Title |
Extensive Ethnic Variation and Linkage Disequilibrium at the FCGR2/3 Locus: Different Genetic Associations Revealed in Kawasaki Disease
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Published in |
Frontiers in immunology, March 2019
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DOI | 10.3389/fimmu.2019.00185 |
Pubmed ID | |
Authors |
Sietse Q. Nagelkerke, Carline E. Tacke, Willemijn B. Breunis, Michael W. T. Tanck, Judy Geissler, Eileen Png, Long T. Hoang, Joris van der Heijden, Ahmad N. M. Naim, Rae S. M. Yeung, Michael L. Levin, Victoria J. Wright, David P. Burgner, Anne-Louise Ponsonby, Justine A. Ellis, Rolando Cimaz, Chisato Shimizu, Jane C. Burns, Karin Fijnvandraat, C. Ellen van der Schoot, Timo K. van den Berg, Martin de Boer, Sonia Davila, Martin L. Hibberd, Taco W. Kuijpers, The International Kawasaki Disease Genetics Consortium, Nagib Dahdah, Isabelle Kone-Paut |
Abstract |
The human Fc-gamma receptors (FcγRs) link adaptive and innate immunity by binding immunoglobulin G (IgG). All human low-affinity FcγRs are encoded by the FCGR2/3 locus containing functional single nucleotide polymorphisms (SNPs) and gene copy number variants. This locus is notoriously difficult to genotype and high-throughput methods commonly used focus on only a few SNPs. We performed multiplex ligation-dependent probe amplification for all relevant genetic variations at the FCGR2/3 locus in >4,000 individuals to define linkage disequilibrium (LD) and allele frequencies in different populations. Strong LD and extensive ethnic variation in allele frequencies was found across the locus. LD was strongest for the FCGR2C-ORF haplotype (rs759550223+rs76277413), which leads to expression of FcγRIIc. In Europeans, the FCGR2C-ORF haplotype showed strong LD with, among others, rs201218628 (FCGR2A-Q27W, r2 = 0.63). LD between these two variants was weaker (r2 = 0.17) in Africans, whereas the FCGR2C-ORF haplotype was nearly absent in Asians (minor allele frequency <0.005%). The FCGR2C-ORF haplotype and rs1801274 (FCGR2A-H131R) were in weak LD (r2 = 0.08) in Europeans. We evaluated the importance of ethnic variation and LD in Kawasaki Disease (KD), an acute vasculitis in children with increased incidence in Asians. An association of rs1801274 with KD was previously shown in ethnically diverse genome-wide association studies. Now, we show in 1,028 European KD patients that the FCGR2C-ORF haplotype, although nearly absent in Asians, was more strongly associated with susceptibility to KD than rs1801274 in Europeans. Our data illustrate the importance of interpreting findings of association studies concerning the FCGR2/3 locus with knowledge of LD and ethnic variation. |
X Demographics
Geographical breakdown
Country | Count | As % |
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United States | 1 | 50% |
Unknown | 1 | 50% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Members of the public | 1 | 50% |
Scientists | 1 | 50% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Unknown | 65 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 14 | 22% |
Researcher | 10 | 15% |
Student > Master | 9 | 14% |
Student > Bachelor | 5 | 8% |
Other | 3 | 5% |
Other | 3 | 5% |
Unknown | 21 | 32% |
Readers by discipline | Count | As % |
---|---|---|
Biochemistry, Genetics and Molecular Biology | 11 | 17% |
Medicine and Dentistry | 10 | 15% |
Immunology and Microbiology | 7 | 11% |
Agricultural and Biological Sciences | 4 | 6% |
Pharmacology, Toxicology and Pharmaceutical Science | 3 | 5% |
Other | 8 | 12% |
Unknown | 22 | 34% |