Transcriptomics,Genomics

Dataset Information

19

White Blood Cell Differentials Enrich Whole Blood Expression Data in the Context of Acute Cardiac Allograft Rejection


ABSTRACT: Acute cardiac allograft rejection is a serious complication of heart transplantation. Investigating molecular processes in whole blood via microarrays is a promising avenue of research in transplantation, particularly due to the non-invasive nature of blood sampling. However, whole blood is a complex tissue and the consequent heterogeneity in composition amongst samples is ignored in traditional microarray analysis. This complicates the biological interpretation of microarray data. Here we have applied a statistical deconvolution approach, cell-specific significance analysis of microarrays (csSAM), to whole blood samples from subjects either undergoing acute heart allograft rejection (AR) or not (NR). We identified eight differentially expressed probe-sets significantly correlated to monocytes (mapping to 6 genes, all down-regulated in ARs versus NRs) at a false discovery rate (FDR) <= 15%. None of the genes identified are present in a biomarker panel of acute heart rejection previously published by our group and discovered in the same data. Overall design: A single treatable acute rejection (International Society for Heart & Lung Transplantation, ISHLT grade >=2R) sample from each of 10 subjects and one non-rejection sample (ISHLT grade = 0R) from 16 subjects who did not have treatable acute rejection at any time within the first six months post-transplant were selected for analysis. Groups had similar mean age (48 ± 14 and 50 ± 16 in ARs and NRs, respectively) and were mainly composed of Caucasian subjects. NRs were more predominantly male (14/16 subjects) compared to ARs (6/10 subjects).

INSTRUMENT(S): [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array

SUBMITTER: Scott Tebbutt  

PROVIDER: GSE87301 | GEO | 2016-09-24

SECONDARY ACCESSION(S): PRJNA344299

REPOSITORIES: GEO

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Publications

White blood cell differentials enrich whole blood expression data in the context of acute cardiac allograft rejection.

Shannon Casey P CP   Hollander Zsuzsanna Z   Wilson-McManus Janet J   Balshaw Robert R   Ng Raymond T RT   McMaster Robert R   McManus Bruce M BM   Keown Paul A PA   Tebbutt Scott J SJ  

Bioinformatics and biology insights 20120410


Acute cardiac allograft rejection is a serious complication of heart transplantation. Investigating molecular processes in whole blood via microarrays is a promising avenue of research in transplantation, particularly due to the non-invasive nature of blood sampling. However, whole blood is a complex tissue and the consequent heterogeneity in composition amongst samples is ignored in traditional microarray analysis. This complicates the biological interpretation of microarray data. Here we have  ...[more]

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