Association analysis of copy numbers of FC-gamma receptor genes for rheumatoid arthritis and other immune-mediated phenotypes

Lude Franke, Hanane El Bannoudi, Diahann T S L Jansen, Klaas Kok, Gosia Trynka, Dorothee Diogo, Morris Swertz, Karin Fransen, Rachel Knevel, Javier Gutierrez-Achury, Lisbeth Ärlestig, Jeffrey D Greenberg, Joel Kremer, Dimitrios A Pappas, Alexandros Kanterakis, Rinse K Weersma, Annette H M van der Helm-van Mil, Viktor Guryev, Solbritt Rantapää-Dahlqvist, Peter K GregersenRobert M Plenge, Cisca Wijmenga, Tom W-J Huizinga, Andreea Ioan-Facsinay, Rene E M Toes, Alexandra Zhernakova

Research output: Contribution to journalArticleAcademicpeer-review

19 Citations (Scopus)


Segmental duplications (SDs) comprise about 5% of the human genome and are enriched for immune genes. SD loci often show copy numbers variations (CNV), which are difficult to tag with genotyping methods. CNV in the Fcγ receptor region (FCGR) has been suggested to be associated with rheumatic diseases. The objective of this study was to delineate association of FCGR-CNV with rheumatoid arthritis (RA), coeliac disease and Inflammatory bowel disease incidence. We developed a method to accurately quantify CNV in SD loci based on the intensity values from the Immunochip platform and applied it to the FCGR locus. We determined the method's validity using three independent assays: segregation analysis in families, arrayCGH, and whole genome sequencing. Our data showed the presence of two separate CNVs in the FCGR locus. The first region encodes FCGR2A, FCGR3A and part of FCGR2C gene, the second encodes another part of FCGR2C, FCGR3B and FCGR2B. Analysis of CNV status in 4578 individuals with RA and 5457 controls indicated association of duplications in the FCGR3B gene in antibody-negative RA (P=0.002, OR=1.43). Deletion in FCGR3B was associated with increased risk of antibody-positive RA, consistently with previous reports (P=0.023, OR=1.23). A clear genotype-phenotype relationship was observed: CNV polymorphisms of the FCGR3A gene correlated to CD16A expression (encoded by FCGR3A) on CD8 T-cells. In conclusion, our method allows determining the CNV status of the FCGR locus, we identified association of CNV in FCGR3B to RA and showed a functional relationship between CNV in the FCGR3A gene and CD16A expression.European Journal of Human Genetics advance online publication, 13 May 2015; doi:10.1038/ejhg.2015.95.

Original languageEnglish
Pages (from-to)263-270
Number of pages8
JournalEuropean Journal of Human Genetics
Issue number2
Early online date13-May-2015
Publication statusPublished - 2016

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