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Wiley, Human Mutation: Variation, Informatics and Disease, 2(35), p. 248-256, 2013

DOI: 10.1002/humu.22471

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A 129-kb Deletion on Chromosome 12 Confers Substantial Protection Against Rheumatoid Arthritis, Implicating the GeneSLC2A3

Journal article published in 2013 by Colin D. Veal, Katherine E. Reekie, Johnny C. Lorentzen, Peter K. Gregersen, Leonid Padyukov ORCID, Anthony J. Brookes
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

PMCID: PMC3995011 ; We describe a copy-number variant (CNV) for which deletion alleles confer a protective affect against rheumatoid arthritis (RA). This CNV reflects net unit deletions and expansions to a normal two-unit tandem duplication located on human chr12p13.31, a region with conserved synteny to the rat RA susceptibility quantitative trait loci Oia2. Genotyping, using the paralogue ratio test and SNP intensity data, in Swedish samples (2,403 cases, 1,269 controls) showed that the frequency of deletion variants is significantly lower in cases (P = 0.0012, OR = 0.442 [95%CI 0.258-0.755]). Reduced frequencies of deletion variants were also seen in replication materials comprising 9,201 UK samples (1,846 cases, 7,355 controls) and 2,963 US samples (906 controls, 1,967 cases) (Mantel-Haenszel P = 0.036, OR = 0.559 [95%CI 0.323-0.966]). Combining the three datasets produces a Mantel-Haenszel OR of 0.497 (P