Family-based whole-genome sequencing identifies compound heterozygous protein-coding and noncoding mutations in tetralogy of Fallot

• Published in: Gene Vol. 741; p. 144555
• Main Authors: Wang, Yifeng, Jiang, Tao, Tang, Pushi, Wu, Yifei, Jiang, Zhu, Dai, Juncheng, Gu, Yayun, Xu, Jing, Da, Min, Ma, Hongxia, Jin, Guangfu, Mo, Xuming, Li, Qingguo, Wang, Xiaowei, Hu, Zhibin
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 30.05.2020
• Subjects: Clinical genetics; Compound heterozygous mutations; Exons - genetics; Female; Heterozygote; Humans; Male; Mutation - genetics; Open Reading Frames - genetics; Pedigree; Tetralogy of fallot; Tetralogy of Fallot - genetics; Tetralogy of Fallot - pathology; Whole Genome Sequencing; WGS; Whole genome sequencing; TOF; INDEL; NCC; Compound heterozygous mutations; Clinical genetics; sgRNA; NS-CHD; SNV; cDNA; Tetralogy of fallot; CHD
• ISSN: 0378-1119; 1879-0038
• DOI: 10.1016/j.gene.2020.144555

•Family-based WGS was performed to detect the genetic architecture of TOF.•A newly identified compound heterozygous pattern in TOF probands was establised.•Noncoding mutation in regulatory element was firstly involved in the pattern.•The noncoding mutation increased silencer activity to reduce NOTCH1 expression.•The compound heterozygous pattern in this study may increase the penetrance of TOF. Tetralogy of Fallot (TOF) is one of most serious cyanotic congenital heart disease (CHD) and the prevalence is estimated to be 1 in 3000 live births worldwide. Though multiple studies have found genetic variants as risk factors for TOF, they could only explain a small fraction of the pathogenesis. Here, we performed whole genome sequencing (WGS) for 6 individuals derived from 2 families to evaluate pathogenic mutations located in both coding and noncoding regions. We characterized the annotated deleterious coding mutations and impaired noncoding mutations in regulatory elements by various data analysis. Additionally, functional assays were conducted to validate function regulatory elements and noncoding mutations. Interestingly, a compound heterozygous pattern with pathogenic coding and noncoding mutations was identified in probands. In proband 1, biallelic mutations (g.139409115A > T, encoding p.Asn685Ile; g.139444949C > A) in NOTCH1 exon and its regulatory element were detected. In vitro experiments revealed that the regulatory element acted as a silencer and the noncoding mutation decreased the expression of NOTCH1. In proband 2, we also found compound heterozygous mutations (g. 216235029C > T, encoding p.Val2281Met; g. 216525154A > C) which potentially regulated the function of FN1 gene. In summary, our study firstly reported an instance of newly identified noncoding mutation in regulatory element within the compound heterozygous pattern in TOF. The results provided a deeper understanding of TOF genetic architectures.