6 ◾ Bioinformatics
and captured by a sensor or a camera. Figure 1.2 shows the steps of pyrosequencing after
adding the DNA fragments to the wells, where sequencing takes place by incorporating a
known nucleotide to the growing complementary strand each time and releasing of PPI
that is translated into a light signal, which is detected by a camera.
1.2.2.2 Ion Torrent Technology
The Ion Torrent sequencers are manufactured by Thermo Fisher Scientific. The Ion Torrent
sequencing method is similar to the Roche 454 sequencing in the first steps: fragmenta-
tion, DNA denaturing, adaptor ligation, and the use of beads in microwells with primers.
However, instead of solving the nucleotide order of the DNA template by capturing the
light released by inorganic pyrophosphate as in Roche 454 sequencing, the Ion Torrent
method depends on the pH signal of the hydrogen ions released every time a nucleotide
is incorporated in the DNA template. The microwells are in a microchip provided with
the so-called ion sensitive layer (pH sensor). This layer is able to detect the hydrogen ions
(protons). There are four solutions for the four kinds of nucleotides (dATP, dCTP, dGTP,
and dTTP). During the Ion Torrent sequencing, the four nucleotide solutions are added
sequentially. If the nucleotide is incorporated, a hydrogen ion (H+) will be released chang-
ing the pH of the solution and a signal will be generated; otherwise, no change in the pH
or a signal (Figure 1.3). The base call is based on this signal. Each time, the microwells are
washed to remove the free nucleotides before adding a new nucleotide solution.
1.2.2.3 AB SOLiD Technology
The Applied Biosystem SOLiD is based on the sequential ligation with dye-labeled oligos.
SOLiD stands for Sequencing by Oligonucleotide Ligation and Detection. This technology
was developed by Fisher Scientific. It depends on the DNA ligase that has the ability to
incorporate nucleotides in the DNA template. The DNA library preparation is similar to
FIGURE 1.2 Pyrosequencing and base calling.