Background. The persistent presence of antiphospholipid antibodies (APA) may lead to the development of primary or secondary antiphospholipid syndrome. Although the genetic basis of APA has been suggested, the identity of the underlying genes is largely unknown. In this study, we have performed a genome-wide association study (GWAS) in an effort to identify susceptibility loci/genes for three main APA: anticardiolipin antibodies (ACL), lupus anticoagulant (LAC), and anti-β2 glycoprotein I antibodies (anti-β2GPI). Methods. DNA samples were genotyped using the Affymetrix 6.0 array containing 906,600 single-nucleotide polymorphisms (SNPs). Association of SNPs with the antibody status (positive/negative) was tested using logistic regression under the additive model. Results. We have identified a number of suggestive novel loci with . Although they do not meet the conservative threshold of genome-wide significance, many of the suggestive loci are potential candidates for the production of APA. We have replicated the previously reported associations of HLA genes and APOH with APA but these were not the top loci. Conclusions. We have identified a number of suggestive novel loci for APA that will stimulate follow-up studies in independent and larger samples to replicate our findings. 1. Introduction Antiphospholipid antibodies (APA) are a heterogeneous group of antibodies that are detected in a variety of conditions, including primary antiphospholipid syndrome (APS) and systemic lupus erythematosus (SLE) [1]. The term antiphospholipid antibodies is a misnomer as APA present in autoimmune disease, like SLE, do not bind to phospholipids but recognize phospholipid-binding proteins [2]. Patients with persistent APA who develop pregnancy complications or thrombosis are considered to have primary APS and those who develop these complications in the presence of autoimmune disease are classified having secondary APS. Since the definition of APS is not limited to a single APA assay, it is required to measure more than one APA. Indeed, currently recognized laboratory criteria for APS include having one or more of three APA, including anticardiolipin antibodies (ACL), lupus anticoagulant (LAC), or anti-β2 glycoprotein I antibodies (anti-β2GPI) in conjunction with the presence of thrombosis or pregnancy loss [3]. Although the genetic basis of APA [4] and APS [5] has been suggested, the underlying genetic factors have not been clearly established. Understanding the genetic bases of various APA may help to delineate the mechanisms for APS. The objective of this study was to
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