title: Use of RNA sequencing to evaluate rheumatic disease patients.
abstract: Studying the factors that control gene expression is of substantial importance for rheumatic diseases with poorly understood etiopathogenesis. In the past, gene expression microarrays have been used to measure transcript abundance on a genome-wide scale in a particular cell, tissue or organ. Microarray analysis has led to gene signatures that differentiate rheumatic diseases, and stages of a disease, as well as response to treatments. Nowadays, however, with the advent of next-generation sequencing methods, massive parallel sequencing of RNA tends to be the technology of choice for gene expression profiling, due to several advantages over microarrays, as well as for the detection of non-coding transcripts and alternative splicing events. In this review, we describe how RNA sequencing enables unbiased interrogation of the abundance and complexity of the transcriptome, and present a typical experimental workflow and bioinformatics tools that are often used for RNA sequencing analysis. We also discuss different uses of this next-generation sequencing technology to evaluate rheumatic disease patients and investigate the pathogenesis of rheumatic diseases such as rheumatoid arthritis, systemic lupus erythematosus, juvenile idiopathic arthritis and Sjögren's syndrome.
authors.affiliation: Biological Sciences Department, New York City College of Technology, City University of New York, New York, NY, 11201, USA. egiannopoulou@citytech.cuny.edu.|Arthritis and Tissue Degeneration Program and the David Z Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, 10021, USA. egiannopoulou@citytech.cuny.edu.
authors.forename: Eugenia G
authors.initials: EG
authors.lastname: Giannopoulou
authors.affiliation: HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine and Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, 10021, USA. ole2001@med.cornell.edu.
authors.forename: Olivier
authors.initials: O
authors.lastname: Elemento
authors.affiliation: Arthritis and Tissue Degeneration Program and the David Z Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, 10021, USA. ivashkivl@hss.edu.
authors.forename: Lionel B
authors.initials: LB
authors.lastname: Ivashkiv
mesh_terms: D020869:Gene Expression Profiling / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D012216:Rheumatic Diseases / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*