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Solid sequencing

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SOLiD (Sequencing by Oligonucleotide Ligation and Detection) is a next-generation sequencing technology developed by Life Technologies and has been commercially available since 2008. These next generation technologies generate hundreds of millions to billions of small sequence reads at one time. Well-known examples of such DNA sequencing methods include 454 pyrosequencing (introduced in 2005, generating millions of 200-400bp reads in 2009), the Solexa system (introduced in 2006, generating hundreds of millions of 50-100bp reads in 2009) and the SOLiD system (introduced in 2007, generating billions of 50bp 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]

<h2>Chemistry</h2>

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.

<ul>

<li><~~a title~~span style="~~2 Base Encoding" href="/wiki/2_Base_Encoding"><font~~ color=": #~~0645ad~~000000">2 Base Encoding</~~font></a~~span></li> <li><~~a class~~span style="~~mw-redirect" title="Next-generation sequencing" href="/wiki/Next-generation_sequencing"><font~~ color=": #~~0645ad~~000000">Next-generation sequencing</~~font></a~~span></li> <li><~~a title~~span style="~~Applied Biosystems" href="/wiki/Applied_Biosystems"><font~~ color=": #~~0645ad~~000000">Applied Biosystems</~~font></a~~span></li> <li><~~a title~~span style="~~Illumina (company)" href="/wiki/Illumina_(company)"><font~~ color=": #~~0645ad~~000000">Illumina (company)</~~font></a~~span></li> <li><~~a title="454 Life Sciences" href~~span style="~~/wiki/454_Life_Sciences"><font~~ color=": #~~0645ad~~000000">454 Life Sciences</~~font></a~~span></li>

</ul>

<h2>References</h2>

<ol>

<li id="cite_note-0"><a href="#cite_ref-0">^</a> Valouev A, Ichikawa J, Tonthat T, et al. (July 2008). <a class="external text" rel="nofollow" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2493394~~" rel="nofollow~~">"A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning"</a>. Genome Research 18 (7): 1051–63. <a title="Digital object identifier" href="/wiki/Digital_object_identifier">doi</a>:<a class="external text" rel="nofollow" href="http://dx.doi.org/10.1101%2Fgr.076463.108~~" rel="nofollow~~">10.1101/gr.076463.108</a>. <a class="mw-redirect" title="PubMed Identifier" href="/wiki/PubMed_Identifier">PMID</a> <a class="external text" rel="nofollow" href="http://www.ncbi.nlm.nih.gov/pubmed/18477713~~" rel="nofollow~~">18477713</a>.<span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=A+high-resolution%2C+nucleosome+position+map+of+C.+elegans+reveals+a+lack+of+universal+sequence-dictated+positioning&rft.jtitle=Genome+Research&rft.aulast=Valouev+A%2C+Ichikawa+J%2C+Tonthat+T%2C+%27%27et+al.%27%27&rft.au=Valouev+A%2C+Ichikawa+J%2C+Tonthat+T%2C+%27%27et+al.%27%27&rft.date=July+2008&rft.volume=18&rft.issue=7&rft.pages=1051%E2%80%9363&rft_id=info:doi/10.1101%2Fgr.076463.108&rft_id=info:pmid/18477713&rfr_id=info:sid/en.wikipedia.org:ABI_Solid_Sequencing"> </li> <li id="cite_note-1"><a href="#cite_ref-1">^</a> 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. <a title="Digital object identifier" href="/wiki/Digital_object_identifier">doi</a>:<a class="external text" rel="nofollow" href="http://dx.doi.org/10.1038%2Fnmeth.1223~~" rel="nofollow~~">10.1038/nmeth.1223</a>. <a class="mw-redirect" title="PubMed Identifier" href="/wiki/PubMed_Identifier">PMID</a> <a class="external text" rel="nofollow" href="http://www.ncbi.nlm.nih.gov/pubmed/18516046~~" rel="nofollow~~">18516046</a>.<span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Stem+cell+transcriptome+profiling+via+massive-scale+mRNA+sequencing&rft.jtitle=Nature+Methods&rft.aulast=Cloonan+N%2C+Forrest+AR%2C+Kolle+G%2C+%27%27et+al.%27%27&rft.au=Cloonan+N%2C+Forrest+AR%2C+Kolle+G%2C+%27%27et+al.%27%27&rft.date=July+2008&rft.volume=5&rft.issue=7&rft.pages=613%E2%80%939&rft_id=info:doi/10.1038%2Fnmeth.1223&rft_id=info:pmid/18516046&rfr_id=info:sid/en.wikipedia.org:ABI_Solid_Sequencing"> </li> <li id="cite_note-2"><a href="#cite_ref-2">^</a> 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. <a title="Digital object identifier" href="/wiki/Digital_object_identifier">doi</a>:<a class="external text" rel="nofollow" href="http://dx.doi.org/10.1038%2Fnmeth.1315~~" rel="nofollow~~">10.1038/nmeth.1315</a>. <a class="mw-redirect" title="PubMed Identifier" href="/wiki/PubMed_Identifier">PMID</a> <a class="external text" ~~href~~rel="nofollow" href="http://www.ncbi.nlm.nih.gov/pubmed/19349980~~" rel="nofollow~~">19349980</a>.<span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=mRNA-Seq+whole-transcriptome+analysis+of+a+single+cell&rft.jtitle=Nature+Methods&rft.aulast=Tang+F%2C+Barbacioru+C%2C+Wang+Y%2C+%27%27et+al.%27%27&rft.au=Tang+F%2C+Barbacioru+C%2C+Wang+Y%2C+%27%27et+al.%27%27&rft.date=May+2009&rft.volume=6&rft.issue=5&rft.pages=377%E2%80%9382&rft_id=info:doi/10.1038%2Fnmeth.1315&rft_id=info:pmid/19349980&rfr_id=info:sid/en.wikipedia.org:ABI_Solid_Sequencing"> </li> <li id="cite_note-3"><a href="#cite_ref-3">^</a> McKernan KJ, Peckham HE, Costa GL, et al. (September 2009). <a class="external text" rel="nofollow" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2752135~~" rel="nofollow~~">"Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding"</a>. Genome Research 19 (9): 1527–41. <a title="Digital object identifier" href="/wiki/Digital_object_identifier">doi</a>:<a class="external text" rel="nofollow" href="http://dx.doi.org/10.1101%2Fgr.091868.109~~" rel="nofollow~~">10.1101/gr.091868.109</a>. <a class="mw-redirect" title="PubMed Identifier" href="/wiki/PubMed_Identifier">PMID</a> <a class="external text" rel="nofollow" href="http://www.ncbi.nlm.nih.gov/pubmed/19546169~~" rel="nofollow~~">19546169</a>.<span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Sequence+and+structural+variation+in+a+human+genome+uncovered+by+short-read%2C+massively+parallel+ligation+sequencing+using+two-base+encoding&rft.jtitle=Genome+Research&rft.aulast=McKernan+KJ%2C+Peckham+HE%2C+Costa+GL%2C+%27%27et+al.%27%27&rft.au=McKernan+KJ%2C+Peckham+HE%2C+Costa+GL%2C+%27%27et+al.%27%27&rft.date=September+2009&rft.volume=19&rft.issue=9&rft.pages=1527%E2%80%9341&rft_id=info:doi/10.1101%2Fgr.091868.109&rft_id=info:pmid/19546169&rfr_id=info:sid/en.wikipedia.org:ABI_Solid_Sequencing"> </li>

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<h2>Further reading</h2>

<ul>

<li>Mardis ER (2008). "Next-generation DNA sequencing methods". Annual Review of Genomics and Human Genetics 9: 387–402. <a title="Digital object identifier" href="/wiki/Digital_object_identifier">doi</a>:<a class="external text" rel="nofollow" href="http://dx.doi.org/10.1146%2Fannurev.genom.9.081307.164359~~" rel="nofollow~~">10.1146/annurev.genom.9.081307.164359</a>. <a class="mw-redirect" title="PubMed Identifier" href="/wiki/PubMed_Identifier">PMID</a> <a class="external text" rel="nofollow" href="http://www.ncbi.nlm.nih.gov/pubmed/18576944~~" rel="nofollow~~">18576944</a>.<span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Next-generation+DNA+sequencing+methods&rft.jtitle=Annual+Review+of+Genomics+and+Human+Genetics&rft.aulast=Mardis+ER&rft.au=Mardis+ER&rft.date=2008&rft.volume=9&rft.pages=387%E2%80%93402&rft_id=info:doi/10.1146%2Fannurev.genom.9.081307.164359&rft_id=info:pmid/18576944&rfr_id=info:sid/en.wikipedia.org:ABI_Solid_Sequencing"> </li> <li>Mardis ER (2009). <a class="external text" rel="nofollow" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2684661~~" rel="nofollow~~">"New strategies and emerging technologies for massively parallel sequencing: applications in medical research"</a>. Genome Medicine 1 (4): 40. <a title="Digital object identifier" href="/wiki/Digital_object_identifier">doi</a>:<a class="external text" rel="nofollow" href="http://dx.doi.org/10.1186%2Fgm40~~" rel="nofollow~~">10.1186/gm40</a>. <a class="mw-redirect" title="PubMed Identifier" href="/wiki/PubMed_Identifier">PMID</a> <a class="external text" rel="nofollow" href="http://www.ncbi.nlm.nih.gov/pubmed/19435481~~" rel="nofollow~~">19435481</a>.<span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=New+strategies+and+emerging+technologies+for+massively+parallel+sequencing%3A+applications+in+medical+research&rft.jtitle=Genome+Medicine&rft.aulast=Mardis+ER&rft.au=Mardis+ER&rft.date=2009&rft.volume=1&rft.issue=4&rft.pages=40&rft_id=info:doi/10.1186%2Fgm40&rft_id=info:pmid/19435481&rfr_id=info:sid/en.wikipedia.org:ABI_Solid_Sequencing"> </li>

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<h2>External links</h2>

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<li><a class="external text" rel="nofollow" href="http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_061241.pdf~~" rel="nofollow~~">"The SOLiD 3 System: Enabling the Next Generation of Science"</a>. <a title="Life Technologies" href="/wiki/Life_Technologies">Life Technologies</a>. 2009. <a class="external free" rel="nofollow" href="http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_061241.pdf~~" rel="nofollow~~">http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_061241.pdf</a>. Retrieved January 27, 2010.<span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=bookitem&rft.btitle=The+SOLiD+3+System%3A+Enabling+the+Next+Generation+of+Science&rft.atitle=&rft.date=2009&rft.pub=%5B%5BLife+Technologies%5D%5D&rft_id=http%3A%2F%2Fwww3.appliedbiosystems.com%2Fcms%2Fgroups%2Fmcb_marketing%2Fdocuments%2Fgeneraldocuments%2Fcms_061241.pdf&rfr_id=info:sid/en.wikipedia.org:ABI_Solid_Sequencing"> </li> <li><a class="external text" rel="nofollow" href="http://marketing.appliedbiosystems.com/mk/get/SOLID_ACCURACY_Landing?CID=BN-88889-NAHomePage~~" rel="nofollow~~">"The SOLiD 3 Plus System"</a>. <a title="Life Technologies" href="/wiki/Life_Technologies">Life Technologies</a>. 2009. <a class="external free" rel="nofollow" href="http://marketing.appliedbiosystems.com/mk/get/SOLID_ACCURACY_Landing?CID=BN-88889-NAHomePage~~" rel="nofollow~~">http://marketing.appliedbiosystems.com/mk/get/SOLID_ACCURACY_Landing?CID=BN-88889-NAHomePage</a>. Retrieved January 27, 2010.</li>

</ul>

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