title: Prioritizing and selecting likely novel miRNAs from NGS data.
abstract: Small non-coding RNAs play a key role in many physiological and pathological processes. Since 2004, miRNA sequences have been catalogued in miRBase, which is currently in its 21st version. We investigated sequence and structural features of miRNAs annotated in the miRBase and compared them between different versions of this reference database. We have identified that the two most recent releases (v20 and v21) are influenced by next-generation sequencing based miRNA predictions and show significant deviation from miRNAs discovered prior to the high-throughput profiling period. From the analysis of miRBase, we derived a set of key characteristics to predict new miRNAs and applied the implemented algorithm to evaluate novel blood-borne miRNA candidates. We carried out 705 individual whole miRNA sequencings of blood cells and collected a total of 9.7 billion reads. Using miRDeep2 we initially predicted 1452 potentially novel miRNAs. After excluding false positives, 518 candidates remained. These novel candidates were ranked according to their distance to the features in the early miRBase versions allowing for an easier selection of a subset of putative miRNAs for validation. Selected candidates were successfully validated by qRT-PCR and northern blotting. In addition, we implemented a web-server for ranking potential miRNA candidates, which is available at:www.ccb.uni-saarland.de/novomirank.
authors.affiliation: Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany.
authors.forename: Christina
authors.initials: C
authors.lastname: Backes
authors.affiliation: Internal Medicine II, University Hospital Heidelberg, Heidelberg, Germany.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Meder
authors.affiliation: Department of Human Genetics, Saarland University, Homburg, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Hart
authors.affiliation: Department of Human Genetics, Saarland University, Homburg, Germany.
authors.forename: Nicole
authors.initials: N
authors.lastname: Ludwig
authors.affiliation: Department of Human Genetics, Saarland University, Homburg, Germany.
authors.forename: Petra
authors.initials: P
authors.lastname: Leidinger
authors.affiliation: Internal Medicine II, University Hospital Heidelberg, Heidelberg, Germany.
authors.forename: Britta
authors.initials: B
authors.lastname: Vogel
authors.affiliation: Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany.
authors.forename: Valentina
authors.initials: V
authors.lastname: Galata
authors.affiliation: University Hospital Zurich, Department of Neurology and University of Zurich, Switzerland.
authors.forename: Patrick
authors.initials: P
authors.lastname: Roth
authors.affiliation: Department of Virology, Saarland University Medical School, Homburg, Germany.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Menegatti
authors.affiliation: Department of Virology, Saarland University Medical School, Homburg, Germany.
authors.forename: Friedrich
authors.initials: F
authors.lastname: Grässer
authors.affiliation: Department of Neurology, Charité Universitätsmedizin Berlin, Germany.
authors.forename: Klemens
authors.initials: K
authors.lastname: Ruprecht
authors.affiliation: Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany.
authors.forename: Mustafa
authors.initials: M
authors.lastname: Kahraman
authors.affiliation: Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Grossmann
authors.affiliation: Internal Medicine II, University Hospital Heidelberg, Heidelberg, Germany.
authors.forename: Jan
authors.initials: J
authors.lastname: Haas
authors.affiliation: Department of Human Genetics, Saarland University, Homburg, Germany.
authors.forename: Eckart
authors.initials: E
authors.lastname: Meese
authors.affiliation: Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany andreas.keller@ccb.uni-saarland.de.
authors.forename: Andreas
authors.initials: A
authors.lastname: Keller
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D001773:Blood Cells / Q000737:chemistry / Q000378:metabolism; D015152:Blotting, Northern; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D035683:MicroRNAs / Q000097:blood / Q000235:genetics*; D008969:Molecular Sequence Data; D060888:Real-Time Polymerase Chain Reaction; D017423:Sequence Analysis, RNA / Q000706:statistics & numerical data*; D012984:Software; D059467:Transcriptome
chemical_list: D035683:MicroRNAs