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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.'',〔Jay Shendure et al. (2005) Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome. Science 309(5741) , 1728 - 1732〕 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,〔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.〕 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.〔(Article: Reagents,Methods and Libraries for Bead-Based Sequencing )〕 and Valouev et al.〔(Article: A high-resolution, nucleosome position map of C. elegans reveals a lack of universal... )〕 Cloonan et al.〔(Article: Stem cell transcriptome profiling via massive-scale mRNA sequencing )〕 and Smith et al.〔Rapid whole-genome mutational profiling using next-generation sequencing technologies, Genome Research, 2008 18:1638-1642〕 ==General features== The general steps common to many of these next-generation sequencing techniques include: # Random fragmentation of genomic DNA # Immobilization of single DNA fragments on a solid support like a bead or a planar solid surface # Amplification of DNA fragments on the solid surface using PCR and making polymerase colonies〔Chetverin, NAR, 1993, Vol.21, No. 10 2349-2353〕 # Sequencing and subsequent in situ interrogation after each cycle using fluorescence scanning or chemiluminescence.〔MATTHEW E. HUDSON (2008) Sequencing breakthroughs for genomic ecology and evolutionary biology. Molecular Ecology Resources 8 (1) , 3–17〕 In 1988, Whiteley ''et al.'' demonstrated the use of fluorescently labeled oligonucleotide ligation for the detection of DNA variants.〔Whiteley US patent number 4,883,750〕 In 1995 Macevicz〔Macevicz US patent number 5,750,341〕 demonstrated repeated ligation of oligonucleotides to detect contiguous DNA variants. In 2003, Dressman ''et al.''〔Transforming single DNA molecules into fluorescent magnetic particles fr detection and enumeration of genetic variations,PNAS July 22, 2004 Vol. 100 no. 15, 8817-8822〕 demonstrated the use of emulsion PCR to generate millions of clonally amplified beads which one could perform these repeated ligation assays on. In 2005, Shendure ''et al.'' performed a sequencing procedure which combined Whiteley and Dressman techniques performing ligation of fluorescent labeled "8 base degenerate" 9-mer probes which distinguished a different base according to the probes label and non degenerate base. This process was repeated (without regenerating an extendable end as in Macevicz) using identical primers but with probes with labels which identified different non-degenerate base to sequence 6bp reads in 5->3 direction and 7bp reads in the 3->5 direction. 抄文引用元・出典: フリー百科事典『 ウィキペディア（Wikipedia）』 ■ウィキペディアで「2 base encoding」の詳細全文を読む スポンサード リンク
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