Biology Reference
In-Depth Information
Cloud computing allows a user to rent processing time on a computer cluster;
the user can load software and access to the cluster by disk or by the internet.
Software is being developed that makes it possible to analyze an entire genome
using cloud computing and a laptop (
Nature Biotechnology
2010
).
7.11.2 Third-Generation Sequencing
Although NextGen sequencing has provided scientific advances using high-
throughput methods at a greatly reduced cost compared with Sanger sequenc-
ing, even NextGen sequencing methods cannot provide all the answers
geneticists want (
Harris et al. 2008, Eid et al. 2009, Pettersson et al. 2009, Schadt
et al. 2010, Ghose 2012
). Several third-generation sequencing technologies
are being developed that will further reduce costs and the time required to
sequence genomes (
Bennett et al. 2005
).
Second-generation sequencing techniques involve sequencing by synthesis,
relying on PCR to grow clusters of a given DNA template, attaching the clus-
ters of DNA templates to a solid surface that is then imaged as the clusters are
sequenced by synthesis in a phased approach. By contrast, third-generation
technologies are attempting to sequence
single molecules
of DNA so that biases
introduced by PCR amplification are eliminated (
Harris et al. 2008
). The goal is
to increase read length from tens of base pairs to thousands of base pairs per
read and to reduce the time from days to hours or minutes (
Schadt et al. 2010
).
Thus, the goal is higher throughput, faster turnaround, longer read lengths to
enhance assembly, higher accuracy rates, the need for smaller amounts of start-
ing material, and lower cost. Using such methods, the human genome, in the-
ory, could be sequenced for
<
US$100 (
Schadt et al. 2010
).
One approach to third-generation sequencing involves ion sequencing, in
which each well lies above an ion-sensitive metallic oxide layer coupled to an
electronic sensor that registers tiny and transient pH changes in each well as
determined by the base sequence (
Robison 2011
).
The Ion Torrent Personal Genome Machine (PGM) costs
≈
US$50,000 and relies
on detection of the release of hydrogen ions when DNA polymerase adds a
nucleotide during DNA synthesis. The DNA is present in up to a million or more
microwells that are flooded with each of the four nucleotides in succession. If
the nucleotide complements that of the DNA template, it is incorporated, result-
ing in a hydrogen ion that is detected by a pH sensor and translated into a volt-
age change recorded by a semiconductor sensor. In January 2012, Ion Torrent
released a more powerful machine, Ion Proton, that can “churn out a human
