A Systematic Comparison and Evaluation of High Density Exon Arrays and RNA-seq technology in Unraveling the Peripheral Blood Transcriptome of Sickle Cell Disease.

Sickle cell transcriptome was analyzed using whole blood clinical specimens on the Affymetrix Human Exon 1.0 ST arrays and Illuminas deep sequencing technologies. Data analysis indicated a strong concordance (R=0.64) between exon array and RNA-seq in both gene level and exon level expression of transcripts. The magnitude of fold changes in the expression levels for the differentially expressed genes (p<0.05) was found to be higher in RNA-seq than microarrays. However, the arrays outperformed the sequencing technology in the detection of low abundant transcripts. In addition to examining the expression level changes of transcripts, RNA-seq technology was able to identify sequence variation in the expressed transcripts. We also demonstrate herein the ability of RNA-seq technology to discover novel expression outside of the annotated genes.

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Raghavachari N, Barb J, Yang Y, Liu P, Woodhouse K, Levy D, O'Donnell CJ, Munson PJ, Kato GJ