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Whole genome expression profiling based on paraffin embedded tissue of a large DLBCL cohort

ABSTRACT: Gene expression profiling was carried out for RNA extracted from Formalin-fixed, paraffin embedded (FFPE) biopsies for 1311 patients with diffuse large b-cell lymphoma (DLBCL) using the Illumina DASL platform.

ORGANISM(S): Homo sapiens

PROVIDER: GSE181063 | GEO | 2021/07/30

REPOSITORIES: GEO

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Whole genome expression profiling based on paraffin embedded tissue can be used to classify diffuse large b-cell lymphoma and predict clinical outcome

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Whole genome expression profiling based on paraffin embedded tissue can be used to classify diffuse large b-cell lymphoma and predict clinical outcome

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Project description:Diffuse large B-cell lymphoma (DLBCL) exhibits heterogeneous clinical outcomes even in tumors of the same stage and with similar pathological characteristics. A substantial number of patients with DLBCL still fail to be cured despite recent improvements in therapy. In this study, we used formalin fixed paraffin embedded (FFPE) tumor samples for microarray gene expression profiling to develop robust prognostic profiles for DLBCL. We performed a retrospective microarray gene expression profiling study of FFPE from a cohort of DLBCL patients using the whole genome cDNA mediated Annealing, Selection and Ligation (WG-DASL) assay. After removing poor-quality samples, data from 164 patients were used for statistical analyses to develop and validate a prognostic gene expression signature using a gradient lasso and leave-one-out cross-validation process.

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Project description:Tissue sample acquisition is a limiting step in many studies. There are many thousands of formalin fixed paraffin embedded archival blocks collected around the world, but in contrast relatively few fresh frozen samples in tumor banks. Once samples are fixed in formalin the RNA is degraded and traditional methods for gene expression profiling are not suitable. In this study we have evaluated the whole genome DASL assay from Illumina to perform transcriptomic analysis from archived breast tumor tissue fixed in formalin paraffin embedded blocks. We profiled 76 familial breast tumors from cases carrying a BRCA1, BRCA2 or ATM mutation, or from non-BRCA1/2 families. We found that replicate samples correlated well with each other (r2=0.9-0.98). In 12/15 cases, the matched formalin-fixed and frozen samples predicted the same tumor molecular subtypes with confidence. These results demonstrate that the whole genome DASL assay is a valuable tool to profile degraded RNA from archival FFPE material. This assay will enable transcriptomic analysis of a large number of archival samples that are stored in pathology archives around the globe and consequently will have the potential to improve our understanding and characterisation of many diseases. RNA was extracted from FFPE Familial breast tumours and analysed using the WG-DASL assay for Illumina.

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