Genome-wide analysis of copy number variation in type 1 diabetes

PLoS ONE

Volumn 5, Issue 11, 2010, Pages

  Grayson, Britney L ^a   Smith, Mary Ellen ^b   Thomas, James W ^a,b   Wang, Lily ^a   Dexheimer, Phil ^a   Jeffrey, Joy ^c   Fain, Pamela R ^c   Nanduri, Priyaanka ^c   Eisenbarth, George S ^c   Aune, Thomas M ^a,b  

^a VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b VANDERBILT UNIVERSITY MEDICAL CENTER   (United States)

^c UNIVERSITY OF COLORADO DENVER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; ARTICLE; AUTOIMMUNITY; BINDING SITE; CHROMOSOME 6P; CONTROLLED STUDY; COPY NUMBER VARIATION; GENE CLUSTER; GENE DELETION; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC VARIABILITY; HUMAN; INSULIN DEPENDENT DIABETES MELLITUS; MAJOR CLINICAL STUDY; POLYMERASE CHAIN REACTION; PROTEIN BINDING; QUANTITATIVE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; CHROMOSOME 13; CHROMOSOME 2; CHROMOSOME 6; CHROMOSOME 7; CHROMOSOME 8; CHROMOSOME DELETION; COHORT ANALYSIS; DNA MICROARRAY; GENE FREQUENCY; GENETIC PREDISPOSITION; GENETICS; METHODOLOGY; MONOZYGOTIC TWINS; RISK FACTOR; TWINS;

ADULT; CHROMOSOME DELETION; CHROMOSOMES, HUMAN, PAIR 13; CHROMOSOMES, HUMAN, PAIR 2; CHROMOSOMES, HUMAN, PAIR 6; CHROMOSOMES, HUMAN, PAIR 7; CHROMOSOMES, HUMAN, PAIR 8; COHORT STUDIES; DIABETES MELLITUS, TYPE 1; DNA COPY NUMBER VARIATIONS; GENE DELETION; GENE FREQUENCY; GENETIC PREDISPOSITION TO DISEASE; GENETIC VARIATION; GENOME-WIDE ASSOCIATION STUDY; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; RISK FACTORS; TWINS, MONOZYGOTIC;

EID: 78649745154     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0015393     Document Type: Article

References (39)

1. Alberti KGMM, Zimmet PZ, Consultation WHO (1998) Definition, diagnosis and classification of diabetes mellitus and its complications. Part 1: diagnosis and classification of diabetes mellitus. Provisional report of a WHO Consultation. Diabetic Medicine 15: 539-553.
2. Bluestone JA, Herold K, Eisenbarth G (2010) Genetics, pathogenesis and clinical interventions in type 1 diabetes. Nature 464: 1293-1300.
3. Redondo MJ, Jeffrey J, Fain PR, Eisenbarth GS, Orban T (2008) Concordance for Islet Autoimmunity among Monozygotic Twins. New England Journal of Medicine 359: 2849-2850.
4. Hyttinen V, Kaprio J, Kinnunen L, Koskenvuo M, Tuomilehto J (2003) Genetic Liability of Type 1 Diabetes and the Onset Age Among 22,650 Young Finnish Twin Pairs: A Nationwide Follow-Up Study. Diabetes 52: 1052-1055.
5. Lleo A, Invernizzi P, Gao B, Podda M, Gershwin ME (2010) Definition of human autoimmunity - autoantibodies versus autoimmune disease. Autoimmunity Reviews 9: A259-A266.
6. Davies JL, Kawaguchi Y, Bennett ST, Copeman JB, Cordell HJ, et al. (1994) A genome-wide search for human type 1 diabetes susceptibility genes. Nature 371: 130-136.
7. Tisch R, McDevitt H (1996) Insulin-Dependent Diabetes Mellitus. Cell 85: 291-297.
8. Pugliese A, Gianani R, Moromisato R, Awdeh ZL, Alper CA, et al. (1995) HLADQB1* 0602 Is Associated with Dominant Protection From Diabetes Even Among Islet Cell Antibody-Positive First-Degree Relatives of Patients with IDDM. Diabetes 44: 608-613.
9. Wellcome Trust CCC (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447: 661-678.
10. Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, et al. (2004) Detection of large-scale variation in the human genome. Nat Genet 36: 949-951.
11. Sebat J, Lakshmi B, Troge J, Alexander J, Young J, et al. (2004) Large-scale copy number polymorphism in the human genome. Science 305: 525-528.
12. Lupski JR, de Oca-Luna RM, Slaugenhaupt S, Pentao L, Guzzetta V, et al. (1991) DNA duplication associated with Charcot-Marie-Tooth disease type 1A. Cell 66: 219-232.
13. International Human Genome Sequencing C (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921.
14. The International SNP Map WG (2001) A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409: 928-933.
15. Rudd MK, Keene J, Bunke B, Kaminsky EB, Adam MP, et al. (2009) Segmental duplications mediate novel, clinically relevant chromosome rearrangements. Human Molecular Genetics 18: 2957-2962.
16. Piotrowski A, Bruder CEG, Andersson R, Diaz de Ståhl T, Menzel U, et al. (2008) Somatic mosaicism for copy number variation in differentiated human tissues. Human Mutation 29: 1118-1124.
17. Han K, Lee J, Meyer TJ, Remedios P, Goodwin L, et al. (2008) L1 recombination-associated deletions generate human genomic variation. Proceedings of the National Academy of Sciences 105: 19366-19371.
18. Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, et al. (2007) Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315: 848-853.
19. Cahan P, Li Y, Izumi M, Graubert TA (2009) The impact of copy number variation on local gene expression in mouse hematopoietic stem and progenitor cells. Nature Genetics 41: 430-437.
20. Schuster-Böckler B, Conrad D, Bateman A. (2010) Dosage Sensitivity Shapes the Evolution of Copy-Number Varied Regions. PLoS ONE 5: e9474.
21. Baranzini SE, Mudge J, van Velkinburgh JC, Khankhanian P, Khrebtukova I, et al. (2010) Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis. Nature 464: 1351-1356.
22. Bruder CEG, Piotrowski A, Gijsbers AACJ, Andersson R, Erickson S, et al. (2008) Phenotypically Concordant and Discordant Monozygotic Twins Display Different DNA Copy-Number-Variation Profiles. The American Journal of Human Genetics 82: 763-771.
23. Javierre BM, Fernandez AF, Richter J, Al-Shahrour F, Martin-Subero JI, et al. (2010) Changes in the pattern of DNA methylation associate with twin discordance in systemic lupus erythematosus. Genome Research 20: 170-179.
24. Kaminsky ZA, Tang T, Wang S-C, Ptak C, Oh GHT, et al. (2009) DNA methylation profiles in monozygotic and dizygotic twins. Nat Genet 41: 240-245.
25. Grozeva D, Kirov G, Ivanov D, Jones IR, Jones L, et al. (2010) Rare Copy Number Variants: A Point of Rarity in Genetic Risk for Bipolar Disorder and Schizophrenia. Archives of General Psychiatry 67: 318-327.
26. Willcocks LC, Lyons PA, Clatworthy MR, Robinson JI, Yang W, et al. (2008) Copy number of FCGR3B, which is associated with systemic lupus erythematosus, correlates with protein expression and immune complex uptake. J Exp Med 205: 1573-1582.
27. Korn JM, Kuruvilla FG, McCarroll SA, Wysoker A, Nemesh J, et al. (2008) Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs. Nat Genet 40: 1253-1260.
28. McCarroll SA, Kuruvilla FG, Korn JM, Cawley S, Nemesh J, et al. (2008) Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat Genet 40: 1166-1174.
29. Szigeti K, Garcia CA, Lupski JR (2006) Charcot-Marie-Tooth disease and related hereditary polyneuropathies: Molecular diagnostics determine aspects of medical management. Genetics in Medicine 8: 86-92.
30. Ovcharenko I, Nobrega MA, Loots GG, Stubbs L (2004) ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes. Nucleic Acids Research 32: W280-286.
31. Barrett JC, Clayton DG, Concannon P, Akolkar B, Cooper JD, et al. (2009) Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes. Nat Genet 41: 703-707.
32. Hindorff LA, Junkins HA, Hall PN, Mehta JP, Manolio TA. A Catalog of Published Genome-Wide Association Studies. Available: www.genome.gov/gwastudies.
33. Baisch J, Weeks T, Giles R, Hoover M, Stastny P, et al. (1990) Analysis of HLADQ genotypes and susceptibility in insulin-dependent diabetes mellitus. New England Journal of Medicine 322: 1836-1841.
34. Wellcome Trust CCC (2010) Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature 464: 713-720.
35. Bashiardes S, Veile R, Allen M, Wise C, Dobbs M, et al. (2004) SNTG1, the gene encoding c1-syntrophin: a candidate gene for idiopathic scoliosis. Human Genetics 115: 81-89.
36. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, et al. (2002) The Human Genome Browser at UCSC. Genome Research 12: 996-1006.
37. Arnett FC, Edworthy SM, Bloch DA, Mcshane DJ, Fries JF, et al. (1988) The american rheumatism association 1987 revised criteria for the classification of rheumatoid arthritis. Arthritis Rheum 31: 315-324.
38. McDonald WI, Compston A, Edan G, Goodkin D, Hartung HP, et al. (2001) Recommended diagnostic criteria for multiple sclerosis: Guidelines from the international panel on the diagnosis of multiple sclerosis. Annals of Neurology 50: 121-127.
39. Polman CH, Reingold SC, Edan G, Filippi M, Hartung HP, et al. (2005) Diagnostic criteria for multiple sclerosis: 2005 revisions to the ''McDonald Criteria''. Annals of Neurology 58: 840-846.