Next-generation sequencing identifies novel microRNAs in peripheral blood of lung cancer patients

Molecular BioSystems

Volumn 7, Issue 12, 2011, Pages 3187-3199

  Keller, Andreas ^a,b,c   Backes, Christina ^a,b   Leidinger, Petra ^b   Kefer, Nathalie ^a   Boisguerin, Valesca ^a   Barbacioru, Catalin ^d   Vogel, Britta ^e   Matzas, Mark ^a   Huwer, Hanno ^f   Katus, Hugo A ^e   Stähler, Cord ^a,c   Meder, Benjamin ^e   Meese, Eckart ^b  

^a Biomarker Discovery Center Heidelberg   (Germany)

^b SAARLAND UNIVERSITY   (Germany)

^c SIEMENS AG   (Germany)

^d Life Technologies Corporation   (United States)

^e UNIVERSITY OF HEIDELBERG   (Germany)

^f Voelklingen Heart Center   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; TRANSCRIPTOME; TUMOR MARKER;

ADULT; AGED; ARTICLE; BLOOD; FEMALE; GENE EXPRESSION PROFILING; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; LUNG TUMOR; MALE; METHODOLOGY; MIDDLE AGED; NUCLEOTIDE SEQUENCE; SEQUENCE ANALYSIS;

ADULT; AGED; BASE SEQUENCE; FEMALE; GENE EXPRESSION PROFILING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; LUNG NEOPLASMS; MALE; MICRORNAS; MIDDLE AGED; SEQUENCE ANALYSIS, RNA; TRANSCRIPTOME; TUMOR MARKERS, BIOLOGICAL;

EID: 80755147170     PISSN: 1742206X     EISSN: 17422051     Source Type: Journal    
DOI: 10.1039/c1mb05353a     Document Type: Article

References (38)

1. B. Meder et al., MicroRNA signatures in total peripheral blood as novel biomarkers for acute myocardial infarction Basic Res. Cardiol. 2011 106 1 13 23
2. P. Leidinger et al., High-throughput miRNA profiling of human melanoma blood samples BMC Cancer 2010 10 262
3. A. Keller et al., Multiple sclerosis: microRNA expression profiles accurately differentiate patients with relapsing-remitting disease from healthy controls PLoS One 2009 4 10 e7440
4. A. Keller et al., miRNAs in lung cancer - studying complex fingerprints in patient's blood cells by microarray experiments BMC Cancer 2009 9 353
5. S. F. Hausler et al., Whole blood-derived miRNA profiles as potential new tools for ovarian cancer screening Br. J. Cancer 103 5 693 700
6. A. Keller et al., Toward the blood-borne miRNome of human diseases Nat. Methods 2011 8 10 841 843
7. Z. Hu et al., Serum microRNA signatures identified in a genome-wide serum microRNA expression profiling predict survival of non-small-cell lung cancer J. Clin. Oncol. 2010 28 10 1721 1726
8. C. Zhang et al., Expression profile of MicroRNAs in serum: A fingerprint for esophageal squamous cell carcinoma Clin. Chem. 2010 56 12 1871 1879
9. R. Liu et al., A five-microRNA signature identified from genome-wide serum microRNA expression profiling serves as a fingerprint for gastric cancer diagnosis Eur. J. Cancer 2011 47 5 784 791
10. L. M. Li et al., Serum microRNA profiles serve as novel biomarkers for HBV infection and diagnosis of HBV-positive hepatocarcinoma Cancer Res. 2010 70 23 9798 9807
11. Q. Ge et al., Sequencing circulating miRNA in maternal plasma with modified library preparation Clin. Chim. Acta 2011 412 21-22 1989 1994
12. S. S. Luo et al., Human villous trophoblasts express and secrete placenta-specific microRNAs into maternal circulation via exosomes Biol. Reprod. 2009 81 4 717 729
13. C. Vaz et al., Analysis of microRNA transcriptome by deep sequencing of small RNA libraries of peripheral blood BMC Genomics 2010 11 288
14. S. Griffiths-Jones miRBase: the microRNA sequence database Methods Mol. Biol. 2006 342 129 138
15. S. Griffiths-Jones et al., miRBase: tools for microRNA genomics Nucleic Acids Res. 2008 36 database issue D154 D158 (Pubitemid 351149713)
16. S. Griffiths-Jones et al., miRBase: microRNA sequences, targets and gene nomenclature Nucleic Acids Res. 2006 34 database issue D140 D144
17. M. R. Friedlander et al., Discovering microRNAs from deep sequencing data using miRDeep Nat. Biotechnol. 2008 26 4 407 415 (Pubitemid 351501815)
18. L. A. Goff et al., Ago2 immunoprecipitation identifies predicted microRNAs in human embryonic stem cells and neural precursors PLoS One 2009 4 9 e7192
19. E. Bonnet et al., Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences Bioinformatics 2004 20 17 2911 2917 (Pubitemid 39619182)
20. S. F. Altschul et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 1997 25 17 3389 3402 (Pubitemid 27359211)
21. L. Lestrade M. J. Weber et al., snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs Nucleic Acids Res. 2006 34 database issue D158 D162
22. C. Liu et al., NONCODE: an integrated knowledge database of non-coding RNAs Nucleic Acids Res. 2005 33 database issue D112 D115 (Pubitemid 40207841)
23. R. Team, R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing, Vienna, 2008
24. A. J. Enright et al., MicroRNA targets in Drosophila GenomeBiology 2003 5 1 R1
25. A. Keller et al., GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments BMC Bioinformatics 2008 9 552
26. C. Backes et al., GeneTrail - advanced gene set enrichment analysis Nucleic Acids Res. 2007 35 W186 W192
27. B. John et al., Human MicroRNA targets PLoS Biol. 2004 2 11 e363
28. D. Karolchik et al., The UCSC Table Browser data retrieval tool Nucleic Acids Res. 2004 32 database issue D493 D496 (Pubitemid 38081706)
29. P. Roth et al., A specific miRNA signature in the peripheral blood of glioblastoma patients J. Neurochem. 2011 118 3 449 457
30. M. Kanehisa S. Goto KEGG: kyoto encyclopedia of genes and genomes Nucleic Acids Res. 2000 28 1 27 30 (Pubitemid 30047706)
31. C. Backes et al., A dictionary on microRNAs and their putative target pathways Nucleic Acids Res. 2010 38 13 4476 4486
32. T. Babak et al., Probing microRNAs with microarrays: tissue specificity and functional inference RNA 2004 10 11 1813 1819 (Pubitemid 39426380)
33. J. Lu et al., MicroRNA expression profiles classify human cancers Nature 2005 435 7043 834 838 (Pubitemid 40839735)
34. T. A. Fehniger et al., Next-generation sequencing identifies the natural killer cell microRNA transcriptome Genome Res. 20 11 1590 1604
35. X. Chen et al., Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases Cell Res. 2008 18 10 997 1006
36. N. Hooten et al., microRNA expression patterns reveal differential expression of target genes with age PLoS One 5 5 e10724
37. T. Tomankova M. Petrek E. Kriegova Involvement of microRNAs in physiological and pathological processes in the lung Respir. Res. 11 159
38. F. Schembri et al., MicroRNAs as modulators of smoking-induced gene expression changes in human airway epithelium Proc. Natl. Acad. Sci. U. S. A. 2009 106 7 2319 2324