Transcriptome sequencing of the Microarray Quality Control (MAQC) RNA reference samples using next generation sequencing

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• 作者：Shrinivasrao P Mane (1)
  Clive Evans (1)
  Kristal L Cooper (1)
  Oswald R Crasta (1)
  Otto Folkerts (1)
  Stephen K Hutchison (2)
  Timothy T Harkins (3)
  Danielle Thierry-Mieg (4)
  Jean Thierry-Mieg (4)
  Roderick V Jensen (5)
  
• 刊名：BMC Genomics
• 出版年：2009
• 出版时间：December 2009
• 年：2009
• 卷：10
• 期：1
• 全文大小：537KB
• 参考文献：1. Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, Baker SC, Collins PJ, de Longueville F, Kawasaki ES, Lee KY, / et al.: The MicroArray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements. / Nature Biotech 2006,24(9):1151-161. CrossRef
  2. Canales RD, Luo Y, Willey JC, Austermiller B, Barbacioru CC, Boysen C, Hunkapiller K, Jensen RV, Knight CR, Lee KY, / et al.: Evaluation of DNA microarray results with quantitative gene expression platforms. / Nature Biotech 2006,24(9):1115-122. CrossRef
  3. Wold B, Myers RM: Sequence census methods for functional genomics. / Nature Methods 2008, 5:19-1. CrossRef
  4. Shendure J: The beginning of the end for microarrays? / Nature Methods 2008,5(7):585-87. CrossRef
  5. Bainbridge MN, Warren RL, Hirst M, Romanuik T, Zeng T, Go A, Delaney A, Griffith M, Hickenbotham M, Magrini V, / et al.: Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach. / BMC Genomics 2006, 7:246. CrossRef
  6. Emrich SJ, Barbazuk WB, Li L, Schnable PS: Gene discovery and annotation using LCM-54 transcriptome sequencing. / Genome Res 2007,17(1):69-3. CrossRef
  7. Weber AP, Weber KL, Carr K, Wilkerson C, Ohlrogge JB: Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing. / Plant Physiology 2007,144(1):32-2. CrossRef
  8. Sugarbaker DJ, Richards WG, Gordon GJ, Dong L, De Rienzo A, Maulik G, Glickman JN, Chirieac LR, Hartman ML, Taillon BE, / et al.: Transcriptome sequencing of malignant pleural mesothelioma tumors. / Proc Natl Acad Sci USA 2008,105(9):3521-526. CrossRef
  9. Mao C, Evans C, Jensen RV, Sobral BW: Identification of new genes in Sinorhizobium meliloti using the Genome Sequencer FLX system. / BMC Microbiol 2008, 8:72. CrossRef
  10. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M: The transcriptional landscape of the yeast genome defined by RNA sequencing. / Science 2008,320(5881):1344-349. CrossRef
  11. Wilhelm BT, Marguerat S, Watt S, Schubert F, Wood V, Goodhead I, Penkett CJ, Rogers J, Bahler J: Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. / Nature 2008,453(7199):1239-243. CrossRef
  12. Cloonan N, Forrest AR, Kolle G, Gardiner BB, Faulkner GJ, Brown MK, Taylor DF, Steptoe AL, Wani S, Bethel G, / et al.: Stem cell transcriptome profiling via massive-scale mRNA sequencing. / Nature Methods 2008,5(7):613-19. CrossRef
  13. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B: Mapping and quantifying mammalian transcriptomes by RNA-Seq. / Nat Methods 2008,5(7):621-28. CrossRef
  14. Rosenkranz R, Borodina T, Lehrach H, Himmelbauer H: Characterizing the mouse ES cell transcriptome with Illumina sequencing. / Genomics 2008,92(4):187-94. CrossRef
  15. Morin R, Bainbridge M, Fejes A, Hirst M, Krzywinski M, Pugh T, McDonald H, Varhol R, Jones S, Marra M: Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. / Biotechniques 2008,45(1):81-4. CrossRef
  16. Mudge J, Miller NA, Khrebtukova I, Lindquist IE, May GD, Huntley JJ, Luo S, Zhang L, van Velkinburgh JC, Farmer AD, / et al.: Genomic convergence analysis of schizophrenia: mRNA sequencing reveals altered synaptic vesicular transport in post-mortem cerebellum. / PLoS ONE 2008,3(11):e3625. CrossRef
  17. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, / et al.: Genome sequencing in microfabricated high-density picolitre reactors. / Nature 2005,437(7057):376-80.
  18. Thierry-Mieg D, Thierry-Mieg J: AceView: a comprehensive cDNA-supported gene and transcripts annotation. / Genome Biology 2006.,7(Suppl 1): S12 11-4
  19. McClintick JN, Edenberg HJ: Effects of filtering by Present call on analysis of microarray experiments. / BMC Bioinformatics 2006, 7:49. CrossRef
  20. Graveley BR: Power Sequencing. / Nature 2008, 453:1197-198. CrossRef
  21. Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, Scherf M, Seifert M, Borodina T, Soldatov A, Parkhomchuk D, / et al.: A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. / Science 2008,321(5891):956-60. CrossRef
  22. Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ: Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. / Nat Genet 2008,40(12):1413-415. CrossRef
  23. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB: Alternative isoform regulation in human tissue transcriptomes. / Nature 2008,456(7221):470-76. CrossRef
  24. Salehi-Ashtiani K, Yang X, Derti A, Tian W, Hao T, Lin C, Makowski K, Shen L, Murray RR, Szeto D, / et al.: Isoform discovery by targeted cloning, 'deep-well' pooling and parallel sequencing. / Nat Methods 2008,5(7):597-00. CrossRef
  25. Harris TD, Buzby PR, Babcock H, Beer E, Bowers J, Braslavsky I, Causey M, Colonell J, Dimeo J, Efcavitch JW, / et al.: Single-molecule DNA sequencing of a viral genome. / Science 2008,320(5872):106-09. CrossRef
  26. Lundquist PM, Zhong CF, Zhao P, Tomaney AB, Peluso PS, Dixon J, Bettman B, Lacroix Y, Kwo DP, McCullough E, / et al.: Parallel confocal detection of single molecules in real time. / Opt Lett 2008,33(9):1026-028. CrossRef
  27. Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM, Wang MD, Zhang K, Mitra RD, Church GM: Accurate multiplex polony sequencing of an evolved bacterial genome. / Science 2005,309(5741):1728-732. CrossRef
  28. Denoeud F, Aury JM, Da Silva C, Noel B, Rogier O, Delledonne M, Morgante M, Valle G, Wincker P, Scarpelli C, / et al.: Annotating genomes with massive-scale RNA sequencing. / Genome Biol 2008,9(12):R175. CrossRef
  29. Bemmo A, Benovoy D, Kwan T, Gaffney DJ, Jensen RV, Majewski J: Gene Expression and Isoform Variation Analysis using Affymetrix Exon Arrays. / BMC Genomics 2008,9(1):529. CrossRef
  
• 作者单位：Shrinivasrao P Mane (1)
  Clive Evans (1)
  Kristal L Cooper (1)
  Oswald R Crasta (1)
  Otto Folkerts (1)
  Stephen K Hutchison (2)
  Timothy T Harkins (3)
  Danielle Thierry-Mieg (4)
  Jean Thierry-Mieg (4)
  Roderick V Jensen (5)
  
  1. Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, 24061, USA
  2. 454 Life Sciences, Inc., 20 Commercial Street, Branford, CT, 06405, USA
  3. Roche Applied Science, Indianapolis, IN, 46250, USA
  4. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, USA
  5. Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
  

文摘

Background Transcriptome sequencing using next-generation sequencing platforms will soon be competing with DNA microarray technologies for global gene expression analysis. As a preliminary evaluation of these promising technologies, we performed deep sequencing of cDNA synthesized from the Microarray Quality Control (MAQC) reference RNA samples using Roche's 454 Genome Sequencer FLX. Results We generated more that 3.6 million sequence reads of average length 250 bp for the MAQC A and B samples and introduced a data analysis pipeline for translating cDNA read counts into gene expression levels. Using BLAST, 90% of the reads mapped to the human genome and 64% of the reads mapped to the RefSeq database of well annotated genes with e-values ?10-20. We measured gene expression levels in the A and B samples by counting the numbers of reads that mapped to individual RefSeq genes in multiple sequencing runs to evaluate the MAQC quality metrics for reproducibility, sensitivity, specificity, and accuracy and compared the results with DNA microarrays and Quantitative RT-PCR (QRTPCR) from the MAQC studies. In addition, 88% of the reads were successfully aligned directly to the human genome using the AceView alignment programs with an average 90% sequence similarity to identify 137,899 unique exon junctions, including 22,193 new exon junctions not yet contained in the RefSeq database. Conclusion Using the MAQC metrics for evaluating the performance of gene expression platforms, the ExpressSeq results for gene expression levels showed excellent reproducibility, sensitivity, and specificity that improved systematically with increasing shotgun sequencing depth, and quantitative accuracy that was comparable to DNA microarrays and QRTPCR. In addition, a careful mapping of the reads to the genome using the AceView alignment programs shed new light on the complexity of the human transcriptome including the discovery of thousands of new splice variants.