1. ¹Genetic Epidemiology Unit, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
2. ²Arthritis and Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
3. ³Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
4. ⁴Oklahoma University Health Sciences Center, Oklahoma City, OK, USA
5. ⁵VA medical Center, Oklahoma City, OK, USA

Correspondence: Dr SK Nath, Genetic Epidemiology Unit, Arthritis and Immunology Research Program, Oklahoma Medical Research Foundation, 1025 NE 13th Street, Oklahoma City, OK 73104, USA. E-mail: Swapan-Nath@omrf.org

Received 30 December 2008; Revised 18 March 2009; Accepted 18 March 2009; Published online 23 April 2009.

Abstract

Systemic Lupus Erythematosus (SLE) disproportionately affects minorities, such as Hispanic Americans (HA). Prevalence of SLE is 3–5 times higher in HA than in European-derived populations and have more active disease at the time of diagnosis, with more serious organ system involvement. HA is an admixed population, it is possible that there is an effect of admixture on the relative risk of the disease. This admixture can create substantial increase of linkage disequilibrium (LD) in both magnitude and range, which can provide a unique opportunity for admixture mapping. The main objectives of this study are to (a) estimate hidden population structure in HA individuals; (b) estimate individual ancestry proportions and its impact on SLE risk; (c) assess impact of admixture on ITGAM association, a recently identified SLE susceptibility gene; and (d) estimate power of admixture mapping in HA. Our dataset contained 1125 individuals, of whom 884 (657 SLE cases and 227 controls) were self-classified as HA. Using 107 unlinked ancestry informative markers (AIMs), we estimated hidden population structure and individual ancestry in HA. Out of 5671 possible pairwise LD, 54% were statistically significant, indicating recent population admixture. The best-fitted model for HA was a four-population model with average ancestry of European (48%), American-Indian (AI) (40%), African (8%) and a fourth population (4%) with unknown ancestry. We also identified significant higher risk associated with AI ancestry (odds ratio (OR)=4.84, P=0.0001, 95% CI (confidence interval)=2.14–10.95) on overall SLE. We showed that ITGAM is associated as a risk factor for SLE (OR=2.06, P=8.74 10^-5, 95% CI=1.44–2.97). This association is not affected by population substructure or admixture. We have shown that HA have great potential and are an appropriate population for admixture mapping. As expected, the case-only design is more powerful than case–control design, for any given admixture proportion or ancestry risk ratio.