Effect of copy number variants on outcomes for infants with single ventricle heart defects

Abstract

Background: Human genomes harbor copy number variants (CNVs), which are regions of DNA gains or losses. Although pathogenic CNVs are associated with congenital heart disease (CHD), their effect on clinical outcomes is unknown. This study sought to determine whether pathogenic CNVs among infants with single ventricle physiology were associated with inferior neurocognitive and somatic growth outcomes.

Methods and results: Genomic DNAs from 223 subjects of 2 National Heart, Lung, and Blood Institute-sponsored randomized clinical trials in infants with single ventricle CHD and 270 controls from The Cancer Genome Atlas project were analyzed for rare CNVs>300 kb using array comparative genomic hybridization. Neurocognitive and growth outcomes at 14 months from the CHD trials were compared among subjects with and without pathogenic CNVs. Putatively pathogenic CNVs, comprising 25 duplications and 6 deletions, had a prevalence of 13.9%, significantly greater than the 4.4% rate of such CNVs among controls. CNVs associated with genomic disorders were found in 13 cases but not in controls. Several CNVs likely to be causative of single ventricle CHD were observed, including aberrations altering the dosage of GATA4, MYH11, and GJA5. Subjects with pathogenic CNVs had worse linear growth, and those with CNVs associated with known genomic disorders had the poorest neurocognitive and growth outcomes. A minority of children with pathogenic CNVs were noted to be dysmorphic on clinical genetics examination.

Conclusions: Pathogenic CNVs seem to contribute to the cause of single ventricle forms of CHD in ≥10% of cases and are clinically subtle but adversely affect outcomes in children harboring them.

Keywords: DNA copy number variantiations; congenital cardiac defect; hypoplastic left heart syndrome; outcome.

Figure 1

Workflow for aCGH studies. Starting with the available cohorts from the Infants with Single Ventricle and the Single Ventricle Reconstruction-Extension trials of the Pediatric Heart Network, the flow of statistical and genetic analyses is outlined. All pathogenic CNVs identified were successfully confirmed via secondary methods.

Figure 2

Pathogenic deletion and duplication CNVs likely causative for CHD defects. (A) 1.5-Mb deletion CNV at 12p13.33 affecting 223 consecutive probes. (B) 1.6-Mb duplication CNV at 16p13.12-p13.11 affecting 124 consecutive probes and altering MYH11. For each 244K array clone, the Cy3/Cy5 signal intensity ratios are plotted. The green and red dots correspond to log2 ratios of ≤ −0.25 (loss) and ≥ 0.25 (gain), respectively. All chromosomes are depicted according to hg18.

Figure 2

Pathogenic deletion and duplication CNVs likely causative for CHD defects. (A) 1.5-Mb deletion CNV at 12p13.33 affecting 223 consecutive probes. (B) 1.6-Mb duplication CNV at 16p13.12-p13.11 affecting 124 consecutive probes and altering MYH11. For each 244K array clone, the Cy3/Cy5 signal intensity ratios are plotted. The green and red dots correspond to log2 ratios of ≤ −0.25 (loss) and ≥ 0.25 (gain), respectively. All chromosomes are depicted according to hg18.

Figure 3

Schematic illustration of the 16p13.1 region. The smallest region of overlap (SRO) between the three duplications (shown in blue) and the deletion (shown in red) at 16p13.1 is 758 kb. This region includes eight genes, including MYH11 and ABCC6. MYH11 encodes the smooth muscle myosin, heavy chain.