Feb 3, 2016

A novel approach to identifying marker genes and estimating the cellular composition of whole blood from gene expression profiles

BioRxiv : the Preprint Server for Biology
Casey P. ShannonScott J. Tebbutt

Abstract

Measuring genome-wide changes in transcript abundance in circulating peripheral whole blood cells is a useful way to study disease pathobiology and may help elucidate biomarkers and molecular mechanisms of disease. The sensitivity and interpretability of analyses carried out in this complex tissue, however, are significantly affected by its dynamic heterogeneity. It is therefore desirable to quantify this heterogeneity, either to account for it or to better model interactions that may be present between the abundance of certain transcripts, some cell types and the indication under study. Accurate enumeration of the many component cell types that make up peripheral whole blood can be costly, however, and may further complicate the sample collection process. Many approaches have been developed to infer the composition of a sample from high-dimensional transcriptomic and, more recently, epigenetic data. These approaches rely on the availability of isolated expression profiles for the cell types to be enumerated. These profiles are platform-specific, suitable datasets are rare, and generating them is expensive. No such dataset exists on the Affymetrix Gene ST platform. We present a freely-available, and open source, multi-response ...Continue Reading

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Mentioned in this Paper

Biological Markers
Study
Whole Blood
Genome
1beta-(p-hydroxyphenyl acetyl)-15-O-beta-D-glucopyranosyl-5alpha, 6betaH-eudesma-3-en-12, 6alpha-olide
Profile (Lab Procedure)
Gene Expression
Study of Epigenetics
Specimen Collection
Whole Blood Specimen

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