2 Base Encoding

2 Base Encoding, also called SOLiD (Sequencing by Oligonucleotide Ligation and Detection), is a next-generation sequencing technology developed by Applied Biosystems and has been commercially available since 2008. These technologies generate hundreds of thousands of small sequence reads at one time. Well-known examples of such DNA sequencing methods include 454 pyrosequencing (introduced in 2005), the Solexa system (introduced in 2006) and the SOLiD system (introduced in 2007). 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 100,000,000 bases/machine/day in 2006.

Similar to Shendure et al., 2-base encoding is based on ligation sequencing rather than sequencing by synthesis. However, instead of using fluorescent labeled 9-mer probes that distinguish only 6 bases, 2-base encoding takes advantage of fluorescent labeled 8-mer probes that distinguish the two 3 prime most bases but can be cycled similar to the Macevicz method, thus greater than 6bp reads can be obtained (25-50bp published, 50bp in NCBI in Feb 2008). The 2 base encoding enables reading each base twice without performing twice the work. The technique is described by McKernan, Blanchard, Kotler and Costa. and Valouev et al. Cloonan et al. and Smith et al.