Blood transcriptome changes after stroke in an African American population

Annals of Clinical and Translational Neurology
Robert MellerRoger P Simon

Abstract

Molecular diagnostic medicine holds much promise to change point of care treatment. An area where additional diagnostic tools are needed is in acute stroke care, to assist in diagnosis and prognosis. Previous studies using microarray-based gene expression analysis of peripheral blood following stroke suggests this approach may be effective. Next-generation sequencing (NGS) approaches have expanded genomic analysis and are not limited to previously identified genes on a microarray chip. Here, we report on a pilot NGS study to identify gene expression and exon expression patterns for the prediction of stroke diagnosis and prognosis. We recruited 28 stroke patients and 28 age- and sex-matched hypertensive controls. RNA was extracted from 3 mL blood samples, and RNA-Seq libraries were assembled and sequenced. Bioinformatical analysis of the aligned RNA data reveal exonic (30%), intronic (36%), and novel RNA components (not currently annotated: 33%). We focused our study on patients with confirmed middle cerebral artery occlusion ischemic stroke (n = 17). On the basis of our observation of differential splicing of gene transcripts, we used all exonic RNA expression rather than gene expression (combined exons) to build prediction mod...Continue Reading

References

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Citations

Jul 20, 2016·Journal of Investigative Medicine : the Official Publication of the American Federation for Clinical Research·An Zhou
Dec 16, 2016·Journal of Equine Science·Teruaki TozakiShun-Ichi Nagata
Apr 14, 2018·Journal of Cerebral Blood Flow and Metabolism : Official Journal of the International Society of Cerebral Blood Flow and Metabolism·Boryana StamovaFrank R Sharp
Jun 14, 2018·Aging and Disease·Chengjie ZhangLing Wei
Aug 25, 2018·Dose-response : a Publication of International Hormesis Society·Rehana K LeakMelvin E Andersen

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Methods Mentioned

BETA
blood draw
chip
RNA seq
PCA
pull down

Software Mentioned

Seq
Partek Genomics Studio
R
Genome viewer
LifeScope Software
Cuffmerge
Whole Transcriptome Analysis
Partek
Ref
Cufflinks

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