Phenotype-specific effect of chromosome 1q21.1 rearrangements and GJA5 duplications in 2436 congenital heart disease patients and 6760 controls

Abstract

Recurrent rearrangements of chromosome 1q21.1 that occur via non-allelic homologous recombination have been associated with variable phenotypes exhibiting incomplete penetrance, including congenital heart disease (CHD). However, the gene or genes within the ~1 Mb critical region responsible for each of the associated phenotypes remains unknown. We examined the 1q21.1 locus in 948 patients with tetralogy of Fallot (TOF), 1488 patients with other forms of CHD and 6760 ethnically matched controls using single nucleotide polymorphism genotyping arrays (Illumina 660W and Affymetrix 6.0) and multiplex ligation-dependent probe amplification. We found that duplication of 1q21.1 was more common in cases of TOF than in controls [odds ratio (OR) 30.9, 95% confidence interval (CI) 8.9-107.6); P = 2.2 × 10(-7)], but deletion was not. In contrast, deletion of 1q21.1 was more common in cases of non-TOF CHD than in controls [OR 5.5 (95% CI 1.4-22.0); P = 0.04] while duplication was not. We also detected rare (n = 3) 100-200 kb duplications within the critical region of 1q21.1 in cases of TOF. These small duplications encompassed a single gene in common, GJA5, and were enriched in cases of TOF in comparison to controls [OR = 10.7 (95% CI 1.8-64.3), P = 0.01]. These findings show that duplication and deletion at chromosome 1q21.1 exhibit a degree of phenotypic specificity in CHD, and implicate GJA5 as the gene responsible for the CHD phenotypes observed with copy number imbalances at this locus.

Figure 1.

The 1q21.1 region (adaptation from the UCSC hg18 Genome Browser) and the summary of findings in TOF and non-TOF mixed CHD cohort. (A) The region of 1q21.1 is complex (143.5–147.5 Mb is shown) due to the presence of extensive segmental duplication blocks and the existing gaps in the reference human genome sequence (NCBI Build 36.1). The largest pair of segmental duplications with >99% homology that mediates most of the rearrangements in this locus is indicated by large orange arrows. (B) RefSeq genes in the region. The critical region is indicated by translucent gray block. (C) The coverage of the Illumina 660W-Quad (the main platform used in this study) and the location of the custom-designed MLPA probes used in this study are shown. (D) Overview of 1q21.1 duplications (blue bars) and deletions (red bars) identified in our study. The cardiac phenotype is shown after the patient identifier. TGA, transposition of the great arteries; MV, mitral valve dysplasia with ventricular septal defect; ASD, atrial septal defect.

Figure 2.

Small duplications encompassing GJA5 within the critical region of 1q21.1. Five CNVs were identified within the critical region of 1q21.1 in 948 TOF and 1488 non-TOF CHD cases. Rare duplications of 100–200 kb in size (shown as blue bars) were found in 3/948 TOF cases encompassing a single gene in common: GJA5. Probands LEU-30 and LEU-98 were found to be distantly related, with estimated genome-wide IBD sharing probabilities for sharing (0,1,2) alleles IBD to be (0.8581, 0.1369, 0.0050). However, their estimated IBD-sharing probabilities within the 3 Mb region surrounding GJA5 are considerably higher (0, 0.64, 0.36), and both of them carry duplications with identical breakpoints. Thus, these two observations are likely to represent one ancestral duplication event. Appropriate correction for the distant relatedness of these two individuals was made in the statistical analyses (see Supplementary Material). In 1488 non-TOF CHD cases, a triplication variant (blue bar) encompassing GJA5 was found in one patient with PA and one deletion variant (red bar) encompassing the last exon of a non-coding LOC100289211 gene was found in one patient with transposition of the great arteries (TGA). RefSeq genes in the region, the coverage for the Illumina660W platform and location of the MLPA probes are indicated in the hg18 UCSC Genome Browser (http:// genome.ucsc.edu).