title: Ultra-high throughput sequencing-based small RNA discovery and discrete statistical biomarker analysis in a collection of cervical tumours and matched controls.
abstract: BACKGROUND
  Ultra-high throughput sequencing technologies provide opportunities both for discovery of novel molecular species and for detailed comparisons of gene expression patterns. Small RNA populations are particularly well suited to this analysis, as many different small RNAs can be completely sequenced in a single instrument run.
  
  
  RESULTS
  We prepared small RNA libraries from 29 tumour/normal pairs of human cervical tissue samples. Analysis of the resulting sequences (42 million in total) defined 64 new human microRNA (miRNA) genes. Both arms of the hairpin precursor were observed in twenty-three of the newly identified miRNA candidates. We tested several computational approaches for the analysis of class differences between high throughput sequencing datasets and describe a novel application of a log linear model that has provided the most effective analysis for this data. This method resulted in the identification of 67 miRNAs that were differentially-expressed between the tumour and normal samples at a false discovery rate less than 0.001.
  
  
  CONCLUSIONS
  This approach can potentially be applied to any kind of RNA sequencing data for analysing differential sequence representation between biological sample sets.
authors.affiliation: Department of Statistics, Stanford University, Stanford, California 94305-4065, USA.
authors.forename: Daniela
authors.initials: D
authors.lastname: Witten
authors.forename: Robert
authors.initials: R
authors.lastname: Tibshirani
authors.forename: Sam Guoping
authors.initials: SG
authors.lastname: Gu
authors.forename: Andrew
authors.initials: A
authors.lastname: Fire
authors.forename: Weng-Onn
authors.initials: WO
authors.lastname: Lui
mesh_terms: D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D018076:DNA, Complementary / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D015723:Gene Library; D016014:Linear Models; D035683:MicroRNAs / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D018076:DNA, Complementary; D035683:MicroRNAs
references.citation: Science. 2001 Oct 26;294(5543):862-4
references.pmid: 11679672
references.citation: Nature. 2000 Feb 24;403(6772):901-6
references.pmid: 10706289
references.citation: Cell. 2003 Apr 4;113(1):25-36
references.pmid: 12679032
references.citation: Nat Biotechnol. 2008 Apr;26(4):407-15
references.pmid: 18392026
references.citation: PLoS One. 2007 Oct 10;2(10):e1020
references.pmid: 17925868
references.citation: Br J Cancer. 2009 Mar 24;100(6):1002-11
references.pmid: 19293812
references.citation: Cell. 2007 Jun 29;129(7):1401-14
references.pmid: 17604727
references.citation: Clin Chem. 2008 Oct;54(10):1696-704
references.pmid: 18719201
references.citation: Nature. 2006 Jul 13;442(7099):199-202
references.pmid: 16751776
references.citation: Nature. 2008 Jun 5;453(7196):803-6
references.pmid: 18463630
references.citation: Nat Struct Mol Biol. 2006 Dec;13(12):1097-101
references.pmid: 17099701
references.citation: J Cell Sci. 2002 Dec 15;115(Pt 24):4891-900
references.pmid: 12432076
references.citation: Nature. 2003 Dec 18;426(6968):845-9
references.pmid: 14685240
references.citation: Nat Rev Genet. 2007 Nov;8(11):884-96
references.pmid: 17943195
references.citation: Plant Cell Physiol. 2008 Apr;49(4):493-500
references.pmid: 18344228
references.citation: Science. 2008 May 23;320(5879):1023-4
references.pmid: 18467555
references.citation: Cancer Res. 2005 Aug 15;65(16):7065-70
references.pmid: 16103053
references.citation: Genes Dev. 2008 Jan 1;22(1):26-36
references.pmid: 18172163
references.citation: Nat Med. 1995 Jun;1(6):578-82
references.pmid: 7585126
references.citation: Genome Res. 2008 Jun;18(6):957-64
references.pmid: 18469162
references.citation: Cell. 2008 Apr 4;133(1):116-27
references.pmid: 18342361
references.citation: Nature. 2007 Jul 5;448(7149):83-6
references.pmid: 17589500
references.citation: Nat Methods. 2005 Apr;2(4):269-76
references.pmid: 15782219
references.citation: Nat Struct Mol Biol. 2008 Apr;15(4):354-63
references.pmid: 18376413
references.citation: Nat Rev Mol Cell Biol. 2008 Mar;9(3):219-30
references.pmid: 18270516
references.citation: Mol Cancer Res. 2003 Oct;1(12):882-91
references.pmid: 14573789
references.citation: Genome Biol. 2006;7(4):R27
references.pmid: 16594986
references.citation: Cancer Res. 2007 Sep 15;67(18):8699-707
references.pmid: 17875710
references.citation: Nature. 2006 Jul 13;442(7099):203-7
references.pmid: 16751777
references.citation: Genome Res. 2008 Apr;18(4):610-21
references.pmid: 18285502
references.citation: Curr Biol. 2003 Apr 29;13(9):790-5
references.pmid: 12725740
references.citation: Science. 2001 Oct 26;294(5543):853-8
references.pmid: 11679670
references.citation: Cell. 1993 Dec 3;75(5):843-54
references.pmid: 8252621
references.citation: Urol Oncol. 2007 Sep-Oct;25(5):387-92
references.pmid: 17826655
references.citation: Science. 2006 Jul 21;313(5785):363-7
references.pmid: 16778019
references.citation: Cancer Res. 2008 Oct 1;68(19):7846-54
references.pmid: 18829540
references.citation: Cell. 1993 Dec 3;75(5):855-62
references.pmid: 8252622
references.citation: Mol Cell. 2007 Mar 23;25(6):792-3
references.pmid: 17386255
references.citation: Proc Natl Acad Sci U S A. 2002 May 14;99(10):6567-72
references.pmid: 12011421
references.citation: EMBO Rep. 2008 Jun;9(6):582-9
references.pmid: 18483486
references.citation: Nucleic Acids Res. 2003 Jul 1;31(13):3406-15
references.pmid: 12824337
references.citation: Genes Dev. 2008 Apr 1;22(7):894-907
references.pmid: 18381893
references.citation: PLoS One. 2008 Jul 02;3(7):e2557
references.pmid: 18596939
references.citation: Genes Dev. 2008 Jan 1;22(1):8-13
references.pmid: 18172160
references.citation: RNA. 2005 Mar;11(3):241-7
references.pmid: 15701730
references.citation: Science. 2001 Oct 26;294(5543):858-62
references.pmid: 11679671
references.citation: Int J Cancer. 2009 Mar 15;124(6):1358-65
references.pmid: 19065659
references.citation: Oncogene. 2008 Apr 17;27(18):2575-82
references.pmid: 17998940
references.citation: Proc Natl Acad Sci U S A. 2008 Jun 10;105(23):7964-9
references.pmid: 18524951
references.citation: Transl Oncol. 2008 Dec;1(4):202-8
references.pmid: 19043531
references.citation: Cell. 2007 Jul 13;130(1):89-100
references.pmid: 17599402
references.citation: Science. 2007 Feb 23;315(5815):1137-40
references.pmid: 17322061
references.citation: Cancer Res. 2007 Jul 1;67(13):6031-43
references.pmid: 17616659
references.citation: Mol Cell. 2007 Oct 26;28(2):328-36
references.pmid: 17964270
references.citation: Methods. 2008 Jan;44(1):13-21
references.pmid: 18158128
references.citation: Proc Natl Acad Sci U S A. 2008 Dec 9;105(49):19300-5
references.pmid: 19033458
references.citation: PLoS One. 2008;3(10):e3420
references.pmid: 18923704
references.citation: Nature. 2008 Jun 5;453(7196):793-7
references.pmid: 18463636
references.citation: Nature. 2008 Jun 5;453(7196):798-802
references.pmid: 18463631
references.citation: Nucleic Acids Res. 2009 Apr;37(5):1672-81
references.pmid: 19153141
references.citation: Nat Cell Biol. 2008 May;10(5):593-601
references.pmid: 18376396
references.citation: Science. 1999 Oct 29;286(5441):950-2
references.pmid: 10542148
references.citation: Science. 2007 Jan 12;315(5809):241-4
references.pmid: 17124291
references.citation: PLoS One. 2009;4(4):e5311
references.pmid: 19390579
references.citation: Proc Natl Acad Sci U S A. 1996 Jan 9;93(1):479-84
references.pmid: 8552665
references.citation: Cancer Genet Cytogenet. 2001 Nov;131(1):48-53
references.pmid: 11734318
references.citation: Clin Cancer Res. 2008 May 1;14(9):2535-42
references.pmid: 18451214
references.citation: J Biol Chem. 2008 May 30;283(22):14910-4
references.pmid: 18411277
references.citation: Genes Dev. 2008 Jan 1;22(1):14-9
references.pmid: 18172161
references.citation: Genome Res. 2008 Nov;18(11):1787-97
references.pmid: 18849523
references.citation: Genes Chromosomes Cancer. 2007 Apr;46(4):373-84
references.pmid: 17243165
references.citation: Nature. 2008 May 22;453(7194):539-43
references.pmid: 18404146
references.citation: Gene. 2003 May 8;309(2):65-70
references.pmid: 12758122