Clinical genetic risk variants inform a functional protein interaction network for tetralogy of Fallot

Abstract

BackgroundTetralogy of Fallot (TOF), the most common cyanotic heart defect in newborns, has evidence of multiple genetic contributing factors. Identifying variants that are clinically relevant is essential to understand patient-specific disease susceptibility and outcomes, and could contribute to delineating pathomechanisms. Methods and ResultsWe used a clinically-driven strategy and current guidelines to re-analyze exome sequencing data from 811 probands with TOF, focused on identifying rare loss-of-function and other likely pathogenic variants in congenital heart disease (CHD) genes. In addition to confirming a major contribution of likely pathogenic variants in FLT4 (VEGFR3; n=14) and NOTCH1 (n=11), we identified 1-3 such variants in each of 21 other CHD genes, including ATRX, DLL4, EP300, GATA6, JAG1, NF1, PIK3CA, RAF1, RASA1, SMAD2, and TBX1. There were also three emerging CHD/TOF candidate genes with multiple loss-of-function variants in this cohort: KDR (n=4), IQGAP1 (n=3), and GDF1 (n=8). In total, these variants were identified in 64 probands (7.9%). Using the 26 composite genes in a STRING protein interaction enrichment analysis revealed a biologically relevant network (p-value 3.3e-16), with VEGFR2 (KDR) and NOTCH1 representing central nodes. Variants associated with arrhythmias/sudden death and/or heart failure indicated factors that could influence long-term outcomes. ConclusionsThe results are relevant to precision medicine for TOF. They suggest considerable clinical yield from genome-wide sequencing, and further evidence for KDR as a CHD/TOF gene and VEGF and Notch signaling as mechanisms in human disease. Harnessing genetic heterogeneity of single gene defects could inform etiopathogenesis and help prioritize novel candidate genes for TOF.