Common variation in ISL1 confers genetic susceptibility for human congenital heart disease

Abstract

Congenital heart disease (CHD) is the most common birth abnormality and the etiology is unknown in the overwhelming majority of cases. ISLET1 (ISL1) is a transcription factor that marks cardiac progenitor cells and generates diverse multipotent cardiovascular cell lineages. The fundamental role of ISL1 in cardiac morphogenesis makes this an exceptional candidate gene to consider as a cause of complex congenital heart disease. We evaluated whether genetic variation in ISL1 fits the common variant-common disease hypothesis. A 2-stage case-control study examined 27 polymorphisms mapping to the ISL1 locus in 300 patients with complex congenital heart disease and 2,201 healthy pediatric controls. Eight genic and flanking ISL1 SNPs were significantly associated with complex congenital heart disease. A replication study analyzed these candidate SNPs in 1,044 new cases and 3,934 independent controls and confirmed that genetic variation in ISL1 is associated with risk of non-syndromic congenital heart disease. Our results demonstrate that two different ISL1 haplotypes contribute to risk of CHD in white and black/African American populations.

Figure 1. ISL1 SNP associations with CHD on chromosome 5.

a) Analysis of SNP data within and surrounding ISL1 in stage 1 yielded 8 SNPs that were significantly associated with CHD in an ethnically heterogeneous US population. ORs, 95%CIs and P values significant at = 0.05 are depicted in black. Non-significant ORs, 95% CIs and P values are depicted in grey. The yellow highlighted region indicates the location of ISL1 on chromosome 5. Labeled SNPs: (a) rs6867206, (b) rs4865656, (c) rs6869844, (d) rs2115322, (e) rs6449600, (f) rs3762977, (g) IVS1+17C>T, (h) rs1017, (i) rs6449612. b) Analysis of SNP data within and surrounding ISL1 in stage 2 US whites yielded10 SNPs that were significantly associated with CHD in an initial analysis of an ethnically heterogeneous US population. ORs, 95%CIs and P values significant at = 0.05 are depicted in black. Non-significant ORs, 95% CIs and P values are depicted in grey. The yellow highlighted region indicates the location of ISL1 on chromosome 5. Labeled SNPs: a) rs6867206, b) rs4865656, c) rs6869844, d) rs2115322, e) rs6449600, f) rs3762977 †, g) IVS1+17C>T †, h) rs1017 †, i) rs6449612. † SNP genotypes determined by imputation.

Figure 2. ISL1 haplotypes and risk of congenital heart disease by race/ethnicity.

a) The A-C-T risk haplotype in white stage 1 (US) and stage 2 (US, Canada, Netherlands) populations. Odds ratios (95% CIs) for each stage are denoted by black boxes (gray lines). Summary OR estimates are represented by black diamonds, where diamond width corresponds to 95% CI bounds. Box and diamond heights are inversely proportional to precision of the OR estimate. b) The G-C-T risk haplotype in black/African American stage 1 (US) and stage 2 (US) populations. Odds ratios (95% CIs) are denoted as in 2a.