ABI Solid Sequencing - Wikipedia, the free encyclopedia
http://en.wikipedia.org/wiki/ABI_Solid_Sequencing
ABI Solid Sequencing
From Wikipedia, the free encyclopedia
SOLiD (Sequencing by Oligonucleotide Ligation and Detection) is a next-generation DNA
sequencing technology developed by Life Technologies and has been commercially available since
2006. This next generation technology generates hundreds of millions to billions of small sequence
reads at one time.
This method should not be confused with "sequencing by synthesis," a principle used by Roche-454
pyrosequencing (introduced in 2005, generating millions of 200-400bp reads in 2009), and the
Solexa system (now owned by Illumina) (introduced in 2006, generating hundreds of millions of
50-100bp reads in 2009)
These methods have reduced the cost from $0.01/base in 2004 to nearly $0.0001/base in 2006 and
increased the sequencing capacity from 1,000,000 bases/machine/day in 2004 to more than
5,000,000,000 bases/machine/day in 2009. Over 30 publications exist describing its use first for
nucleosome positioning from Valouev et al.,[1] transcriptional profiling or strand sensitive RNA-Seq
with Cloonan et al.,[2] single cell transcriptional profiling with Tang et al.[3] and ultimately human
resequencing with McKernan et al.[4]
The method used by this machine (sequencing-by-ligation) has been reported to have some issue
sequencing palindromic sequences. [5]
Contents
1 Chemistry
2 Throughput and Accuracy
3 Applications
4 See also
5 References
6 Further reading
7 External links
Chemistry
A library of DNA fragments is prepared from the sample to be sequenced, and are used to prepare
clonal bead populations. That is, only one species of fragment will be present on the surface of each
magnetic bead. The fragments attached to the magnetic beads will have a universal P1 adapter
sequence attached so that the starting sequence of every fragment is both known and identical.
Emulsion PCR takes place in microreactors containing all the necessary reagents for PCR. The
resulting PCR products attached to the beads are then covalently bound to a glass slide.
Primers hybridize to the P1 adapter sequence within the library template. A set of four fluorescently
labelled di-base probes compete for ligation to the sequencing primer. Specificity of the di-base
probe is achieved by interrogating every 1st and 2nd base in each ligation reaction. Multiple cycles
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ABI Solid Sequencing - Wikipedia, the free encyclopedia
http://en.wikipedia.org/wiki/ABI_Solid_Sequencing
of ligation, detection and cleavage are performed with the number of cycles determining the eventual
read length. Following a series of ligation cycles, the extension product is removed and the template
is reset with a primer complementary to the n-1 position for a second round of ligation cycles.
Five rounds of primer reset are completed for each sequence tag. Through the primer reset process,
each base is interrogated in two independent ligation reactions by two different primers. For
example, the base at read position 5 is assayed by primer number 2 in ligation cycle 2 and by primer
number 3 in ligation cycle 1.
Throughput and Accuracy
According to ABI, the SOLiD 3plus platform yields 60 gigabases of usable DNA data per run. Due
to the two base encoding system, an inherent accuracy check is built into the technology and offers
99.94% accuracy. The chemistry of the systems also means that it is not hindered by homopolymers
unlike the Roche 454 FLX system and so large and difficult homopolymer repeat regions are no
longer a problem to sequence.
Applications
Naturally the technology will be used to sequence DNA, but because of the high parallel nature of all
next generation technologies they also have applications in transcriptomics and epigenomics.
Microarrays have been the mainstay of the transcriptomics world for the last ten years and array
based technology has branched out to other areas. But they are limited in that only information can
be obtained for probes that are on the chip. Only information for organisms for which chips are
available can obtained, and they come with all the problems of hybridizing large numbers of
molecules (differing hybridizing temperatures).
Transcriptomics by next gen sequencing will mean these barriers no longer hold true. Any organism's
entire transcriptome could be potentially sequenced in one run (for very small bacterial genomes)
and not only would the identification of each transcript be available but expression profiling is
possible as quantitative reads can also be achieved.
Chromatin immunoprecipitation (ChIP) is a method for determining transcription factor binding sites
and DNA-protein interactions. It has in the past been combined with array technology (ChIP-chip)
with some success. Next gen sequencing can also be applied in this area. Methylation
immunoprecipitation (MeDIP) can also be performed and also on arrays.
The ability to learn more about methylation and TF binding sites on a genome wide scale is a
valuable resource and could teach us much about disease and molecular biology in general.
See also
2 Base Encoding
Next-generation sequencing
Applied Biosystems
Illumina (company)
454 Life Sciences
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ABI Solid Sequencing - Wikipedia, the free encyclopedia
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References
1. ^ Valouev A, Ichikawa J, Tonthat T, et al. (July 2008). "A high-resolution, nucleosome position map of
C. elegans reveals a lack of universal sequence-dictated positioning". Genome Research 18 (7): 1051–63.
doi:10.1101/gr.076463.108 (http://dx.doi.org/10.1101%2Fgr.076463.108). PMC 2493394
(//www.ncbi.nlm.nih.gov/pmc/articles/PMC2493394). PMID 18477713 (//www.ncbi.nlm.nih.gov
/pubmed/18477713).
2. ^ Cloonan N, Forrest AR, Kolle G, et al. (July 2008). "Stem cell transcriptome profiling via
massive-scale mRNA sequencing". Nature Methods 5 (7): 613–9. doi:10.1038/nmeth.1223
(http://dx.doi.org/10.1038%2Fnmeth.1223). PMID 18516046 (//www.ncbi.nlm.nih.gov/pubmed
/18516046).
3. ^ Tang F, Barbacioru C, Wang Y, et al. (May 2009). "mRNA-Seq whole-transcriptome analysis of a
single cell". Nature Methods 6 (5): 377–82. doi:10.1038/nmeth.1315 (http://dx.doi.org
/10.1038%2Fnmeth.1315). PMID 19349980 (//www.ncbi.nlm.nih.gov/pubmed/19349980).
4. ^ McKernan KJ, Peckham HE, Costa GL, et al. (September 2009). "Sequence and structural variation in
a human genome uncovered by short-read, massively parallel ligation sequencing using two-base
encoding". Genome Research 19 (9): 1527–41. doi:10.1101/gr.091868.109 (http://dx.doi.org
/10.1101%2Fgr.091868.109). PMC 2752135 (//www.ncbi.nlm.nih.gov/pmc/articles/PMC2752135).
PMID 19546169 (//www.ncbi.nlm.nih.gov/pubmed/19546169).
5. ^ Yu-Feng Huang, Sheng-Chung Chen, Yih-Shien Chiang, Tzu-Han Chen & Kuo-Ping Chiu (2012).
"Palindromic sequence impedes sequencing-by-ligation mechanism". BMC systems biology. 6 Suppl 2:
S10. doi:10.1186/1752-0509-6-S2-S10 (http://dx.doi.org/10.1186%2F1752-0509-6-S2-S10).
PMID 23281822 (//www.ncbi.nlm.nih.gov/pubmed/23281822).
Further reading
Mardis ER (2008). "Next-generation DNA sequencing methods". Annual Review of Genomics
and Human Genetics 9: 387–402. doi:10.1146/annurev.genom.9.081307.164359
(http://dx.doi.org/10.1146%2Fannurev.genom.9.081307.164359). PMID 18576944
(//www.ncbi.nlm.nih.gov/pubmed/18576944).
Mardis ER (2009). "New strategies and emerging technologies for massively parallel
sequencing: applications in medical research". Genome Medicine 1 (4): 40. doi:10.1186/gm40
(http://dx.doi.org/10.1186%2Fgm40). PMC 2684661 (//www.ncbi.nlm.nih.gov/pmc/articles
/PMC2684661). PMID 19435481 (//www.ncbi.nlm.nih.gov/pubmed/19435481).
External links
"The SOLiD 3 System: Enabling the Next Generation of Science"
(http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents
/generaldocuments/cms_061241.pdf). Life Technologies. 2009. Retrieved January 27, 2010.
"The SOLiD 3 Plus System" (http://marketing.appliedbiosystems.com/mk/get
/SOLID_ACCURACY_Landing?CID=BN-88889-NAHomePage). Life Technologies. 2009.
Retrieved January 27, 2010.
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