The Genotype and Phenotype (GaP) registry: a living biobank for the analysis of quantitative traits

Immunologic Research

Volumn 63, Issue 1-3, 2015, Pages 107-112

  Gregersen, Peter K ^a   Klein, Gila ^a   Keogh, Mary ^a   Kern, Marlena ^a   DeFranco, Margaret ^a   Simpfendorfer, Kim R ^a   Kim, Sun Jung ^a   Diamond, Betty ^a  

^a FEINSTEIN INSTITUTE FOR MEDICAL RESEARCH   (United States)

Author keywords

Autoimmune disease; Biorepository; Endophenotype; GWAS

Indexed keywords

NON RECEPTOR PROTEIN TYROSINE PHOSPHATASE 22; BLK PROTEIN, HUMAN; CSK TYROSINE-PROTEIN KINASE; MICRORNA; PRDM1 PROTEIN, HUMAN; PROTEIN TYROSINE KINASE; PTPN22 PROTEIN, HUMAN; REPRESSOR PROTEIN;

ALLELE; ARTICLE; AUTOIMMUNE DISEASE; CLINICAL DATA REPOSITORY; DISEASE PREDISPOSITION; ENDOPHENOTYPE; GENE EXPRESSION; GENE FUNCTION; GENE LOCUS; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC DATABASE; GENETIC MARKER; GENETIC RISK; GENETIC VARIABILITY; GENOTYPE; GENOTYPE AND PHENOTYPE REGISTRY; HUMAN; IMMUNE SYSTEM; IMMUNOLOGICAL TOLERANCE; IMMUNOREGULATION; NONHUMAN; PRIORITY JOURNAL; PTPN22 GENE; QUANTITATIVE TRAIT; SINGLE NUCLEOTIDE POLYMORPHISM; BIOBANK; GENETIC ASSOCIATION STUDY; GENETIC POLYMORPHISM; GENETIC PREDISPOSITION; GENETICS; METABOLISM; PHENOTYPE; REGISTER;

AUTOIMMUNE DISEASES; BIOLOGICAL SPECIMEN BANKS; GENETIC ASSOCIATION STUDIES; GENETIC PREDISPOSITION TO DISEASE; GENOTYPE; HUMANS; MICRORNAS; PHENOTYPE; POLYMORPHISM, GENETIC; PROTEIN TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 22; QUANTITATIVE TRAIT, HERITABLE; REGISTRIES; REPRESSOR PROTEINS; SRC-FAMILY KINASES;

EID: 84947494424     PISSN: 0257277X     EISSN: 15590755     Source Type: Journal    
DOI: 10.1007/s12026-015-8711-8     Document Type: Article

References (33)

1. Evangelou M, Smyth DJ, Fortune MD, Burren OS, Walker NM, Guo H, Onengut-Gumuscu S, Chen WM, Concannon P, Rich SS, et al. A method for gene-based pathway analysis using genomewide association study summary statistics reveals nine new type 1 diabetes associations. Genet Epidemiol. 2014;38:661–70.
2. Jostins L, Ripke S, Weersma RK, Duerr RH, McGovern DP, Hui KY, Lee JC, Schumm LP, Sharma Y, Anderson CA, et al. Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature. 2012;491:119–24.
3. Okada Y, Wu D, Trynka G, Raj T, Terao C, Ikari K, Kochi Y, Ohmura K, Suzuki A, Yoshida S, et al. Genetics of rheumatoid arthritis contributes to biology and drug discovery. Nature. 2014;506:376–81.
4. Lessard CJ, Adrianto I, Ice JA, Wiley GB, Kelly JA, Glenn SB, Adler AJ, Li H, Rasmussen A, Williams AH, et al. Identification of IRF8, TMEM39A, and IKZF3-ZPBP2 as susceptibility loci for systemic lupus erythematosus in a large-scale multiracial replication study. Am J Hum Genet. 2012;90:648–60.
5. Ripke S, O’Dushlaine C, Chambert K, Moran JL, Kahler AK, Akterin S, Bergen SE, Collins AL, Crowley JJ, Fromer M, et al. Genome-wide association analysis identifies 13 new risk loci for schizophrenia. Nat Genet. 2013;45:1150–9.
6. Lambert JC, Ibrahim-Verbaas CA, Harold D, Naj AC, Sims R, Bellenguez C, DeStafano AL, Bis JC, Beecham GW, Grenier-Boley B, et al. Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer’s disease. Nat Genet. 2013;45:1452–8.
7. Kraja AT, Chasman DI, North KE, Reiner AP, Yanek LR, Kilpelainen TO, Smith JA, Dehghan A, Dupuis J, Johnson AD, et al. Pleiotropic genes for metabolic syndrome and inflammation. Mol Genet Metab. 2014;112:317–38.
8. Raj T, Kuchroo M, Replogle JM, Raychaudhuri S, Stranger BE, De Jager PL. Common risk alleles for inflammatory diseases are targets of recent positive selection. Am J Hum Genet. 2013;92:517–29.
9. Beecham AH, Patsopoulos NA, Xifara DK, Davis MF, Kemppinen A, Cotsapas C, Shah TS, Spencer C, Booth D, Goris A, et al. Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis. Nat Genet. 2013;45:1353–60.
10. Fairfax BP, Makino S, Radhakrishnan J, Plant K, Leslie S, Dilthey A, Ellis P, Langford C, Vannberg FO, Knight JC. Genetics of gene expression in primary immune cells identifies cell type-specific master regulators and roles of HLA alleles. Nat Genet. 2012;44:502–10.
11. Dendrou CA, Plagnol V, Fung E, Yang JH, Downes K, Cooper JD, Nutland S, Coleman G, Himsworth M, Hardy M, et al. Cell-specific protein phenotypes for the autoimmune locus IL2RA using a genotype-selectable human bioresource. Nat Genet. 2009;41:1011–5.
12. Di Meglio P, Di Cesare A, Laggner U, Chu CC, Napolitano L, Villanova F, Tosi I, Capon F, Trembath RC, Peris K, et al. The IL23R R381Q gene variant protects against immune-mediated diseases by impairing IL-23-induced Th17 effector response in humans. PLoS One. 2011;6:e17160.
13. Manjarrez-Orduno N, Marasco E, Chung SA, Katz MS, Kiridly JF, Simpfendorfer KR, Freudenberg J, Ballard DH, Nashi E, Hopkins TJ, et al. CSK regulatory polymorphism is associated with systemic lupus erythematosus and influences B-cell signaling and activation. Nat Genet. 2012;44:1227–30.
14. Putterman C, Diamond B. Immunization with a peptide surrogate for double-stranded DNA (dsDNA) induces autoantibody production and renal immunoglobulin deposition. J Exp Med. 1998;188:29–38.
15. Gregersen PK, Amos CI, Lee AT, Lu Y, Remmers EF, Kastner DL, Seldin MF, Criswell LA, Plenge RM, Holers VM, et al. REL, encoding a member of the NF-kappaB family of transcription factors, is a newly defined risk locus for rheumatoid arthritis. Nat Genet. 2009;41:820–3.
16. Hom G, Graham RR, Modrek B, Taylor KE, Ortmann W, Garnier S, Lee AT, Chung SA, Ferreira RC, Pant PV, et al. Association of systemic lupus erythematosus with C8orf13-BLK and ITGAM-ITGAX. N Engl J Med. 2008;358:900–9.
17. Simpfendorfer KR, Olsson LM, Manjarrez Orduno N, Khalili H, Simeone AM, Katz MS, Lee AT, Diamond B, Gregersen PK. The autoimmunity-associated BLK haplotype exhibits cis-regulatory effects on mRNA and protein expression that are prominently observed in B cells early in development. Hum Mol Genet. 2012;21:3918–25.
18. Samuelson EM, Laird RM, Maue AC, Rochford R, Hayes SM. Blk haploinsufficiency impairs the development, but enhances the functional responses, of MZ B cells. Immunol Cell Biol. 2012;90:620–9.
19. Samuelson EM, Laird RM, Papillion AM, Tatum AH, Princiotta MF, Hayes SM. Reduced B lymphoid kinase (Blk) expression enhances proinflammatory cytokine production and induces nephrosis in C57BL/6-lpr/lpr mice. PLoS One. 2014;9:e92054.
20. Simpfendorfer KR, Armstead BE, Shih A, Li W, Curran M, Manjarrez-Orduno N, Lee AT, Diamond B, Gregersen PK. Autoimmune disease associated haplotypes of BLK exhibit lowered thresholds for B-cell activation and expansion of immunoglobulin class switched B-cells. Arthritis Rheumatol. 2015;67. doi:10.1002/art.39301.
21. Kim SJ, Gregersen PK, Diamond B. Regulation of dendritic cell activation by microRNA let-7c and BLIMP1. J Clin Investig. 2013;123:823–33.
22. Bottini N, Peterson EJ. Tyrosine phosphatase PTPN22: multifunctional regulator of immune signaling, development, and disease. Annu Rev Immunol. 2014;32:83–119.
23. Hasegawa K, Martin F, Huang G, Tumas D, Diehl L, Chan AC. PEST domain-enriched tyrosine phosphatase (PEP) regulation of effector/memory T cells. Science. 2004;303:685–9.
24. Rawlings DJ, Dai X, Buckner JH. The role of PTPN22 risk variant in the development of autoimmunity: finding common ground between mouse and human. J Immunol. 2015;194:2977–84.
25. Wang Y, Shaked I, Stanford SM, Zhou W, Curtsinger JM, Mikulski Z, Shaheen ZR, Cheng G, Sawatzke K, Campbell AM, et al. The autoimmunity-associated gene PTPN22 potentiates toll-like receptor-driven, type 1 interferon-dependent immunity. Immunity. 2013;39:111–22.
26. Wang Y, Ewart D, Crabtree JN, Yamamoto A, Baechler EC, Fazeli P, Peterson EJ. PTPN22 variant R620W is associated with reduced toll-like receptor 7-induced type I interferon in systemic lupus erythematosus. Arthritis Rheumatol. 2015;67:2403–14.
27. Bayley R, Kite KA, McGettrick HM, Smith JP, Kitas GD, Buckley CD, Young SP. The autoimmune-associated genetic variant PTPN22 R620W enhances neutrophil activation and function in patients with rheumatoid arthritis and healthy individuals. Ann Rheum Dis. 2015;74:1588–95.
28. Chang HH, Dwivedi N, Nicholas AP, Ho IC. The W620 polymorphism in PTPN22 disrupts its interaction with peptidylarginine deiminase type 4 and enhances citrullination and NETosis. Arthritis Rheumatol. 2015;67:2323–34.
29. Liu CC, Lai CY, Yen WF, Lin YH, Chang HH, Tai TS, Lu YJ, Tsao HW, Ho IC, Miaw SC. Reciprocal regulation of C-Maf tyrosine phosphorylation by Tec and Ptpn22. PLoS One. 2015;10:e0127617.
30. Qu H, Fang X. A brief review on the human encyclopedia of DNA elements (ENCODE) project. Genomics Proteomics Bioinform. 2013;11:135–41.
31. Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ, Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, et al. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods. 2013;10:1213–8.
32. Buenrostro JD, Wu B, Chang HY, Greenleaf WJ. ATAC-seq: a method for assaying chromatin accessibility genome-wide. Curr Protoc Mol Biol. 2015;109:21–9.
33. Qu K, Zaba LC, Giresi PG, Li R, Longmire M, Kim YH, Greenleaf WJ, Chang HY. Individuality and variation of personal regulomes in primary human T cells. Cell Syst. 2015;1:51–61.