RESUMO
Next-generation sequencing (NGS) platforms allow the analysis of hundreds of millions of molecules in a single sequencing run, revolutionizing many research areas. NGS-based microRNA studies enable expression quantification in unprecedented scale without the limitations of closed-platforms. Yet, whereas a massive amount of data produced by these platforms is available, comparisons of quantification/discovery capabilities between platforms are still lacking. Here we compare two NGS-platforms: SOLiD and PGM, by evaluating their microRNA identification/quantification capabilities using two breast-derived cell-lines. A high expression correlation (R2 > 0.9) was achieved, encompassing 97% of the miRNAs, and the few discrepancies in miRNA counts were attributable to molecules that have very low expression. Quantification divergences indicative of artefactual representation were seen for 14 miRNAs (higher in SOLiD-reads) and another 10 miRNAs more abundant in PGM-data. An inspection of these revealed an increased and statistically significant count of uracyls and uracyl-stretches for PGM-enriched miRNAs, compared to SOLiD and to the miRBase. In parallel, adenines and adenine-stretches were enriched for SOLiDderived miRNA reads. We conclude that, whereas both platforms are overall consistent and can be used interchangeably for microRNA expression studies, particular sequence features appear to be indicative of specific platform bias, and their presence in microRNAs should be considered for database-analyses.
RESUMO
INTRODUCTION: Chronic rhinosinusitis with nasal polyps is a multifactorial disease with a complex pathophysiology involving multiple genetic and environmental factors. OBJECTIVE: The purpose of this work review is to focus on the importance of genetic studies in chronic rhinosinusitis with nasal polyps besides the several barriers that exists for its understanding. METHODS: A systematic review on studies of association between single nucleotide polymorphisms and chronic rhinosinusitis with nasal polyps based on a PubMed/Medline and Periódicos CAPES search of all articles published between January 2005 and January 2015 was made. The search was guided on studies containing the terms polymorphisms, rhinosinusitis, and polyps. RESULTS: Two studies found an association of MMP-9 and MMP-2 polymorphisms and chronic rhinosinusitis with nasal polyps, but not in patients with recurrent nasal polyps. Other studies found an association of nasal polyps with MMP-9 polymorphisms, but not with MMP-2 ones. There is evidence of an association of LTC4S, NOS2A, PTGDR, MET, COX-2, OSF-2, and LF polymorphisms and the risk of developing nasal polyps, especially when combined with chronic allergic rhinitis and asthma. CONCLUSION: Genetic studies on chronic rhinosinusitis with nasal polyps are promising and may offer insights into its pathophysiology, which is likely affected by multiple genetic factors.
Assuntos
Pólipos Nasais/genética , Polimorfismo de Nucleotídeo Único , Rinite/genética , Sinusite/genética , Asma/genética , Asma/fisiopatologia , Doença Crônica , Feminino , Estudos de Associação Genética , Humanos , Masculino , Metaloproteinase 2 da Matriz/genética , Metaloproteinase 9 da Matriz/genética , Pólipos Nasais/fisiopatologia , Rinite/fisiopatologia , Fatores de Risco , Sinusite/fisiopatologiaRESUMO
Abstract Introduction: Chronic rhinosinusitis with nasal polyps is a multifactorial disease with a complex pathophysiology involving multiple genetic and environmental factors. Objective: The purpose of this work review is to focus on the importance of genetic studies in chronic rhinosinusitis with nasal polyps besides the several barriers that exists for its understanding. Methods: A systematic review on studies of association between single nucleotide polymorphisms and chronic rhinosinusitis with nasal polyps based on a PubMed/Medline and Periódicos CAPES search of all articles published between January 2005 and January 2015 was made. The search was guided on studies containing the terms polymorphisms, rhinosinusitis, and polyps. Results: Two studies found an association of MMP-9 and MMP-2 polymorphisms and chronic rhinosinusitis with nasal polyps, but not in patients with recurrent nasal polyps. Other studies found an association of nasal polyps with MMP-9 polymorphisms, but not with MMP-2 ones. There is evidence of an association of LTC4S, NOS2A, PTGDR, MET, COX-2, OSF-2, and LF polymorphisms and the risk of developing nasal polyps, especially when combined with chronic allergic rhinitis and asthma. Conclusion: Genetic studies on chronic rhinosinusitis with nasal polyps are promising and may offer insights into its pathophysiology, which is likely affected by multiple genetic factors.
Resumo Introdução: A rinossinusite crônica com pólipos nasais é uma doença multifatorial com uma fisiopatologia complexa envolvendo múltiplos fatores genéticos e ambientais. Objetivo: O objetivo deste trabalho é enfatizar a importância dos estudos genéticos na rinossinusite crônica com pólipos nasais, além das diversas barreiras existentes para sua compreensão. Método: Realizou-se uma revisão sistemática de estudos de associação entre polimorfismos de nucleotídeo único e rinossinusite crônica com pólipos nasais com base em uma busca feita nos bancos de dados PubMed/Medline e Periódicos CAPES de todos os artigos publicados entre janeiro de 2005 e janeiro de 2015. A busca foi direcionada à estudos contendo os termos polimorfismos, rinossinusite e pólipos. Resultados: Dois estudos encontraram uma associação entre os polimorfismos MMP-9 e MMP-2 e rinossinusite crônica com pólipos nasais, mas não em pacientes com pólipos nasais recorrentes. Outros estudos encontraram uma associação de pólipos nasais com polimorfismos MMP-9, mas não com MMP-2. Existem evidências de uma associação dos polimorfismos LTC4S, NOS2A, PTGDR, MET, COX-2, OSF-2 e LF e o risco de desenvolver pólipos nasais, especialmente quando combinados com rinite alérgica crônica e asma. Conclusão: Estudos genéticos sobre rinossinusite crônica com pólipos nasais são promissores e podem oferecer conhecimento sobre sua fisiopatologia, que é provavelmente afetada por múltiplos fatores genéticos.