Rare Copy Number Variations in Adults with Tetralogy of Fallot Implicate Novel Risk Gene Pathways

Abstract

Structural genetic changes, especially copy number variants (CNVs), represent a major source of genetic variation contributing to human disease. Tetralogy of Fallot (TOF) is the most common form of cyanotic congenital heart disease, but to date little is known about the role of CNVs in the etiology of TOF. Using high-resolution genome-wide microarrays and stringent calling methods, we investigated rare CNVs in a prospectively recruited cohort of 433 unrelated adults with TOF and/or pulmonary atresia at a single centre. We excluded those with recognized syndromes, including 22q11.2 deletion syndrome. We identified candidate genes for TOF based on converging evidence between rare CNVs that overlapped the same gene in unrelated individuals and from pathway analyses comparing rare CNVs in TOF cases to those in epidemiologic controls. Even after excluding the 53 (10.7%) subjects with 22q11.2 deletions, we found that adults with TOF had a greater burden of large rare genic CNVs compared to controls (8.82% vs. 4.33%, p = 0.0117). Six loci showed evidence for recurrence in TOF or related congenital heart disease, including typical 1q21.1 duplications in four (1.18%) of 340 Caucasian probands. The rare CNVs implicated novel candidate genes of interest for TOF, including PLXNA2, a gene involved in semaphorin signaling. Independent pathway analyses highlighted developmental processes as potential contributors to the pathogenesis of TOF. These results indicate that individually rare CNVs are collectively significant contributors to the genetic burden of TOF. Further, the data provide new evidence for dosage sensitive genes in PLXNA2-semaphorin signaling and related developmental processes in human cardiovascular development, consistent with previous animal models.

1q21.1 Microduplication expression in adults

“…5 At our center, we detected 1q21.1 duplications in seven (2 male and 5 female) unrelated Caucasian adult probands (median age 51, range 28-62 years) ( Table 1, cases 1-7; Figure 1), three ascertained with schizophrenia 40 and four with TOF. 37 There were no 1q21.1 duplications in 2,357 adult controls, thus the CNV was enriched in both the schizophrenia (odds ratio 15.4 (95% confidence interval 1.6-148.0); P = 0.0155) and TOF (odds ratio 18.9 (95% confidence interval 2.1-169.7); P = 0.0040) cohorts studied. Tables 1 and 2 show the demographic and clinical data available for 27 adults (10 males and 17 females), seven (25.9%) from our center and 20 (74.1%) from the literature reviewed.…”

“…Since the first report of a 1q21.1 duplication in a TOF proband, 23 several studies have now reported that 1q21.1 duplications are enriched in TOF at remarkably similar prevalences: 0.78%, 10 0.84%, 5 and 0.80%. 37 Prevalence results for schizophrenia, autism spectrum disorder, and intellectual disability, although elevated, are less clear. 2,9 Although numbers were small, the majority of children (16 of 26) and adults (8 of 13) with head circumference …”

“…The sample population for identification of 1q21.1 duplications at our center comprised 502 unrelated adults with tetralogy of Fallot (TOF) seen at the Toronto Congenital Cardiac Centre for Adults 37 and 463 unrelated adults with a Diagnostic and Statistical Manual of Mental Disorders 4th Edition (DSM-IV) diagnosis of chronic schizophrenia or schizoaffective disorder ascertained mainly through four eastern Canadian clinics. 40 Lifetime medical history and physical features were directly assessed by researchers blind to genotype using a standard protocol.…”

“…39 Cases of 1q21.1 duplication were confirmed using quantitative PCR and/or clinical microarrays. 37,40 analyses Clinical data on adults from our center and the literature were compiled to identify features present in both populations. Any feature present in two or more subjects from our center or the literature was considered to be possibly associated with the 1q21.1 duplication phenotype.…”

“…5,37 There are now four subjects with TOF reported to have small duplications overlapping GJA5: three 100-200 kb 5 and one 10.3 kb 37 in size. GJA5 encodes connexin 40, a cardiac gap junction protein expressed in the right ventricular outflow tract.…”