Application of panel for Ion Torrent PGM sequencing of genetic disease

Abstract

Objective To identity the pathogenic gene mutation in sporadic dystonia patients through Ion AmliSeq multiplex PCR custom sequence acquisition system and the Ion Torrent PGM high throughput sequencing platform, optimize the examination process, and explore the possibility of genetic diagnosis and clinical intervention of genetic diseases through target sequence capture with high-throughput sequencing. Methods Totally 95 patients who were clinically diagnosed as dystonia in PUMCH were enrolled. After extracting whole genome DNA from their peripheral blood leukocytes, we performed sequence by the Ion Torrent Personal Genome Machine (PGM). Then we used Sanger sequence to validate all the variants. Results Totally 12 chips were used in the study, the sequencing depth was 134±44 and the coverage was 96.12±0.71%. The sequencing cycle of Single chip was 6 hours (sequencing) and the maximum data of single chip could reach 900Mb. Among 95 patients with dystonia, 71 rare variants were detected. The accuracy rate was 41.04% and the false positive rate was 58.96%. The main factor that influenced the quality of sequencing screening was the special sequence structure of DNA, such as the presence of the same polymer. Conclusion Ion Torrent PGM sequencing platform has the advantages of high sequencing throughput, easy operation, fast speed and low cost, which can improve the efficiency of genetic screening for genetic diseases. In a reasonable range of gene number, Ion Torrent PGM will help to provide guidance for the differential diagnosis of dystonia. Key words: high-throughput sequencing; Ion Torrent PGM; panel sequencing