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Giovannetti A, Bianco SD, Traversa A, Panzironi N, Bruselles A, Lazzari S, Liorni N, Tartaglia M, Carella M, Pizzuti A, Mazza T, Caputo V. MiRLog and dbmiR: prioritization and functional annotation tools to study human microRNA sequence variants. Hum Mutat 2022; 43:1201-1215. [PMID: 35583122 PMCID: PMC9546175 DOI: 10.1002/humu.24399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 05/03/2022] [Accepted: 05/11/2022] [Indexed: 11/22/2022]
Abstract
The recent identification of noncoding variants with pathogenic effects suggests that these variations could underlie a significant number of undiagnosed cases. Several computational methods have been developed to predict the functional impact of noncoding variants, but they exhibit only partial concordance and are not integrated with functional annotation resources, making the interpretation of these variants still challenging. MicroRNAs (miRNAs) are small noncoding RNA molecules that act as fine regulators of gene expression and play crucial functions in several biological processes, such as cell proliferation and differentiation. An increasing number of studies demonstrate a significant impact of miRNA single nucleotide variants (SNVs) both in Mendelian diseases and complex traits. To predict the functional effect of miRNA SNVs, we implemented a new meta‐predictor, MiRLog, and we integrated it into a comprehensive database, dbmiR, which includes a precompiled list of all possible miRNA allelic SNVs, providing their biological annotations at nucleotide and miRNA levels. MiRLog and dbmiR were used to explore the genetic variability of miRNAs in 15,708 human genomes included in the gnomAD project, finding several ultra‐rare SNVs with a potentially deleterious effect on miRNA biogenesis and function representing putative contributors to human phenotypes.
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Affiliation(s)
- Agnese Giovannetti
- Laboratory of Clinical Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Salvatore Daniele Bianco
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy.,Unit of Bioinformatics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Alice Traversa
- Laboratory of Clinical Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Noemi Panzironi
- Laboratory of Clinical Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Alessandro Bruselles
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Sara Lazzari
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Niccolò Liorni
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy.,Unit of Bioinformatics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Massimo Carella
- Medical Genetics Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Antonio Pizzuti
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Tommaso Mazza
- Unit of Bioinformatics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Viviana Caputo
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
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