2 base encoding

Two-base encoding scheme. In two-base encoding, each unique pair of bases on the 3' end of the probe is assigned one out of four possible colors. For example, "AA" is assigned to blue, "AC" is assigned to green, and so on for all 16 unique pairs. During sequencing, each base in the template is sequenced twice, and the resulting data are decoded according to this scheme.

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.

2-base encoding is based on ligation sequencing rather than sequencing by synthesis.[1] 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,[2] 50bp in NCBI in Feb 2008). The 2 base encoding enables reading each base twice without performing twice the work.[3][4][5][6]

  1. ^ Jay Shendure et al. (2005) Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome. Science 309(5741), 1728 - 1732
  2. ^ Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. McKernan KJ, Peckham HE, Costa GL, McLaughlin SF, Fu Y, Tsung EF, Clouser CR, Duncan C, Ichikawa JK, Lee CC, Zhang Z, Ranade SS, Dimalanta ET, Hyland FC, Sokolsky TD, Zhang L, Sheridan A, Fu H, Hendrickson CL, Li B, Kotler L, Stuart JR, Malek JA, Manning JM, Antipova AA, Perez DS, Moore MP, Hayashibara KC, Lyons MR, Beaudoin RE, Coleman BE, Laptewicz MW, Sannicandro AE, Rhodes MD, Gottimukkala RK, Yang S, Bafna V, Bashir A, MacBride A, Alkan C, Kidd JM, Eichler EE, Reese MG, De La Vega FM, Blanchard AP. Genome Res. 2009 Sep;19(9):1527-41. Epub 2009 Jun 22.
  3. ^ Patent: Reagents,Methods and Libraries for Bead-Based Sequencing
  4. ^ Article: A high-resolution, nucleosome position map of C. elegans reveals a lack of universal...
  5. ^ Article: Stem cell transcriptome profiling via massive-scale mRNA sequencing
  6. ^ Rapid whole-genome mutational profiling using next-generation sequencing technologies, Genome Research, 2008 18:1638-1642