Associations of Multiple <i>NOTCH4</i> Exonic Variants with Systemic Sclerosis.

Abstract

Findings from previous genome-wide association studies indicated an association of the <i>NOTCH4</i> gene with systemic sclerosis (SSc). This is a followup study to fine-map exonic variants of <i>NOTCH4</i> in SSc. All exons of <i>NOTCH4</i> were sequenced and analyzed in a total of 1006 patients with SSc and 1004 controls of US white ancestry with the Ion Torrent system. Identified SSc-associated variants were confirmed with Sanger sequencing, and then examined in a Chinese Han cohort consisting of 576 patients with SSc and 574 controls. The <i>NOTCH4</i> variants were analyzed for association with SSc as a whole and with SSc clinical and autoantibody subtypes with and without the influence of specific HLA-class II alleles that had been previously identified as major genetic factors in SSc. A total of 12 SSc-associated and SSc subtype-associated exonic variants of <i>NOTCH4</i> were identified in the US cohort. Three of them are nonsynonymous single-nucleotide polymorphisms and 1 is a CTG tandem repeat that encodes for a poly-leucine, all of which are located in the <i>NOTCH4</i> extracellular domain (NECD). Conditional logistic regression analysis on SSc-associated HLA-class II alleles indicated an independent association of the <i>NOTCH4</i> variants with SSc autoantibody subtypes. Analysis of the Chinese cohort supported a genetic contribution of <i>NOTCH4</i> to SSc and its subtypes. Multiple <i>NOTCH4</i> exonic variants were associated with SSc and/or SSc subtypes. Several of these variants encode nonsynonymous sequence changes occurring in the NECD, which implicates a potentially functional effect of <i>NOTCH4</i>.