Next Generation Sequencing Identify Rare Copy Number Variants in Non-syndromic Patent Ductus Arteriosus

Abstract

Patent ductus arteriosus (PDA) is a common congenital cardiovascular malformation with both inherited and acquired causes. Several genes have been reported to be related to PDA, but the molecular pathogenesis is still unclear. Here, we screened a population matched cohort of 39 patients with PDA and 100 healthy children using whole exome sequencing (WES). And identified 10 copy number variants (CNVs) and 20 candidate genes using Gene ontology (GO) functional enrichment analysis. In gene network analysis, we screened 7 pathogenic CNVs of 10 candidate genes (MAP3K1, MYC, VAV2, WDR5, RXRA, APLNR, TJP1, ERCC2, FOSB, CHRNA4). Further analysis of transcriptome array showed that 7 candidate genes (MAP3K1, MYC, VAV2, APLNR, TJP1, FOSB, CHRNA4) were indeed significantly expressed in human embryonic heart. Moreover, CHRNA4 was observed the most important genes. Our data provided rare CNVs as potential genetic cause of PDA in humans and also advance understanding of the genetic components of PDA.

The Interaction Analysis of SNP Variants and DNA Methylation Identifies Novel Methylated Pathogenesis Genes in Congenital Heart Diseases

“…Group 1 included 216 unrelated patients for WES analysis, which consisted of 78 TAPVC, 78 PA/VSD patients, 40 PDA patients, and 20 TOF patients. Data of WES analysis were derived from our previous studies ( Chen et al, 2020 ; Shi et al, 2020 ; Shi et al, 2018 ). Group 2 contained 16 cases (three TAPVC, two PDA, three TOF, three PA, and five healthy children); blood samples were collected, checked, standardized, and analyzed for DNA methylation.…”

“…Whole exome sequencing was applied for sequencing in the first group. WES was carried out using the Agilent Sure Select Target Enrichment kit (V6 58 Mb; Agilent Technologies) for sequence capture and the Illumina HiSeq2500 for sequencing (Illumina) to a target depth of 100 ( Chen et al, 2020 ; Shi et al, 2020 ; Shi et al, 2018 ).…”

“…Previously, we obtained the expression data in homo early embryonic heart at different stages (Carnegie stages 10–16) after medical termination of pregnancy measured with the Affymetrix HTA 2.0 microarray platform ( Chen et al, 2020 ; Shi et al, 2020 ; Shi et al, 2018 ). The expression levels of our methylated candidate genes in human embryonic heart were shown using the median value.…”

Whole‐exome sequencing analysis of patent ductus arteriosus in a Japanese macaque (Macaca fuscata)

“…Moreover, AZGP1 is downregulated during ductal closure 8 . Notably, CSPG4, a crucial proteoglycan for blood vessel development, was classified as a congenital heart defect‐related gene 7,13 . TNFRSF13B, an essential player in B cell development, emerges with uncertain significance within the context of a patient presenting with PDA, as documented in the ClinVar database 14 …”

“…We identified a total of 6227 variants and filtered them based on the annotation, resulting in 1133 variants. Candidate SNVs were filtered using public databases, including OMIM, MalaCards, ClinVar, STRING, the Gene Ontology (GO) database, and relevant literature, to assess their potential relevance to PDA and cardiovascular development, 5,7,8 resulting in a final list of 32 potentially relevant variants (Figure 1). We used the nucleotide BLAST program from NCBI to compare the 32 potentially relevant SNVs with sequences from five reference species (M. fuscata, M. mulatta, M. fascicularis, Papio anubis, and Homo sapiens) to assess the conservation level across species and identify the potential functional consequences of these variants.…”