A Survey of Next-Generation–Sequencing Technologies - Next Generation Sequencing Technologies in Medical Genetics - page 16

produces about 4 TB of raw data. Automation can be used in library preparations via
a Tecan system which integrated a Covaris A and Roche 454 REM e system.

2.6 Benchtop Sequencers

Ion Personal Genome Machine (PGM) and MiSeq were launched by Ion Torrent
and Illumina (Fig. 1.1 ) . They are both small in size and feature fast turnover rates
but limited data throughput. They are suitable for clinical applications and small
laboratories.

2.6.1 Personal Genome Machine (PGM)

In 2010, Ion Torrent released the Ion PGM which is based on semiconductor
sequencing technology (Fig. 1.1 ) . A proton is released when nucleotide incorpora-
tion, by a polymerase, extends a DNA molecule based on complementation.
Nucleotide addition or lack of is detected in the PGM by measuring the pH differ-
ence. Specifi cally, no voltage difference is detected when a nucleotide is added to
the chip. However, the voltage will double if two appropriate nucleotides are added
(Flusberg et al. 2010 ).
The PGM is the fi rst commercial sequencing machine that does not utilize fl uo-
rescence signal detection to obtain sequence information. Consequently, the plat-
form permits higher speed, lower cost, and smaller instrument size. For example, it
can process 200 bp reads in 2 h with sample preparation time that is less than 6 h.
The sequence quality of PGM is more stable, compared to the decreasing quality of
the HiSeq 2000 after 50 cycles, as explained by fl uorescent signal decay. It was
shown that PGM has a stable quality along sequencing reads and a good perfor-
mance on mismatch accuracies, but has rather a bias in detection of indels (Liu et al.
2012 ). Moreover, the GC depth distribution is better in PGM when compared to the
HiSeq 2000. Ion Torrent has already released Ion 314 and 316, and 318 chips. The
chips are different in the number of wells resulting in higher production within the
same sequencing time. The Ion 318 v2 chip enables the production of greater than
1.2-2 Gb data in 2 h with a read length of 400 bp.

2.6.2 Illumina's MiSeq

In 2011, MiSeq, a benchtop sequencer, was launched with shared sequencing tech-
nology with HiSeq 2000 (Fig. 1.1 ) . Its latest output generates 8.5 Gb per run
(2 × 250 bp paired-end reads) in about 39 h. At the end of 2013 it will produce 15 Gb
per run in about 48 h with a length of 300 bp. A compact, all-in-one platform