RNA‐Seq and Human Complex Disease


The Human Genome Project and next‐generation sequencing technologies contributed to identify disease‐causing mutations in Mendelian disorders and susceptibility loci in complex disease. Despite the progresses, studying multifactorial diseases still remains a challenge. Most of the genome‐wide association studies have not explained the causative role of nucleotide variations in complex diseases, and several polymorphisms so far identified have been shown to affect gene expression and alternative splicing. It has highlighted the importance of studying the transcriptome in the context of these diseases.

Ribonucleic acid (RNA)‐sequencing is providing an unprecedented opportunity to quantify in a single experiment – other than gene expression levels – the extent of alternative splicing and allele‐specific expression, as well as to identify novel genes, splice isoforms, chimaeric transcripts, and to investigate noncoding RNAs.

Here, the authors describe the advantages of using RNA‐Seq to study human complex diseases, paying attention to metabolic–cardiovascular disorders, neurodegenerative and neuropsychiatric diseases, and cancer.

Key Concepts:

  • Complex diseases are caused by intricate molecular interactions, involving both genetic and environmental factors. Their aetiology remains mostly unknown.

  • The causative role of single‐nucleotide polymorphisms and of other DNA variations to complex disease susceptibility has not yet been provided.

  • Most of GWAS‐associated SNPs fall in regulatory regions and directly affect gene expression levels and alternative splicing.

  • Transcriptome analysis is emerging as a promising approach to understand the impact of nucleotide variations on gene expression levels and splicing in the diseases' aetiology.

  • RNA‐Seq allows the precise quantification of expression levels of known genes, the identification of novel coding and noncoding transcripts as well as alternative splice isoforms and chimeric transcripts.

  • RNA‐Seq – based on high‐throughput sequencing – overcomes many microarray's drawbacks and represents a promising tool for transcriptomic studies.

  • Whole‐transcriptome analysis by RNA‐Seq is revealing a powerful approach to study complex diseases.

Keywords: RNA‐sequencing; complex diseases; transcriptome; gene expression; next‐generation sequencing

Figure 1.

A schematic representation of a typical RNA‐Seq experiment.

Figure 2.

Examples of RNA‐Seq data from Costa et al. shown in UCSC Genome Browser. (a), (b), and (c) show three different examples of de‐novo identified transcripts. Blue boxes indicate the exons, black blocks and arrowed lines indicate the splice junctions and red peaks represent data ‘coverage’. (a) Shows a new splicing isoform resulting from the skipping of one exon, whose presence is indicated by a novel splice junction (highlighted in red); (b) shows an example of a newly identified exon (green box), whose presence is also supported by two novel splice junctions (in red); a completely unannotated transcribed region is finally indicated in (c). Green arrows show the lack of any gene annotation in RefSeq and Ensembl databases. It is also evident that this newly identified transcript does not overlap any repeated region of the human genome.



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Ciccodicola, Alfredo, Aversa, Rosanna, Esposito, Roberta, and Costa, Valerio(Sep 2013) RNA‐Seq and Human Complex Disease. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0024990]