J Bacteriol Virol.  2014 Jun;44(2):208-213. 10.4167/jbv.2014.44.2.208.

Performance Comparison of Benchtop Next-generation Sequencing Systems

• Na HS

• KMID: 2168697
• DOI: http://doi.org/10.4167/jbv.2014.44.2.208

Abstract

With fast development and wide applications of next generation sequencing (NGS), genomic sequence information is within reach to various research fields. Three benchtop NGS instruments are now available. The 454 GS Junior (Roche), Ion PGM (Life Technologies) and MiSeq (Illumina) are laser-printer sized and offer modest set-up and running costs. By reviewing 2 studies that compared the performance of these instruments, the major characteristics of each benchtop platforms are compared to enable direct comparisons. The 454 GS Junior generated the longest reads and most contiguous assemblies but had the lowest throughput. The Ion Torrent PGM had the highest throughput and fastest run time. The MiSeq had the highest throughput per run and lowest error rates. The Ion Torrent PGM and 454 GS Junior both produced homopolymer-associated indel errors. Although all the platforms allow multiplexing of samples, details of experimental design, library preparation and data analysis may constrain the options. The features of the platforms provide opportunities both to conduct groundbreaking studies and to waste money. Thus, careful considerations should be made before purchasing or using any of them.

Keyword

Next generation sequencing; 454 GS Junior; Ion torrent; MiSeq

MeSH Terms

Research Design
Running
Statistics as Topic

Reference

1). Liu L, Li Y, Li S, Hu N, He Y, Pong R, et al. Comparison of next-generation sequencing systems. J Biomed Biotechnol. 2012; 2012:251–364.

2). Loman NJ, Misra RV, Dallman TJ, Constantinidou C, Gharbia SE, Wain J, et al. Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol. 2012; 30:434–9.

3). Jünemann S, Sedlazeck FJ, Prior K, Albersmeier A, John U, Kalinowski J, et al. Updating benchtop sequencing performance comparison. Nat Biotechnol. 2013; 31:294–6.

4). Koshimizu E, Miyatake S, Okamoto N, Nakashima M, Tsurusaki Y, Miyake N, et al. Performance comparison of bench-top next generation sequencers using microdroplet PCR-based enrichment for targeted sequencing in patients with autism spectrum disorder. PLoS One. 2013; 8:e74167.

5). Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet. 2010; 11:31–46.

6). Glenn TC. Field guide to next-generation DNA sequencers. Mol Ecol Resour. 2011; 11:759–69.

7). Products - Technology: 454 Life Sciences, a Roche Company. 2014. http://my454.com/products/technology.asp.

8). Flusberg BA, Webster DR, Lee JH, Travers KJ, Olivares EC, Clark TA, et al. Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat Methods. 2010; 7:461–5.

9). Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008; 456:53–9.

10). Sanders SJ, Ercan-Sencicek AG, Hus V, Luo R, Murtha MT, Moreno-De-Luca D, et al. Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism. Neuron. 2011; 70:863–85.

11). Beecham J. Annual Research Review: Child and adolescent mental health interventions: a review of progress in economic studies across different disorders. J Child Psychol Psychiatry. 2014.

12). Klei L, Sanders SJ, Murtha MT, Hus V, Lowe JK, Willsey AJ, et al. Common genetic variants, acting additively, are a major source of risk for autism. Mol Autism. 2012; 3:9.

13). Sanders SJ, Murtha MT, Gupta AR, Murdoch JD, Raubeson MJ, Willsey AJ, et al. De novo mutations revealed by whole-exome sequencing are strongly associated with autism. Nature. 2012; 485:237–41.