Volume 5 Number 4 (July 2015)
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IJBBB 2015 Vol.5(4): 264-279 ISSN: 2010-3638
doi: 10.17706/ijbbb.2015.5.4.264-279

Systems Genetics of Complex Diseases Using RNA-Sequencing Methods

Gianluca Mazzoni, Lisette J. A. Kogelman, Prashanth Suravajhala, Haja N. Kadarmideen
Abstract—Next generation sequencing technologies have enabled the generation of huge quantities of biological data, and nowadays extensive datasets at different ‘omics levels have been generated. Systems genetics is a powerful approach that allows to integrate different ‘omics level and understand the biological mechanisms behind complex diseases or traits. In the recent past, transcriptomic studies with microarrays have been replaced with the new powerful RNA-seq technologies. This has led to detection of novel gene transcripts, novel regulatory mechanisms, allele specific gene expression and numerous non-coding RNAs (ncRNAs). The integration of transcriptomics data with genomic data in a systems genetics context represents a valuable possibility to go deep into the causal and regulatory mechanisms that generate complex traits and diseases. However RNA-Seq data have to be treated carefully and the choice of the right methodology could have a great impact on the final results. Furthermore the integration of different level is not trivial. Here we give a comprehensive systems genetics overview of the methods and tools for analysis and the integration of RNA-Seq data including ncRNAs. We focused principally on merits and demerits of tools for post mapping quality control, normalization, differential expression analysis, gene network analysis, and integration of different omics data in order to generate a comprehensive guideline to systems genetics analysis using RNA-Seq data.

Index Terms—Quality control, differential expression, network construction, non-coding RNA, data integration.

Department of Veterinary Clinical and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark.

Cite: Gianluca Mazzoni, Lisette J. A. Kogelman, Prashanth Suravajhala, Haja N. Kadarmideen, "Systems Genetics of Complex Diseases Using RNA-Sequencing Methods," International Journal of Bioscience, Biochemistry and Bioinformatics vol. 5, no. 4, pp. 264-279, 2015.

General Information

ISSN: 2010-3638 (Online)
Abbreviated Title: Int. J. Biosci. Biochem. Bioinform.
Frequency: Quarterly 
DOI: 10.17706/IJBBB
Editor-in-Chief: Prof. Ebtisam Heikal 
Abstracting/ Indexing:  Electronic Journals Library, Chemical Abstracts Services (CAS), Engineering & Technology Digital Library, Google Scholar, and ProQuest.
E-mail: ijbbb@iap.org
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