Allelic expression analysis of the osteoarthritis susceptibility locus that maps to chromosome 3p21 reveals cis-acting eQTLs at GNL3 and SPCS1

BMC Medical Genetics

Volumn 15, Issue 1, 2014, Pages

  Gee, Fiona ^a   Clubbs, Clare F ^a   Raine, Emma V A ^a   Reynard, Louise N ^a   Loughlin, John ^a  

^a NEWCASTLE UNIVERSITY   (United Kingdom)

Author keywords

Allelic imbalance; Genetic risk; Linkage disequilibrium; Osteoarthritis; Single nucleotide polymorphism

Indexed keywords

ARTICLE; CHROMOSOME 3P; CHROMOSOME 3P21; CONTROLLED STUDY; GENE; GENE EXPRESSION; GENE LOCUS; GENETIC ANALYSIS; GENETIC SUSCEPTIBILITY; GLT8D1 GENE; GNL3 GENE; HUMAN; HUMAN TISSUE; ITIH1 GENE; ITIH3 GENE; ITIH4 GENE; MISSENSE MUTATION; MUSTN1 GENE; NEK4 GENE; NT5DC2 GENE; OSTEOARTHRITIS; PBRM1 GENE; SINGLE NUCLEOTIDE POLYMORPHISM; SPCS1 GENE; STAB1 GENE; TMEM110 GENE;

AGED; AGED, 80 AND OVER; ALLELES; ALLELIC IMBALANCE; CARTILAGE; CHROMOSOMES, HUMAN, PAIR 3; FEMALE; GENE EXPRESSION; GENETIC PREDISPOSITION TO DISEASE; GENOTYPE; GTP-BINDING PROTEINS; HUMANS; MALE; MEMBRANE PROTEINS; MIDDLE AGED; NUCLEAR PROTEINS; OSTEOARTHRITIS; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEINS; QUANTITATIVE TRAIT LOCI; TRANSCRIPTION FACTORS;

EID: 84900423002     PISSN: None     EISSN: 14712350     Source Type: Journal    
DOI: 10.1186/1471-2350-15-53     Document Type: Article

References (17)

1. Brandt KD, Dieppe P, Radin EL. Etiopathogenesis of osteoarthritis. Rheum Dis Clin North Am 2008, 34:531-559. 10.1016/j.rdc.2008.05.011, 18687271.
2. Loughlin J. Genetics of osteoarthritis. Curr Opin Rheumatol 2011, 23:479-83. 10.1097/BOR.0b013e3283493ff0, 21709558.
3. arcOGEN Consortium, arcOGEN Collaborators Identification of new susceptibility loci for osteoarthritis (arcOGEN): a genome-wide association study. Lancet 2012, 380:815-823. 3443899, 22763110, arcOGEN Consortium, arcOGEN Collaborators.
4. Kerkhof HJ, Lories RJ, Meulenbelt I, Jonsdottir I, Valdes AM, Arp P, Ingvarsson T, Jhamai M, Jonsson H, Stolk L, Thorleifsson G, Zhai G, Zhang F, Zhu Y, van der Breggen R, Carr A, Doherty M, Doherty S, Felson DT, Gonzalez A, Halldorsson BV, Hart DJ, Hauksson VB, Hofman A, Ioannidis JP, Kloppenburg M, Lane NE, Loughlin J, Luyten FP, Nevitt MC, et al. A genome-wide association study identifies an osteoarthritis susceptibility locus on chromosome 7q22. Arthritis Rheum 2010, 62:499-510. 3354739, 20112360.
5. Nakajima M, Takahashi A, Kou I, Rodriguez-Fontenla C, Gomez-Reino JJ, Furuichi T, Dai J, Sudo A, Uchida A, Fukui N, Kubo M, Kamatani N, Tsunoda T, Malizos KN, Tsezou A, Gonzalez A, Nakamura Y, Ikegawa S. New sequence variants in HLA class II/III region associated with susceptibility to knee osteoarthritis identified by genome-wide association study. PLoS One 2010, 5:e9723. 10.1371/journal.pone.0009723, 2841168, 20305777.
6. Cookson W, Liang L, Abecasis G, Moffatt M, Lathrop M. Mapping complex disease traits with global gene expression. Nat Rev Genet 2009, 10:184-194. 10.1038/nrg2537, 19223927.
7. Montgomery SB, Dermitzakis ET. From expression QTLs to personalized transcriptomics. Nat Rev Genet 2011, 12:277-282.
8. Freedman ML, Monteiro AN, Gayther SA, Coetzee GA, Risch A, Plass C, Casey G, De Biasi M, Carlson C, Duggan D, James M, Liu P, Tichelaar JW, Vikis HG, You M, Mills IG. Principles for the post-GWAS functional characterization of cancer risk loci. Nat Genet 2011, 43:513-518. 10.1038/ng.840, 3325768, 21614091.
9. Egli RJ, Southam L, Wilkins JM, Lorenzen I, Pombo-Suarez M, Gonzalez A, Carr A, Chapman K, Loughlin J. Functional analysis of the osteoarthritis susceptibility-associated GDF5 regulatory polymorphism. Arthritis Rheum 2009, 60:2055-2064. 10.1002/art.24616, 19565498.
10. Wilkins JM, Southam L, Price AJ, Mustafa Z, Carr A, Loughlin J. Extreme context specificity in differential allelic expression. Hum Mol Genet 2007, 16:537-546. 10.1093/hmg/ddl488, 17220169.
11. Ratnayake M, Reynard LN, Raine EV, Santibanez-Koref M, Loughlin J. Allelic expression analysis of the osteoarthritis susceptibility locus that maps to MICAL3. BMC Med Genet 2012, 13:12. 3366887, 22385522.
12. Ronaghi M, Uhlén M, Nyrén P. A sequencing method based on real-time pyrophosphate. Science 1998, 281:363. 365.
13. Boyle AP, Hong EL, Hariharan M, Cheng Y, Schaub MA, Kasowski M, Karczewski KJ, Park J, Hitz BC, Weng S, Cherry JM, Snyder M. Annotation of functional variation in personal genomes using RegulomeDB. Genome Res 2012, 22:1790-1797. 10.1101/gr.137323.112, 3431494, 22955989.
14. Sarig O, Nahum S, Rapaport D, Ishida-Yamamoto A, Fuchs-Telem D, Qiaoli L, Cohen-Katsenelson K, Spiegel R, Nousbeck J, Israeli S, Borochowitz ZU, Padalon-Brauch G, Uitto J, Horowitz M, Shalev S, Sprecher E. Short stature, onychodysplasia, facial dysmorphism, and hypotrichosis syndrome is caused by a POC1A mutation. Am J Hum Genet 2012, 91:337-342. 10.1016/j.ajhg.2012.06.003, 3415554, 22840363.
15. Xu Y, Barter MJ, Swan DC, Rankin KS, Rowan AD, Santibanez-Koref M, Loughlin J, Young DA. Identification of the pathogenic pathways in osteoarthritic hip cartilage: commonality and discord between hip and knee OA. Osteoarthr Cartil 2012, 20:1029-1038. 10.1016/j.joca.2012.05.006, 22659600.
16. Ma H, Pederson T. Nucleostemin: a multiplex regulator of cell-cycle progression. Trends Cell Biol 2008, 18:575-579. 10.1016/j.tcb.2008.09.003, 18951797.
17. Romanova L, Kellner S, Katoku-Kikyo N, Kikyo N. Novel role of nucleostemin in the maintenance of nucleolar architecture and integrity of small nucleolar ribonucleoproteins and the telomerase complex. J Biol Chem 2009, 284:26685-26694. 10.1074/jbc.M109.013342, 2785356, 19648109.