False-negative Possibility in Genetic Test of Congenital Long QT Syndrome by Next-generation Sequencing / 中国循环杂志

ABSTRACT

Objective: To explore the false-negative possibility in genetic test of congenital long QT syndrome (LQTS) by next-generation sequencing (NGS). Methods: A total of 28 genomic DNA samples were collected from 4 laboratories including 2 commercial medical laboratories using HiSeq2000 platform as Lab1,n=6 and Lab2,n=8; 1 commercial research service laboratory using Ion-torrent platform as Lab3,n=8 and 1 academic laboratory using HiSeq2000 platform as Lab 4,n=6. Sequencing coverage in the exons of protein-coding region in 3 main LQTS pathogenic genes as KCNQ1, KCNH2, SCN5A and possible pathogenic variants were quantitatively analyzed. Results: In Lab1, Lab 2 and Lab 4 with HiSeq2000 platform, above 98% protein coding regions in 3 pathogenic genes were covered with>10-fold reads and 90%-95% were covered with>30-fold reads. In 2 commercial medical laboratories, 3.63% and 9.84% protein coding regions of KCNQ1 gene in 14 samples were covered with<10-fold reads and with<30-fold reads; lower than 10-fold covering region was focused in the 1st exon including about 2% known or likely pathogenic variants. In 2 commercial medical laboratories, 2.64% and 15.76% protein coding regions of KCNH2 gene in 14 samples were covered with<10-fold reads and with<30-fold reads; low covering region was located in multiple exons. For the data from Lab 1, as high as 28.56% protein coding regions of KCNH2 gene were covered with<30-fold reads including 113 (19.79%) known or likely pathogenic variants. SCN5A gene had the best coverage of protein coding region, with no<10-fold reads in all 4 Labs and no<30-fold reads in 2 commercial medical laboratories. Conclusion: Currently, NGS has low coverage region in both KCNQ1 and KCNH2 genes, pathogenic variants could be missed and false-negative possibility should be highly alert.