Ion Personal Genome Machine (PGM) and MiSeq were launched by Ion Torrent and Illumina. They are both small in size and feature fast turnover rates but limited data throughput. They are targeted to clinical applications and small labs.

10.5.1 ION PGM FROM ION TORRENT

Ion PGM was released by Ion Torrent at the end of 2010. PGM uses semi­conductor sequencing technology. When a nucleotide is incorporated into the DNA molecules by the polymerase, a proton is released. By detecting the change in pH, PGM recognized whether the nucleotide is added or not. Each time the chip was flooded with one nucleotide after another, if it is not the correct nucleotide, no voltage will be found; if there is 2 nucleotides added, there is double voltage detected [15]. PGM is the first commercial sequencing machine that does not require fluorescence and camera scanning, resulting in higher speed, lower cost, and smaller instru­ment size. Currently, it enables 200 bp reads in 2 hours and the sample preparation time is less than 6 hours for 8 samples in parallel.

An exemplary application of the Ion Torrent PGM sequencer is the identification of microbial pathogens. In May and June of 2011, an ongo­ing outbreak of exceptionally virulent Shiga-toxin — (Stx) producing Esch­erichia coli O104:H4 centered in Germany [16, 17], there were more than 3000 people infected. The whole genome sequencing on Ion Torrent PGM sequencer and HiSeq 2000 helped the scientists to identify the type of E. coli which would directly apply the clue to find the antibiotic resistance. The strain appeared to be a hybrid of two E. coli strains—entero aggre­gative E. coli and entero hemorrhagic E. coli—which may help explain why it has been particularly pathogenic. From the sequencing result of E. coli TY2482 [18], PGM shows the potential of having a fast, but limited throughput sequencer when there is an outbreak of new disease.

In order to study the sequencing quality, mapping rate, and GC depth distribution of Ion Torrent and compare with HiSeq 2000, a high GC Rho — dobacter sample with high GC content (66%) and 4.2 Mb genome was sequenced in these two different sequencers (Table 2). In another experi­ment, E. coli K12 DH10B (NC_010473.1) with GC 50.78% was sequenced by Ion Torrent for analysis of quality value, read length, position accura­cies, and GC distribution (Figure 1).

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All read length distribution, total read num з 577537 Mapped read length distribution Mapped read map length distribution