http://qa.lifesciencedb.jp/questions/349/%E6%96%B0%E5%9E%8B%E3%82%B7%E3%83%BC%E3%82%B1%E3%83%B3%E3%82%B5%E3%83%BC%E3%81%AE%E7%94%9F%E3%83%87%E3%83%BC%E3%82%BF%E3%82%B5%E3%82%A4%E3%82%BA%E3%81%AF%E3%81%A9%E3%82%93%E3%81%AA%E9%A2%A8%E3%81%A7%E3%81%99%E3%81%8B<p><img alt="alt text" src="http://farm6.static.flickr.com/5253/5475238349_f91dd0c290_z.jpg"> [http://www.flickr.com/photos/59261391@N05/5475238349/][2] はしばらく前の議論に使った目安です。　現状はどうなんでしょうか？</p> <p><strong>Kato Kikuya</strong> <strong>Impact of the next generation DNA sequencers</strong> . Int J Clin Exp Med. 2009; 2(2): 193–202. Published online 2009 July 8. Comparison of sequencers (January, 2009). It should be noted that the throughput of each sequencer is improving rapidly</p> <table> <thead> <tr> <th> </th> <th> ABI 3730xI </th> <th> Roche GS FLX </th> <th> Illumina GA </th> <th> ABI SOLiD </th> </tr> </thead> <tbody> <tr> <th> Bases/template </th> <td> ∼1100 </td> <td> ∼400 </td> <td> ∼75 </td> <td> 50 </td> </tr> <tr> <th> Templates/run </th> <td> 96 </td> <td> 1,000,000 </td> <td> 40,000,000 </td> <td> 85,000,000 </td> </tr> <tr> <th> Data production/day </th> <td> 1 MB/day </td> <td> 400MB/run/7.5hr </td> <td> 3,000MB/run/6.5 days </td> <td> 4,000MB/run/6 days </td> </tr> <tr> <th> Maximum samples </th> <td> 96 </td> <td> 16 regions/plate </td> <td> 8 channels/flowcell </td> <td> 16chambers/2 slides </td> </tr> <tr> <th> Sequence reaction </th> <td> Sanger method </td> <td> pyrosequencing </td> <td> Reverse terminator </td> <td> ligation sequencing </td> </tr> </tbody> </table>jaMon, 28 Feb 2011 22:20:49 +0900http://qa.lifesciencedb.jp/questions/349/%E6%96%B0%E5%9E%8B%E3%82%B7%E3%83%BC%E3%82%B1%E3%83%B3%E3%82%B5%E3%83%BC%E3%81%AE%E7%94%9F%E3%83%87%E3%83%BC%E3%82%BF%E3%82%B5%E3%82%A4%E3%82%BA%E3%81%AF%E3%81%A9%E3%82%93%E3%81%AA%E9%A2%A8%E3%81%A7%E3%81%99%E3%81%8B/375<table> <thead> <tr> <th> Method </th> <th> Amplification </th> <th> Read length (base pairs) </th> <th> Templates per run </th> <th> Data production/day </th> <th> Sequence reaction </th> <th> Reference </th> </tr> </thead> <tbody> <tr> <th> ABI 3730xI </th> <td> PCR </td> <td> ~900 to 1,100 </td> <td> 96 </td> <td> 1 Mb/day </td> <td> Sanger method </td> <td> http://www.appliedbyosystems.com </td> </tr> <tr> <th> 454 FLX Roche </th> <td> Emulsion PCR </td> <td> ~400 </td> <td> 1,000,000 </td> <td> 400 Mb/run/7.5 to 8 hours </td> <td> Pyrosequencing </td> <td> http://www.rocheapplied-science.com </td> </tr> <tr> <th> Illumina (Solexa) Genome Analyzer </th> <td> Bridge PCR </td> <td> 36 to 175 </td> <td> 40,000,000 </td> <td> &gt;17 Gb/run/3 to 6 days </td> <td> Reverse terminator </td> <td> http://www.illumina.com </td> </tr> <tr> <th> ABI SOLiD </th> <td> Emulsion PCR </td> <td> ~50 </td> <td> 85,000,000 </td> <td> 10 to 15 Gb/run/6 days </td> <td> Ligation sequencing </td> <td> http://www.appliedbyosystems.com </td> </tr> <tr> <th> Helicos Heliscope </th> <td> None </td> <td> 30 to 35 </td> <td> 800,000,000 </td> <td> 21 to 28 Gb/run/8 days </td> <td> Single molecule sequence by synthesis </td> <td> http://www.helicosbio.com </td> </tr> </tbody> </table> <p><strong>Next-generation sequencing, breast-cancer-research.comJ Reis-Filho - Breast Cancer Research, 2009</strong></p> <table> <thead> <tr> <th colspan="7"> Technologies in development </th> </tr> </thead> <tbody> <tr> <th> Pacific Biosciences </th> <td> None </td> <td> &gt;1,000 </td> <td> NA </td> <td> NA </td> <td> Single molecule real-time DNA sequencing </td> <td> http://www.pacificbiosciences.com </td> </tr> <tr> <th> Intelligent Biosciences </th> <td> Yesa </td> <td> NA </td> <td> NA </td> <td> NA </td> <td> Sequence by synthesis </td> <td> http://www.intelligentbiosystems.com </td> </tr> <tr> <th> Visigen Biotechnologies </th> <td> None </td> <td> NA </td> <td> NA </td> <td> NA </td> <td> Base-specific FRET emission </td> <td> http://www.visigenbio.com </td> </tr> <tr> <th> ZS Genetics </th> <td> None </td> <td> NA </td> <td> NA </td> <td> NA </td> <td> ZSG atomic labelling and electron microscopy </td> <td> http://www.zsgenetics.com </td> </tr> </tbody> </table>okuboMon, 28 Feb 2011 22:20:49 +0900http://qa.lifesciencedb.jp/questions/349/%E6%96%B0%E5%9E%8B%E3%82%B7%E3%83%BC%E3%82%B1%E3%83%B3%E3%82%B5%E3%83%BC%E3%81%AE%E7%94%9F%E3%83%87%E3%83%BC%E3%82%BF%E3%82%B5%E3%82%A4%E3%82%BA%E3%81%AF%E3%81%A9%E3%82%93%E3%81%AA%E9%A2%A8%E3%81%A7%E3%81%99%E3%81%8B/375http://qa.lifesciencedb.jp/questions/349/%E6%96%B0%E5%9E%8B%E3%82%B7%E3%83%BC%E3%82%B1%E3%83%B3%E3%82%B5%E3%83%BC%E3%81%AE%E7%94%9F%E3%83%87%E3%83%BC%E3%82%BF%E3%82%B5%E3%82%A4%E3%82%BA%E3%81%AF%E3%81%A9%E3%82%93%E3%81%AA%E9%A2%A8%E3%81%A7%E3%81%99%E3%81%8B/374<table> <thead> <tr> <th> Platform </th> <th> Company </th> <th> Sequencing data per run (single read) </th> <th> 2 Kb – calculated multiplexing for50x coverage </th> <th> 1 Mb – calculatedmultiplexing for 50x coverage </th> </tr> </thead> <tbody> <tr> <th> GS Junior </th> <td> 454 Sequencing </td> <td> 40 MB </td> <td> 400 </td> <td> approx. 1 </td> </tr> <tr> <th> GS FLX </th> <td> 454 Sequencing </td> <td> 540 MB </td> <td> 5,400 </td> <td> 11 </td> </tr> <tr> <th> MiSeq </th> <td> Illumina </td> <td> 510 MB </td> <td> 5,100 </td> <td> 10 </td> </tr> <tr> <th> GA IIx </th> <td> Illumina </td> <td> 48,000 MB </td> <td> 480,000 </td> <td> 960 </td> </tr> <tr> <th> HiSeq2000 </th> <td> Illumina </td> <td> 100,000 MB </td> <td> 1,000,000 </td> <td> 2,000 </td> </tr> <tr> <th> SOLiD4 </th> <td> Life Technologies </td> <td> 150,000 MB </td> <td> 1,500,000 </td> <td> 3,000 </td> </tr> <tr> <th> AB3730xl </th> <td> Life Technologies </td> <td> 0.08 MB </td> <td> – </td> <td> – </td> </tr> </tbody> </table> <p>Table 1: Overview of the amount of data generated from currently available NGS platforms from the three largest competitors (based on manufacturer’s specifications) along with an estimate of thenumber of samples that could theoretically be analyzed during a single sequencing run. Next-generation Sequencing, Application in Molecular Diagnostics, M.Sc Stefan Kotschote et al., IMGM Laboratories 2011 - imgm.com</p>okuboMon, 28 Feb 2011 22:10:05 +0900http://qa.lifesciencedb.jp/questions/349/%E6%96%B0%E5%9E%8B%E3%82%B7%E3%83%BC%E3%82%B1%E3%83%B3%E3%82%B5%E3%83%BC%E3%81%AE%E7%94%9F%E3%83%87%E3%83%BC%E3%82%BF%E3%82%B5%E3%82%A4%E3%82%BA%E3%81%AF%E3%81%A9%E3%82%93%E3%81%AA%E9%A2%A8%E3%81%A7%E3%81%99%E3%81%8B/374http://qa.lifesciencedb.jp/questions/349/%E6%96%B0%E5%9E%8B%E3%82%B7%E3%83%BC%E3%82%B1%E3%83%B3%E3%82%B5%E3%83%BC%E3%81%AE%E7%94%9F%E3%83%87%E3%83%BC%E3%82%BF%E3%82%B5%E3%82%A4%E3%82%BA%E3%81%AF%E3%81%A9%E3%82%93%E3%81%AA%E9%A2%A8%E3%81%A7%E3%81%99%E3%81%8B/367<p><a href="http://">仲里　SRA 目次</a>をみると　次世代といってもいろいろあるのがよくわかります。数値は実験数です。　経時展開できるともっといいんですけどね </p><table> <thead> <tr> <th> Illumina Genome Analyzer II </th> <th> 19786 </th> </tr> </thead> <tbody> <tr> <th> 454 GS FLX </th> <td> 5815 </td> </tr> <tr> <th> Illumina Genome Analyzer </th> <td> 5191 </td> </tr> <tr> <th> Illumina HiSeq 2000 </th> <td> 2873 </td> </tr> <tr> <th> 454 Titanium </th> <td> 2799 </td> </tr> <tr> <th> GS FLX </th> <td> 709 </td> </tr> <tr> <th> unspecified </th> <td> 577 </td> </tr> <tr> <th> Illumina Genome Analyzer IIx </th> <td> 344 </td> </tr> <tr> <th> AB SOLiD System 3.0 </th> <td> 339 </td> </tr> <tr> <th> 454 GS FLX Titanium </th> <td> 309 </td> </tr> <tr> <th> Solexa 1G Genome Analyzer </th> <td> 268 </td> </tr> <tr> <th> AB SOLiD 4 System </th> <td> 265 </td> </tr> <tr> <th> AB SOLiD System 2.0 </th> <td> 198 </td> </tr> <tr> <th> GS 20 </th> <td> 164 </td> </tr> <tr> <th> AB SOLiD System </th> <td> 118 </td> </tr> <tr> <th> 454 GS 20 </th> <td> 118 </td> </tr> <tr> <th> Helicos HeliScope </th> <td> 16 </td> </tr> <tr> <th> 454 GS </th> <td> 11 </td> </tr> <tr> <th> none </th> <td> 5 </td> </tr> <tr> <th> UNKNOWN </th> <td> 5 </td> </tr> <tr> <th> Total </th> <td> 39910 </td> </tr> <tr> <th> (experiments) </th> </tr> </tbody> </table><p></p>okuboSun, 27 Feb 2011 13:32:30 +0900http://qa.lifesciencedb.jp/questions/349/%E6%96%B0%E5%9E%8B%E3%82%B7%E3%83%BC%E3%82%B1%E3%83%B3%E3%82%B5%E3%83%BC%E3%81%AE%E7%94%9F%E3%83%87%E3%83%BC%E3%82%BF%E3%82%B5%E3%82%A4%E3%82%BA%E3%81%AF%E3%81%A9%E3%82%93%E3%81%AA%E9%A2%A8%E3%81%A7%E3%81%99%E3%81%8B/367http://qa.lifesciencedb.jp/questions/349/%E6%96%B0%E5%9E%8B%E3%82%B7%E3%83%BC%E3%82%B1%E3%83%B3%E3%82%B5%E3%83%BC%E3%81%AE%E7%94%9F%E3%83%87%E3%83%BC%E3%82%BF%E3%82%B5%E3%82%A4%E3%82%BA%E3%81%AF%E3%81%A9%E3%82%93%E3%81%AA%E9%A2%A8%E3%81%A7%E3%81%99%E3%81%8B/351<p>HiSeq約100bpくらいのリードの1レーンシングル分(1ファイル)で25~30GB、ペアエンド分(2ファイル)だとその2倍くらいです。1ラン8レーンなので400~480GBくらいでしょうか。</p>naFri, 25 Feb 2011 14:57:45 +0900http://qa.lifesciencedb.jp/questions/349/%E6%96%B0%E5%9E%8B%E3%82%B7%E3%83%BC%E3%82%B1%E3%83%B3%E3%82%B5%E3%83%BC%E3%81%AE%E7%94%9F%E3%83%87%E3%83%BC%E3%82%BF%E3%82%B5%E3%82%A4%E3%82%BA%E3%81%AF%E3%81%A9%E3%82%93%E3%81%AA%E9%A2%A8%E3%81%A7%E3%81%99%E3%81%8B/351