A Targeted, Next-Generation Genetic Sequencing Study on Tetralogy of Fallot, Combined With Cleft Lip and Palate

BACKGROUND Congenital heart disease (CHD), plus cleft lip and palate (CLP) are currently the most common types of structural malformation in infants. Many genes have been investigated for their involvement in CHD with CLP. Targeted next-generation sequencing can analyze large amounts of genetic information rapidly, and thus address this question. METHODS The authors designed a targeted, next-generation sequencing gene panel for 455 genes previously implicated in CHD or CLP. A single-subject patient served as a genetic source. Variants that affect protein-coding regions were classified into silico and filtered through databases, such as the Single-Nucleotide Polymorphism Database, Yan Huang, the Exome Sequencing Project, and the 1000 Genomes Project. The authors then predicted the function of gene mutations by PolyPhen-2, SIFT, and Mutation Taster. To confirm the related disease genes, the authors surveyed relevant literature on PubMed. Finally, the variant was verified by Sanger sequencing. RESULTS A total of 1520 mutations were successfully found in a patient using combined tetralogy of Fallot and CLP by the targeted next-generation sequencing. However, there were 6 gene mutations (ZNF528, PVRL2, methylenetetrahydrofolate reductase [MTHFR], EVC2, DAND5, CCDC39) that were not found on Single-Nucleotide Polymorphism Database, Yan Huang, Exome Sequencing Project, and 1000 Genomes Project. Four genes (ZNF528, PVRL2, EVC2, CCDC39) were all predicted to be "tolerated," "benign," or "polymorphic" by SIFT, PolyPhen-2, and Mutation Taster. The DAND5 gene was predicted to be "possibly damaging" and "disease causing" respectively by PolyPhen-2 and Mutation Taster, but the SIFT program predicted this mutation to be "tolerated." Likewise, the MTHFR gene mutation was predicted to be "damaging," "possibly damaging," and "disease causing" respectively by SIFT, PolyPhen-2, and Mutation Taster. There is no relevant report about MTHFR gene mutation (c.G586A, p.G196S) on PubMed. CONCLUSION Using targeted, next-generation sequencing technology, the authors identified for the first time a mutation (c.G586A, p.G196S) in the MTHFR gene as a possible cause of TOF and CLP in a patient.