Transcriptomics

Dataset Information

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Kidney transplantation (SMD set)


ABSTRACT: In this study, we examined transcriptional profiles from 3 different microarray platforms, across 103 peripheral blood samples with and without acute rejection, to find a critical gene-set for the diagnosis of acute renal rejection that matched biopsy diagnosis, irrespective of patient demographics, clinical confounders, concomitant infection, immunosuppression usage or sample processing methods. We hypothesized that changes in peripheral blood expression profiles correlate with biopsy-proven rejection, and that these changes could be used as biomarkers for the diagnosis and prediction of acute rejection. Disease State: Acute Rejection (AR#sampleid) or Stable (S#sampleid) samples We performed cross-sectional microarray analysis of 103 matched peripheral blood samples collected at a single time point, timed with a biopsy where acute rejection was either confirmed as present (60 AR samples) or absent (62 STA samples). The samples were hybridized to one of 3 microarray platforms: Affymetrix (n=75 the 54K HG-U133_Plus2 Array), Agilent (n=26, 44K oligo Array) and cDNA array (n=21, ~30K cDNA). Of 103 samples, 14 were used on both Affy and Agilent arrays; 1 was used in cDNA and Agilent array and 2 were used across 3 array platforms. Microarray data generated from 3 array platforms were cross-compared, by mapping common and overlapping transcripts to Human Gene Organization (HUGO) gene names. Significant gene lists on each platform were identified using Significant Analysis of Microarray (SAM, ref) with a common significance threshold of a false discovery rate (FDR) of <10%. This set contains the data for samples hybridized to cDNA arrays.

ORGANISM(S): Homo sapiens  

SUBMITTER: Minnie Sarwal  

PROVIDER: E-GEOD-14357 | ArrayExpress | 2012-12-26

SECONDARY ACCESSION(S): GSE14357PRJNA114471

REPOSITORIES: GEO, ArrayExpress

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Publications

A peripheral blood diagnostic test for acute rejection in renal transplantation.

Li L L   Khatri P P   Sigdel T K TK   Tran T T   Ying L L   Vitalone M J MJ   Chen A A   Hsieh S S   Dai H H   Zhang M M   Naesens M M   Zarkhin V V   Sansanwal P P   Chen R R   Mindrinos M M   Xiao W W   Benfield M M   Ettenger R B RB   Dharnidharka V V   Mathias R R   Portale A A   McDonald R R   Harmon W W   Kershaw D D   Vehaskari V M VM   Kamil E E   Baluarte H J HJ   Warady B B   Davis R R   Butte A J AJ   Salvatierra O O   Sarwal M M MM  

American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons 20121001 10


Monitoring of renal graft status through peripheral blood (PB) rather than invasive biopsy is important as it will lessen the risk of infection and other stresses, while reducing the costs of rejection diagnosis. Blood gene biomarker panels were discovered by microarrays at a single center and subsequently validated and cross-validated by QPCR in the NIH SNSO1 randomized study from 12 US pediatric transplant programs. A total of 367 unique human PB samples, each paired with a graft biopsy for ce  ...[more]

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