest effect on disease risk contribute to the genetic burden. Recently, the completion of the HapMap project, together with the development of new genotyping technologies, has given human geneticists the tools necessary to comprehensively, and in an unbiased manner, search our genome for DNA polymorphisms associated with many autoimmune diseases. Here we review recent progress made in the identification of genetic risk factors for celiac disease, Crohn's disease, multiple sclerosis, rheumatoid arthritis, systemic lupus erythematosus and type-1 diabetes using genome-wide association studies (GWAS). Strikingly, GWAS have increased the number of genetic risk variants associated with these autoimmune diseases from 15 before 2006 to 68 now. We summarize what this new genetic landscape teaches us in terms of the pathogenesis of these diseases, and highlight some of the outstanding challenges ahead. Finally, we open a discussion on ways to best maximize the impact of these genetic discoveries where it matters the most, that is for autoimmune disease patients.
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Affiliation(s)
- Guillaume Lettre
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Divisions of Genetics and Endocrinology and Program in Genomics, Children's Hospital Boston, Boston, MA 02115, USA
| | - John D. Rioux
- Research Center, the Montreal Heart Institute, Université de Montréal, 5000 Bélanger Street, Montréal, Québec H1T 1C8, Canada
- To whom correspondence should be addressed. Tel: +1 5143763330; Fax: +1 5145932539; or or
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340
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Wang K, Chen Z, Tadesse MG, Glessner J, Grant SFA, Hakonarson H, Bucan M, Li M. Modeling genetic inheritance of copy number variations. Nucleic Acids Res 2008; 36:e138. [PMID: 18832372 PMCID: PMC2588508 DOI: 10.1093/nar/gkn641] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Copy number variations (CNVs) are being used as genetic markers or functional candidates in gene-mapping studies. However, unlike single nucleotide polymorphism or microsatellite genotyping techniques, most CNV detection methods are limited to detecting total copy numbers, rather than copy number in each of the two homologous chromosomes. To address this issue, we developed a statistical framework for intensity-based CNV detection platforms using family data. Our algorithm identifies CNVs for a family simultaneously, thus avoiding the generation of calls with Mendelian inconsistency while maintaining the ability to detect de novo CNVs. Applications to simulated data and real data indicate that our method significantly improves both call rates and accuracy of boundary inference, compared to existing approaches. We further illustrate the use of Mendelian inheritance to infer SNP allele compositions in each of the two homologous chromosomes in CNV regions using real data. Finally, we applied our method to a set of families genotyped using both the Illumina HumanHap550 and Affymetrix genome-wide 5.0 arrays to demonstrate its performance on both inherited and de novo CNVs. In conclusion, our method produces accurate CNV calls, gives probabilistic estimates of CNV transmission and builds a solid foundation for the development of linkage and association tests utilizing CNVs.
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Affiliation(s)
- Kai Wang
- Department of Genetics, University of Pennsylvania, Center for Applied Genomics and Division of Human Genetics, The Children's Hospital of Philadelphia, Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA 19104 and Department of Mathematics, Georgetown University, Washington, DC 20057, USA
- *To whom correspondence should be addressed. Tel: 267 426 2378; Fax: 267 426 0363;
| | - Zhen Chen
- Department of Genetics, University of Pennsylvania, Center for Applied Genomics and Division of Human Genetics, The Children's Hospital of Philadelphia, Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA 19104 and Department of Mathematics, Georgetown University, Washington, DC 20057, USA
| | - Mahlet G. Tadesse
- Department of Genetics, University of Pennsylvania, Center for Applied Genomics and Division of Human Genetics, The Children's Hospital of Philadelphia, Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA 19104 and Department of Mathematics, Georgetown University, Washington, DC 20057, USA
| | - Joseph Glessner
- Department of Genetics, University of Pennsylvania, Center for Applied Genomics and Division of Human Genetics, The Children's Hospital of Philadelphia, Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA 19104 and Department of Mathematics, Georgetown University, Washington, DC 20057, USA
| | - Struan F. A. Grant
- Department of Genetics, University of Pennsylvania, Center for Applied Genomics and Division of Human Genetics, The Children's Hospital of Philadelphia, Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA 19104 and Department of Mathematics, Georgetown University, Washington, DC 20057, USA
| | - Hakon Hakonarson
- Department of Genetics, University of Pennsylvania, Center for Applied Genomics and Division of Human Genetics, The Children's Hospital of Philadelphia, Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA 19104 and Department of Mathematics, Georgetown University, Washington, DC 20057, USA
| | - Maja Bucan
- Department of Genetics, University of Pennsylvania, Center for Applied Genomics and Division of Human Genetics, The Children's Hospital of Philadelphia, Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA 19104 and Department of Mathematics, Georgetown University, Washington, DC 20057, USA
| | - Mingyao Li
- Department of Genetics, University of Pennsylvania, Center for Applied Genomics and Division of Human Genetics, The Children's Hospital of Philadelphia, Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA 19104 and Department of Mathematics, Georgetown University, Washington, DC 20057, USA
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Abstract
CONTEXT The endocrine system is a common target in pathogenic autoimmune responses, and there has been recent progress in our understanding, diagnosis, and treatment of autoimmune endocrine diseases. SYNTHESIS Rapid progress has recently been made in our understanding of the genetic factors involved in endocrine autoimmune diseases. Studies on monogenic autoimmune diseases that include endocrine phenotypes like autoimmune polyglandular syndrome type 1 and immune dysregulation, polyendocrinopathy, enteropathy, X-linked have helped reveal the role of key regulators in the maintenance of immune tolerance. Highly powered genetic studies have found and confirmed many new genes outside of the established role of the human leukocyte antigen locus with these diseases, and indicate an essential role of immune response pathways in these diseases. Progress has also been made in identifying new autoantigens and the development of new animal models for the study of endocrine autoimmunity. Finally, although hormone replacement therapy is still likely to be a mainstay of treatment in these disorders, there are new agents being tested for potentially treating and reversing the underlying autoimmune process. CONCLUSION Although autoimmune endocrine disorders are complex in etiology, these recent advances should help contribute to improved outcomes for patients with, or at risk for, these disorders.
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Affiliation(s)
- Mark S Anderson
- University of California-San Francisco Diabetes Center, San Francisco, California 94143-0540, USA.
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343
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Affiliation(s)
- Kahraman Tanriverdi
- From the Department of Medicine, Boston University School of Medicine, Boston, Mass
| | - Jane E. Freedman
- From the Department of Medicine, Boston University School of Medicine, Boston, Mass
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344
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Miyairi I, DeVincenzo JP. Human genetic factors and respiratory syncytial virus disease severity. Clin Microbiol Rev 2008; 21:686-703. [PMID: 18854487 PMCID: PMC2570150 DOI: 10.1128/cmr.00017-08] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
SUMMARY To explain the wide spectrum of disease severity caused by respiratory syncytial virus (RSV) and because of the limitations of animal models to fully parallel human RSV disease, study of genetic influences on human RSV disease severity has begun. Candidate gene approaches have demonstrated associations of severe RSV in healthy infants with genetic polymorphisms that may alter the innate ability of humans to control RSV (surfactants, Toll-like receptor 4, cell surface adhesion molecules, and others) and those that may control differences in proinflammatory responses or enhanced immunopathology (specific cytokines and their receptors). These studies are reviewed. They are valuable since an understanding of the direction of a polymorphism's effect can help construct a meaningful human RSV disease pathogenesis model. However, the direction, degree, and significance of the statistical association for any given gene are equivocal among studies, and the functional significance of specific polymorphisms is often not even known. Polymorphism frequency distribution differences associated with RSV infection arising from diversity in the genetic background of the population may be confounded further by multiple-hypothesis testing and publication bias, as well as the investigator's perceived importance of a particular pathogenic disease process. Such problems highlight the limitation of the candidate gene approach and the need for an unbiased large-scale genome-wide association study to evaluate this important disease.
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Affiliation(s)
- Isao Miyairi
- Department of Pediatrics, University of Tennessee, Memphis, Tennessee 38103, USA
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345
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Concannon P, Onengut-Gumuscu S, Todd JA, Smyth DJ, Pociot F, Bergholdt R, Akolkar B, Erlich HA, Hilner JE, Julier C, Morahan G, Nerup J, Nierras CR, Chen WM, Rich SS. A human type 1 diabetes susceptibility locus maps to chromosome 21q22.3. Diabetes 2008; 57:2858-61. [PMID: 18647951 PMCID: PMC2551699 DOI: 10.2337/db08-0753] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2008] [Accepted: 07/14/2008] [Indexed: 12/31/2022]
Abstract
OBJECTIVE The Type 1 Diabetes Genetics Consortium (T1DGC) has assembled and genotyped a large collection of multiplex families for the purpose of mapping genomic regions linked to type 1 diabetes. In the current study, we tested for evidence of loci associated with type 1 diabetes utilizing genome-wide linkage scan data and family-based association methods. RESEARCH DESIGN AND METHODS A total of 2,496 multiplex families with type 1 diabetes were genotyped with a panel of 6,090 single nucleotide polymorphisms (SNPs). Evidence of association to disease was evaluated by the pedigree disequilibrium test. Significant results were followed up by genotyping and analyses in two independent sets of samples: 2,214 parent-affected child trio families and a panel of 7,721 case and 9,679 control subjects. RESULTS- Three of the SNPs most strongly associated with type 1 diabetes localized to previously identified type 1 diabetes risk loci: INS, IFIH1, and KIAA0350. A fourth strongly associated SNP, rs876498 (P = 1.0 x 10(-4)), occurred in the sixth intron of the UBASH3A locus at chromosome 21q22.3. Support for this disease association was obtained in two additional independent sample sets: families with type 1 diabetes (odds ratio [OR] 1.06 [95% CI 1.00-1.11]; P = 0.023) and case and control subjects (1.14 [1.09-1.19]; P = 7.5 x 10(-8)). CONCLUSIONS The T1DGC 6K SNP scan and follow-up studies reported here confirm previously reported type 1 diabetes associations at INS, IFIH1, and KIAA0350 and identify an additional disease association on chromosome 21q22.3 in the UBASH3A locus (OR 1.10 [95% CI 1.07-1.13]; P = 4.4 x 10(-12)). This gene and its flanking regions are now validated targets for further resequencing, genotyping, and functional studies in type 1 diabetes.
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Affiliation(s)
- Patrick Concannon
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA.
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346
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Kugathasan S, Baldassano RN, Bradfield JP, Sleiman PMA, Imielinski M, Guthery SL, Cucchiara S, Kim CE, Frackelton EC, Annaiah K, Glessner JT, Santa E, Willson T, Eckert AW, Bonkowski E, Shaner JL, Smith RM, Otieno FG, Peterson N, Abrams DJ, Chiavacci RM, Grundmeier R, Mamula P, Tomer G, Piccoli DA, Monos DS, Annese V, Denson LA, Grant SFA, Hakonarson H. Loci on 20q13 and 21q22 are associated with pediatric-onset inflammatory bowel disease. Nat Genet 2008; 40:1211-5. [PMID: 18758464 PMCID: PMC2770437 DOI: 10.1038/ng.203] [Citation(s) in RCA: 246] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2008] [Accepted: 06/16/2008] [Indexed: 02/08/2023]
Abstract
Inflammatory bowel disease (IBD) is a common inflammatory disorder with complex etiology that involves both genetic and environmental triggers, including but not limited to defects in bacterial clearance, defective mucosal barrier and persistent dysregulation of the immune response to commensal intestinal bacteria. IBD is characterized by two distinct phenotypes: Crohn's disease (CD) and ulcerative colitis (UC). Previously reported GWA studies have identified genetic variation accounting for a small portion of the overall genetic susceptibility to CD and an even smaller contribution to UC pathogenesis. We hypothesized that stratification of IBD by age of onset might identify additional genes associated with IBD. To that end, we carried out a GWA analysis in a cohort of 1,011 individuals with pediatric-onset IBD and 4,250 matched controls. We identified and replicated significantly associated, previously unreported loci on chromosomes 20q13 (rs2315008[T] and rs4809330[A]; P = 6.30 x 10(-8) and 6.95 x 10(-8), respectively; odds ratio (OR) = 0.74 for both) and 21q22 (rs2836878[A]; P = 6.01 x 10(-8); OR = 0.73), located close to the TNFRSF6B and PSMG1 genes, respectively.
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Affiliation(s)
- Subra Kugathasan
- Department of Pediatrics, Children's Research Institute and Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
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347
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Hayton K, Su XZ. Drug resistance and genetic mapping in Plasmodium falciparum. Curr Genet 2008; 54:223-39. [PMID: 18802698 DOI: 10.1007/s00294-008-0214-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2008] [Revised: 08/27/2008] [Accepted: 08/28/2008] [Indexed: 11/30/2022]
Abstract
Drug resistance in malaria parasites is a serious public health burden, and resistance to most of the antimalarial drugs currently in use has been reported. A better understanding of the molecular mechanisms of drug resistance is urgently needed to slow or circumvent the spread of resistance, to allow local treatments to be deployed more effectively to prolong the life span of the current drugs, and to develop new drugs. Although mutations in genes determining resistance to drugs such as chloroquine and the antifolates have been identified, we still do not have a full understanding of the resistance mechanisms, and genes that contribute to resistance to many other drugs remain to be discovered. Genetic mapping is a powerful tool for the identification of mutations conferring drug resistance in malaria parasites because most drug-resistant phenotypes were selected within the past 60 years. High-throughput methods for genotyping large numbers of single nucleotide polymorphisms (SNPs) and microsatellites (MSs) are now available or are being developed, and genome-wide association studies for malaria traits will soon become a reality. Here we discuss strategies and issues related to mapping genes contributing to drug resistance in the human malaria parasite Plasmodium falciparum.
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Affiliation(s)
- Karen Hayton
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA.
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348
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Grant SF, Li M, Bradfield JP, Kim CE, Annaiah K, Santa E, Glessner JT, Casalunovo T, Frackelton EC, Otieno FG, Shaner JL, Smith RM, Eckert AW, Imielinski M, Chiavacci RM, Berkowitz RI, Hakonarson H. Association of HMGA2 Gene Variation with Height in Specific Pediatric Age Categories. GENOMICS INSIGHTS 2008. [DOI: 10.4137/gei.s944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Background Recently an association was demonstrated between the single nucleotide polymorphism (SNP), rs1042725, within the HMGA2 locus and height as a consequence of a genome wide association (GWA) study of this trait in adults; this observation was also reported in children aged 7–11 years old. Objective We examined in our Caucasian childhood cohort the effects of two strong surrogates for this SNP at this locus with height, rs8756 and rs7968902, with respect to the same pediatric age category but also in children grouped separately as younger and older. Methods Utilizing data from an ongoing GWA study in our cohort of 2,619 Caucasian children with measurements for height, we investigated the association of the previously reported variation at the HMGA2 locus with this height treated as a quantitative trait (age and sex corrected) in childhood in the 2–6 (n = 706), 7–11 (n = 617) and 12–18 (n = 1293) years old categories. Results The minor alleles of rs8756 and rs7968902 respectively (strong surrogates for rs1042725 i.e. r 2 = 0.873 and 0.761 in the CEU HapMap respectively) were significantly associated with height in the 7–11 years old age group ( P = 3.53 × 10–3 and 2.82 × 10–4, respectively) However in the 2–6 and 12–18 years old age groups, no association was observed. Conclusions We observe a strong association with height in same age group of 7–11 years old as has been previously reported. However, in the under 7s and the over 11s, no such association was observed.
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Affiliation(s)
- Struan F.A. Grant
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, U.S.A
- Department of Pediatrics and Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, U.S.A
- Department of Pediatrics University of Pennsylvania, School of Medicine, Philadelphia, Pennsylvania 19104, U.S.A
| | - Mingyao Li
- Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, U.S.A
| | - Jonathan P. Bradfield
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, U.S.A
| | - Cecilia E. Kim
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, U.S.A
| | - Kiran Annaiah
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, U.S.A
| | - Erin Santa
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, U.S.A
| | - Joseph T. Glessner
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, U.S.A
| | - Tracy Casalunovo
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, U.S.A
| | - Edward C Frackelton
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, U.S.A
| | - F. George Otieno
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, U.S.A
| | - Julie L. Shaner
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, U.S.A
| | - Ryan M. Smith
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, U.S.A
| | - Andrew W. Eckert
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, U.S.A
| | - Marcin Imielinski
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, U.S.A
| | - Rosetta M. Chiavacci
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, U.S.A
| | - Robert I. Berkowitz
- Behavioral Health Center and Department of Child and Adolescent Psychiatry, The Children's Hospital of Philadelphia, Philadelphia PA 19104, U.S.A
- Center for Weight and Eating Disorders, Department of Psychiatry, University of Pennsylvania, Philadelphia PA 19104, U.S.A
| | - Hakon Hakonarson
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, U.S.A
- Department of Pediatrics and Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, U.S.A
- Department of Pediatrics University of Pennsylvania, School of Medicine, Philadelphia, Pennsylvania 19104, U.S.A
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Abstract
Autoimmune diseases are chronic disorders initiated by a loss of immunologic tolerance to self-antigens. They cluster within families, and patients may be diagnosed with more than one disease, suggesting pleiotropic genes are involved in the aetiology of different diseases. To identify potential loci, which confer susceptibility to autoimmunity independent of disease phenotype, we pooled results from genome-wide linkage studies, using the genome scan meta-analysis method (GSMA). The meta-analysis included 42 independent studies for 11 autoimmune diseases, using 7350 families with 18 291 affected individuals. In addition to the HLA region, which showed highly significant genome-wide evidence for linkage, we obtained suggestive evidence for linkage on chromosome 16, with peak evidence at 10.0-19.8 Mb. This region may harbour a pleiotropic gene (or genes) conferring risk for several diseases, although no such gene has been identified through association studies. We did not identify evidence for linkage at several genes known to confer increased risk to different autoimmune diseases (PTPN22, CTLA4), even in subgroups of diseases consistently found to be associated with these genes. The relative risks conferred by variants in these genes are modest (<1.5 in most cases), and even a large study like this meta-analysis lacks power to detect linkage. This study illustrates the concept that linkage and association studies have power to identify very different types of disease-predisposing variants.
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350
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Butty V, Campbell C, Mathis D, Benoist C. Impact of diabetes susceptibility loci on progression from pre-diabetes to diabetes in at-risk individuals of the diabetes prevention trial-type 1 (DPT-1). Diabetes 2008; 57:2348-59. [PMID: 18556337 PMCID: PMC2518486 DOI: 10.2337/db07-1736] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2007] [Accepted: 06/05/2008] [Indexed: 12/14/2022]
Abstract
OBJECTIVE The unfolding of type 1 diabetes involves a number of steps: defective immunological tolerance, priming of anti-islet autoimmunity, and destruction of insulin-producing beta-cells. A number of genetic loci contribute to susceptibility to type 1 diabetes, but it is unclear which stages of the disease are influenced by the different loci. Here, we analyzed the frequency of type 1 diabetes-risk alleles among individuals from the Diabetes Prevention Trial-Type 1 (DPT-1) clinical trial, which tested a preventive effect of insulin in at-risk relatives of diabetic individuals, all of which presented with autoimmune manifestations but only one-third of which eventually progressed to diabetes. RESEARCH DESIGN AND METHODS In this study, 708 individuals randomized into DPT-1 were genotyped for 37 single nucleotide polymorphisms in diabetes susceptibility loci. RESULTS Susceptibility alleles at loci expected to influence immunoregulation (PTPN22, CTLA4, and IL2RA) did not differ between progressors and nonprogressors but were elevated in both groups relative to general population frequencies, as was the INS promoter variant. In contrast, HLA DQB1*0302 and DQB1*0301 differed significantly in progressors versus nonprogressors (DQB*0302, 42.6 vs. 34.7%, P = 0.0047; DQB*0301, 8.6 vs. 14.3%, P = 0.0026). Multivariate analysis of the factors contributing to progression demonstrated that initial titers of anti-insulin autoantibodies (IAAs) could account for some (P = 0.0016) but not all of this effect on progression (P = 0.00038 for the independent effect of the number of DQB*0302 alleles). The INS-23 genotype was most strongly associated with anti-IAAs (median IAA levels in TT individuals, 60 nU/ml; AT, 121; and AA, 192; P = 0.000037) and only suggestively to the outcome of oral insulin administration. CONCLUSIONS With the exception of HLA, most susceptibility loci tested condition the risk of autoimmunity rather than the risk of failed immunoregulation that results in islet destruction. Future clinical trials might consider genotyping INS-23 in addition to HLA alleles as disease/treatment response modifier.
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Affiliation(s)
- Vincent Butty
- From the Section on Immunology and Immunogenetics, Joslin Diabetes Center, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Christopher Campbell
- From the Section on Immunology and Immunogenetics, Joslin Diabetes Center, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Diane Mathis
- From the Section on Immunology and Immunogenetics, Joslin Diabetes Center, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Christophe Benoist
- From the Section on Immunology and Immunogenetics, Joslin Diabetes Center, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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