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. 2015 Feb;105(2):83-9.
doi: 10.1016/j.ygeno.2014.12.002. Epub 2014 Dec 17.

RNA-Seq identifies novel myocardial gene expression signatures of heart failure

Yichuan Liu  1 , Michael Morley  2 , Jeffrey Brandimarto  3 , Sridhar Hannenhalli  4 , Yu Hu  5 , Euan A Ashley  6 , W H Wilson Tang  7 , Christine S Moravec  8 , Kenneth B Margulies  9 , Thomas P Cappola  10 , Mingyao Li  11 ; MAGNet consortium
Affiliations

RNA-Seq identifies novel myocardial gene expression signatures of heart failure

Yichuan Liu et al. Genomics. 2015 Feb.

Abstract

Heart failure is a complex clinical syndrome and has become the most common reason for adult hospitalization in developed countries. Two subtypes of heart failure, ischemic heart disease (ISCH) and dilated cardiomyopathy (DCM), have been studied using microarray platforms. However, microarray has limited resolution. Here we applied RNA sequencing (RNA-Seq) to identify gene signatures for heart failure from six individuals, including three controls, one ISCH and two DCM patients. Using genes identified from this small RNA-Seq dataset, we were able to accurately classify heart failure status in a much larger set of 313 individuals. The identified genes significantly overlapped with genes identified via genome-wide association studies for cardiometabolic traits and the promoters of those genes were enriched for binding sites for transcriptions factors. Our results indicate that it is possible to use RNA-Seq to classify disease status for complex diseases such as heart failure using an extremely small training dataset.

Keywords: Disease classification; Heart Failure; RNA-seq.

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Conflict of interest statement

Conflict of interest

The authors declare that they have no conflict of interest

Figures

Figure 1
Figure 1. K-means clustering results based on RNA-Seq determined feature vectors
(A) Clustering results for the 231 ISCH/NF individuals. (B) Clustering results for the 218 DCM/NF individuals.
Figure 1
Figure 1. K-means clustering results based on RNA-Seq determined feature vectors
(A) Clustering results for the 231 ISCH/NF individuals. (B) Clustering results for the 218 DCM/NF individuals.
See this image and copyright information in PMC

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