9 Genomic Techniques and How to Apply Them to Marine Questions
321
For more detailed information regarding the Illumina
R
sequencing technology
and the Illumina
R
Genome Analyser and recent developments please refer to the
Illumina
R
website http://www.illumina.com/. The Illumina sequencing platform
includes merged technology from Solexa, Lynx and Manteia SA.
9.1.2.3 SOLiD TM System
Applied Biosystems
R
(ABI) have developed the SOLiD TM System (Supported
Oligonucleotide Ligation and Detection System), which is a genetic analysis
platform that enables massively parallel sequencing of clonally amplified DNA
fragments linked to beads. The SOLiD TM sequencing methodology is based on
sequential ligation with dye-labelled oligonucleotides. The company claims that
this technology provides unmatched accuracy, ultra-high throughput and application
flexibility. The SOLiD TM System features di-base encoding, a proprietary mechanism that interrogates each base twice. The SOLiD TM System generates more than
one gigabase of mapable data per run (Table 9.1). Increased bead yields, improved
bead enrichment methods, higher density bead packing, and improved featurefinding software will allow for rapid gains in throughput from the same system. The
di-base encoding algorithms filter out errors in the raw data following sequencing,
providing built-in error correction.
For more detailed information and recent developments regarding the
SOLiD TM technology and the ABI SOLiD TM system refer to the Applied
Biosystems
R
website https://products.appliedbiosystems.com/index.cfm or http://
solid.appliedbiosystems.com
9.1.3 Other New Advanced Approaches to DNA Sequencing
In August 2007 the National Institutes of Health (NIH) issued a news release
announcing several new grant awards to boost efforts towards next generation
sequencing technologies (http://www.genome.gov). Shendure et al. (2008) have provided a recent overview of DNA sequencing strategies, including approaches such as
microelectrophoresis and mass spectrometry. Here a short overview is presented of
three distinct approaches to DNA sequencing based on two articles from Shendure
et al. (2004, 2008): polony sequencing, sequencing-by-hybridization, and nanopore
sequencing.
9.1.3.1 Open-Source “Polony Sequencing” System
Using the “polymerase colony (polony) Cyclic Sequencing by Synthesis” method it
was possible to resequence an evolved strain of Escherichia coli with less than one
error per million consensus bases (Shendure et al. 2005). The polony resequencing method involves the amplification of short DNA fragments on one-micrometer
magnetic beads using the emulsion polymerase chain reaction (see Section 9.1.2,
pyrosequencing part). The beads are then immobilized in a polyacrylamide gel and
321
For more detailed information regarding the Illumina
R
sequencing technology
and the Illumina
R
Genome Analyser and recent developments please refer to the
Illumina
R
website http://www.illumina.com/. The Illumina sequencing platform
includes merged technology from Solexa, Lynx and Manteia SA.
9.1.2.3 SOLiD TM System
Applied Biosystems
R
(ABI) have developed the SOLiD TM System (Supported
Oligonucleotide Ligation and Detection System), which is a genetic analysis
platform that enables massively parallel sequencing of clonally amplified DNA
fragments linked to beads. The SOLiD TM sequencing methodology is based on
sequential ligation with dye-labelled oligonucleotides. The company claims that
this technology provides unmatched accuracy, ultra-high throughput and application
flexibility. The SOLiD TM System features di-base encoding, a proprietary mechanism that interrogates each base twice. The SOLiD TM System generates more than
one gigabase of mapable data per run (Table 9.1). Increased bead yields, improved
bead enrichment methods, higher density bead packing, and improved featurefinding software will allow for rapid gains in throughput from the same system. The
di-base encoding algorithms filter out errors in the raw data following sequencing,
providing built-in error correction.
For more detailed information and recent developments regarding the
SOLiD TM technology and the ABI SOLiD TM system refer to the Applied
Biosystems
R
website https://products.appliedbiosystems.com/index.cfm or http://
solid.appliedbiosystems.com
9.1.3 Other New Advanced Approaches to DNA Sequencing
In August 2007 the National Institutes of Health (NIH) issued a news release
announcing several new grant awards to boost efforts towards next generation
sequencing technologies (http://www.genome.gov). Shendure et al. (2008) have provided a recent overview of DNA sequencing strategies, including approaches such as
microelectrophoresis and mass spectrometry. Here a short overview is presented of
three distinct approaches to DNA sequencing based on two articles from Shendure
et al. (2004, 2008): polony sequencing, sequencing-by-hybridization, and nanopore
sequencing.
9.1.3.1 Open-Source “Polony Sequencing” System
Using the “polymerase colony (polony) Cyclic Sequencing by Synthesis” method it
was possible to resequence an evolved strain of Escherichia coli with less than one
error per million consensus bases (Shendure et al. 2005). The polony resequencing method involves the amplification of short DNA fragments on one-micrometer
magnetic beads using the emulsion polymerase chain reaction (see Section 9.1.2,
pyrosequencing part). The beads are then immobilized in a polyacrylamide gel and