Evaluation and selection of a non-PCR based technology for improved gene expression profiling from clinical formalin-fixed, paraffin-embedded samples

Bioanalysis ◽  
2016 ◽  
Vol 8 (22) ◽  
pp. 2305-2316 ◽  
Author(s):  
Zhenhao Qi ◽  
Lisu Wang ◽  
Aiqing He ◽  
Manling Ma-Edmonds ◽  
John Cogswell
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Formalin Fixed ◽  
Selection Of

Gene Expression Profiling Using the Illumina ‘DASL’ Platform on RNA Extracted From Formalin Fixed Paraffin Embedded (FFPE) Tissue Identifies Distinct Prognostic Groups In CHOP-R Treated DLBCL

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 2485-2485
Author(s):  
Sharon Barrans ◽  
Lisa Worrillow ◽  
Matthew Care ◽  
Simon Crouch ◽  
Alex Smith ◽  
...  
Keyword(s):  
Gene Expression ◽  
B Cell ◽  
Gene Expression Profiling ◽  
Gene Expression Data ◽  
Expression Profiling ◽  
Expression Data ◽  
Formalin Fixed Paraffin ◽  
Prognostic Groups ◽  
Formalin Fixed Paraffin Embedded ◽  
Formalin Fixed

Abstract Abstract 2485 Diffuse large B cell lymphoma (DLBCL) is a heterogenous disease, which has been subclassified into germinal centre (GCB) and activated B-cell (ABC) type using gene expression profiling. This has been shown to separate DLBCL into distinct prognostic sub-groups in patients treated with either CHOP or CHOP-R therapy. Previous studies have required the use of fresh or frozen samples for the extraction of RNA of sufficient quality to permit whole genome expression analysis. The Illumina ‘DASL' platform allows for highly reproducible gene expression data to be generated from FFPE material, which opens up large series' of retrospective data for detailed expression studies. The aim of this study was therefore to determine whether the Illumina DASL platform could yield reproducible results on formalin fixed paraffin embedded (FFPE) biopsies from a large series of archival CHOP-R treated DLBCL samples. RNA was extracted from paraffin sections using the Ambion Recoverall extraction kit, with 179/206 (87%) of cases yielding >200ng of RNA sufficient for DASL analysis. The DASL assay was performed according to Illumina protocols. Using stringent exclusion criteria, 157/179 (88%) cases yielding results that were considered to be of sufficiently high quality to be included in the analysis. To fully assess the reproducibility of the assay, 35 cases were analysed on 2–8 occasions across multiple experimental days. Using Pearson's correlation, with full-linkage clustering, four discrete clusters were identified (n=28, 40, 46 and 43). Of important note, 95% of the samples were seen to cluster more tightly with their repeats than with any other sample, with all duplicated samples being called in the same cluster with 100% accuracy, suggesting that the technique is highly reproducible. Univariate Kaplan-Meier survival analysis showed that the clusters identified patients with very different outcomes. Two of the clusters showed identical survival curves and therefore these clusters were merged to give 3 clusters with 2-year overall survivals (OS) of 51% (n=71), 65% (n=46) and 77% (n=40), log rank p=0.03, with a 3.7 year follow-up. This data supports the use of gene expression profiling to classify DLBCL patients into clinically relevant prognostic groups. The Illumina DASL assay allows for highly reproducible gene expression data to be produced in valuable, archival data series, and also in the context of clinical trials, where the majority of the tissue available for study is FFPE. The patients identified in this study as having a sub-optimal response to CHOP-R should be considered for alternative therapies, which should be validated in the context of a clinical trial. Disclosures: No relevant conflicts of interest to declare.

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