Journal article

Obtaining high quality transcriptome data from formalin-fixed, paraffin-embedded diagnostic prostate tumor specimens

Liesel M FitzGerald, Chol-hee Jung, Ee Ming Wong, JiHoon E Joo, Jodee A Gould, Vivien Vasic, Julie K Bassett, Neil O'Callaghan, Tim Nottle, John Pedersen, Graham G Giles, Melissa C Southey

LABORATORY INVESTIGATION | NATURE PUBLISHING GROUP | Published : 2018

Abstract

Prognostic genomic biomarkers that can be measured at diagnosis to aid choice of treatment options are unavailable for most common cancers. This is due in part to the poor quality and quantity of available diagnostic specimens for discovery research and to limitations in genomic technologies. Recent technical advances now enable high-density molecular analyses using suboptimal biological specimens. Here we describe the optimization of a transcriptome-specific protocol for use with formalin-fixed, paraffin-embedded (FFPE) diagnostic prostate cancer (PrCa) specimens. We applied the Ion AmpliSeq Transcriptome Human Gene Expression Kit (AmpliSeq Kit) to RNA samples extracted from 36 tumor-enrich..

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Grants

Awarded by Cure Cancer Australia/Prostate Cancer Foundation of Australia


Awarded by Australian NHMRC


Awarded by NHMRC


Funding Acknowledgements

This work was supported by a Cure Cancer Australia/Prostate Cancer Foundation of Australia Young Investigators Grant (LMF; YI 1812). MCCS cohort recruitment was funded by VicHealth and Cancer Council Victoria. The MCCS was further supported by Australian NHMRC grants 209057, 251553, and 504711 and by infrastructure provided by Cancer Council Victoria. The RFPCS was supported by NHMRC grant 940394; the EOPCFS, and the Radical Prostatectomy Registry by Cancer Council Victoria and the APC study by NHMRC grant 623204. MCS is an NHMRC senior research fellow (1061177). We like to express our gratitude to the men who took part in the study and to the pathology laboratories in Victoria for their collaboration.