Comparison of two benchtop next generation sequencing platforms for mutation screening in patients with epilepsy

Abstract

Objective We performed mutation screening in patients with epilepsy by using two benchtop next-generation sequencing platforms, Illumina MiSeq and Ion Torrent PGM. The same target capture system was used, together with standard reagents, software and hardware for each of the platforms. Here we compared their performance and discussed the advantages and disadvantages of each sequencer, optimized the process of mutation screening and provided suggestions for sequencing platform selection. Methods The peripheral blood of 30 patients with epilepsy was collected after obtaining informed consent, and genomic DNA was extracted. Ion Xpress™ Plus gDNA Fragment Library Preparation kit and Illumina TruSeq DNA LT sample prep kit were used for library preparation in 8 and 22 samples, respectively. Coding region sequences of 428 target genes were enriched by NimbleGen target capture system and sequenced either on Illumina MiSeq or Ion Torrent PGM. Output data from PGM were analyzed by Ion Torrent Suite3.2 for alignment and variants extraction, while data from Miseq were analyzed by BWA-MEM and Samtools. Results Up to 12 samples could be sequenced on Illumina Miseq per run, with total throughput more than 5 Gb, 137x mean coverage sequencing depth, 96.4% capture efficiency rate on target regions and 2056±9.042 variants detected per sample, and the whole test period lasted for 6 days. Comparatively, up to 8 samples per 318 v2 chip could be sequenced on PGM, with total throughput about 1.4 Gb, 70x mean coverage sequencing depth, 96.1% capture efficiency rate on target regions and 3028±678.9 variants detected per sample, and the test period was 6 days. Conclusion Targeted sequence capture combined with next generation sequencing could be an efficient tool for rapid mutation detection in epilepsy. All two benchtop next-generation sequencers evaluated here could generate usable sequences; however there are some differences between the qualities of their data. Ion Torrent PGM is more flexible and cost effective, while Illumina MiSeq is suitable for large sample size detection and with higher throughput and more accuracy. Key words: Benchtop next-generation sequencer; MiSeq; PGM