Imperial College London
Alternate

PROFESSOR H. TERENCE COOK

Faculty of Medicine, Department of Immunology and Inflammation

Emeritus Professor
 
 
 
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Contact

 

+44 (0)20 3313 2009t.h.cook

 
 
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Assistant

 

Miss Claudia Rocchi +44 (0)20 3313 2315

 
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Location

 

9N9Commonwealth BuildingHammersmith Campus

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Summary

 

Publications

Citation

BibTex format

@inproceedings{Toulza:2019:10.1016/j.humimm.2019.07.050,
author = {Toulza, F and Dominy, K and Galliford, J and Cook, T and McLean, A and Roufosse, C},
doi = {10.1016/j.humimm.2019.07.050},
pages = {52--52},
publisher = {Elsevier},
title = {OR48 Gene expression analysis in renal transplant biopsies: Comparison of split samples and different techniques},
url = {http://dx.doi.org/10.1016/j.humimm.2019.07.050},
year = {2019}
}
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RIS format (EndNote, RefMan)

TY  - CPAPER
AB  - AimThe Banff Classification for Allograft Pathology includes increased expression of genes associated with antibody-mediated rejection (AMR) if thoroughly validated in the diagnostic criteria for AMR. There is limited information on how results of gene expression analysis are influenced by sample preservation (formalin-fixation versus RNA later) and gene analysis technique used. Our aim is to compare: 1) Nanostring analysis of samples from the same biopsy split for formalin fixation and paraffin embedding (FFPE) and RNAlater (RL); 2) Nanostring (NS) and Q-PCR of samples preserved in RL.MethodsWe used a custom panel of 219 genes on the NS platform and of 18 genes for Q-PCR. RNA was extracted from 51 renal transplant biopsies, either from the whole sample (RL), or from 3×20-micron sections (FFPE), using a Qiagen kit. Q-PCR was performed with SYBR Green quantification. Correlation was carried out using Spearman rank, with significance set at p<0.01.ResultsComparing the expression of 219 genes using the NS platform between FFPE and RL samples from the same 51 biopsies, we found significant correlation of the expression of the 219 genes in 47/51 samples (92%) (p median=4×10–12 [3×10-56-0.54]); and significant correlation of individual genes between the 2 samples in 163/219 genes (74%) (p median=0.00003 [3.69×10-18-0.98]). Comparing the expression of 18 AMR-tagged genes using NS versus qPCR, from the same pool of RNA in RL (n=51), we found significant correlation in 17/18 genes (94%) (p median=0.032 [0.001–0.966]).ConclusionsMost biopsies (92%) can be split and preserved in FFPE or RL and show good correlation of gene expression results across a range of transcripts using a single platform (NS). However almost a quarter of individual genes showed poor correlation on the same platform (NS) between split samples from the same biopsy in FFPE and RL. This could be because there is genuine variation in levels of expressi
AU  - Toulza,F
AU  - Dominy,K
AU  - Galliford,J
AU  - Cook,T
AU  - McLean,A
AU  - Roufosse,C
DO  - 10.1016/j.humimm.2019.07.050
EP  - 52
PB  - Elsevier
PY  - 2019///
SN  - 0198-8859
SP  - 52
TI  - OR48 Gene expression analysis in renal transplant biopsies: Comparison of split samples and different techniques
UR  - http://dx.doi.org/10.1016/j.humimm.2019.07.050
UR  - http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000489085600048&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=1ba7043ffcc86c417c072aa74d649202
UR  - https://www.sciencedirect.com/science/article/pii/S0198885919307165?via%3Dihub
ER  -
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