Performance comparison of benchtop high-throughput sequencing platforms

Abstract

Three bench-top high-throughput sequencing instruments are now available. The 454 GS Junior (Roche), MiSeq (Illumina) and Ion Torrent PGM (Life Technologies) are laser-printer sized and offer modest set-up and running costs. Each instrument can generate a draft bacterial genome sequence in days, making them attractive for use in the identification and characterization of pathogens in the clinical setting. We compared the performance of these instruments by sequencing isolates of Escherichia coli O104:H4 from the German outbreak of 2011. We compared performance of the platforms, analysing throughput, read length, read error profile and rate, de novo assembly quality and completeness. MiSeq had the highest throughput and lowest error rate. The 454 Junior generated the longest reads and best assemblies. The Ion Torrent PGM produced intermediate throughput with the shortest reads. The Ion Torrent PGM and 454 GS Junior both suffer from errors in homopolymers

Targeted next-generation sequencing as a comprehensive test for patients with and female carriers of DMD/BMD: a multi-population diagnostic study

“…In the near future, with such new platforms as Miseq or Ion Torrent PGM, the testing cycle could be shortened to just a few days. 25 Furthermore, the cost of analyzing an individual sample is much lower than that using MLPA plus Sanger sequencing.…”

Making the genomic leap in HCT: application of second-generation sequencing to clinical advances in hematopoietic cell transplantation

“…As the throughput and read length of SGS continue to improve, soon it will be feasible to sequence the entire MHC in a few reads in just a few hours, eliminating time delay as a barrier to the use of HLA matching data to inform the treatment of solid organ transplant (SOT) recipients (eg, in pre-transplant immunosuppressive dosing). 18 …”

“…They identified that D À/R þ status for one particular GEMA UGT2B17 increased the risk of Grade 2 þ GVHD, a finding that was later replicated in two independent cohorts, together totaling over 1300 patients (combined OR of 2.5). 18 In addition, McCarroll et al showed that UGT2B17 þ HCT recipients, who received hematopoeitic cells from UGT2B17 À/ À donors were seropositive for anti-UGT2B17 antibodies. Moreover, they were able to isolate MHC-bound UGT2B17-derived peptides from the sera of these UGT2B17 mismatched.…”

“…Indeed, SGS can now accomplish the equivalent task in o30 h for the cost of a magnetic resonance imaging scan (B2-3000 USD). 18,56 Although the clinical implementation of SGS technology to routine patient care will require significant upfront costs in equipment acquisition and personnel training, these investments will be worthwhile. In fact, three companies have released benchtop SGS instruments intended to reduce the cost of SGS technology and to increase their accessibility at smaller institutions.…”

“…In fact, three companies have released benchtop SGS instruments intended to reduce the cost of SGS technology and to increase their accessibility at smaller institutions. 18 These portable technologies can sequence an entire human genome (100 Â the size of that of the average E. coli) in just 15 min to 3 h. 57 Such a timeframe makes the use of SGS for infection or MRD monitoring feasible over the course of a clinic visit or on the hospital floor.…”