ABI Solid Sequencing

Main article: 2 base encoding
Library preparation for the SOLiD platform
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.

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 108 - 109 small sequence reads at one time. It uses 2 base encoding to decode the raw data generated by the sequencing platform into sequence data.

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]

  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. PMC 2493394. PMID 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. PMID 18516046. S2CID 19790151.
  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. PMID 19349980. S2CID 16570747.
  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. PMC 2752135. PMID 19546169.
  5. ^ Yu-Feng Huang; Sheng-Chung Chen; Yih-Shien Chiang & Tzu-Han Chen (2012). "Palindromic sequence impedes sequencing-by-ligation mechanism". BMC Systems Biology. 6 (Suppl 2): S10. doi:10.1186/1752-0509-6-S2-S10. PMC 3521181. PMID 23281822.