<p><span style="color: #000000"><b>SOLiD</b> (Sequencing by Oligonucleotide Ligation and Detection) is a next-generation sequencing technology developed by <font color="#0645ad">Life Technologies</font> 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 <font color="#0645ad">pyrosequencing</font> (introduced in 2005, generating millions of 200-400bp reads in 2009), the <font color="#0645ad">Solexa</font> 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.,<sup id="cite_ref-0" class="reference"><font size="2"><font color="#0645ad"><span>[</span>1<span>]</span></font></font></sup> transcriptional profiling or strand sensitive RNA-Seq with Cloonan et al.,<sup id="cite_ref-1" class="reference"><font size="2"><font color="#0645ad"><span>[</span>2<span>]</span></font></font></sup> single cell transcriptional profiling with Tang et al.<sup id="cite_ref-2" class="reference"><font size="2"><font color="#0645ad"><span>[</span>3<span>]</span></font></font></sup> and ultimately human resequencing with McKernan et al.<sup id="cite_ref-3" class="reference"><font size="2"><font color="#0645ad"><span>[</span>4<span>]</span></font></fontsup></supspan></p><p><span style="color: #000000">&nbsp;</span></p><h2><span style="color: #000000"><span id="Chemistry" class="mw-headline">Chemistry</span></span></h2><p><span style="color: #000000">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 <font color="#0645ad">PCR</font> 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.</span></p><p><span style="color: #000000">Primers hybridize to the P1 adapter sequence within the library template. A set of four fluorescently labeled 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 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.</span></p><p><span style="color: #000000">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.</span></p>