Study: Microarray CCP Scores Not a Substitute for qRT-PCR

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Investigators conclude that microarray-generated cell cycle progression score should not be assumed to be a valid surrogate for qRT-PCR-generated scores.
Investigators conclude that microarray-generated cell cycle progression score should not be assumed to be a valid surrogate for qRT-PCR-generated scores.
The following article is part of conference coverage from the 2018 Large Urology Group Practice Association meeting in Chicago, November 1-3. Renal and Urology News' staff will be reporting on presentations dealing with various practice management and clinical topics aimed at community-based urologists. Check back for the latest news from LUGPA 2018.

CHICAGO—Microarray technology for measuring expression of cell cycle progression (CCP) genes in prostate cancer (PCa) tissue compares poorly with qRT-PCR, investigators reported at the 2018 annual meeting of the Large Urology Group Practice Association.

Using either contemporary or archival samples of PCa tissue, Adam Cole, MD, of TruCorp PLLC, and colleagues observed a decrease in pairwise correlations among CCP genes, limited CCP score range, and poor score correlation between platforms, according to a poster presentation.

“As a result, microarray-generated CCP scores should not be assumed to be a valid surrogate for qRT-PCR generated scores for prediction of patient outcome,” they concluded.

In background information provided in the poster, the investigators noted that most studies evaluating CCP gene expression have used qRT-PCR to measure expression levels, which is generally considered the “gold standard” for measuring RNA expression. It is not a highly multiplexed platform, however. As PCa tissue is limited, they noted, that there is interest in evaluating the ability of microarrays to measure CCP gene expression.

Dr Cole and colleagues compared the characteristics of CCP score from RP samples submitted for commercial testing, generated using qRT-PCR, with scores generated from publicly available microarray expression datasets. They compared CCP scores generated by 2 different testing platforms using the same set of 39 contemporary RP samples: qRT-PCR (Myriad Genetic Laboratories) and Cuzick CCP score (Decipher GRID microarray, GenomeDx).

The average CCP gene pairwise correlation in the commercial RP cohort was 0.67, whereas the pairwise CCP gene correlations in the microarray studies were significantly lower, ranging from 0.17 to 0.58.

In addition, the centered CCP score in the commercial cohort ranged from -2 to 3, with a standard deviation of 0.79. In contrast, the center CCP score range in microarray studies was highly truncated, with SD ranging from 0.12 to 0.46.

Using contemporary clinical samples to compare microarray- and qRT-PCR-based proliferation scores from the same formalin-fixed paraffin-embedded tissue blocks, the investigators found that the between-platform correlation was only 0.60. The range of the microarray-based score was severely truncated compared with scores from qRT-PCR, they reported.

Visit Renal and Urology News' conference section for continuous coverage from LUGPA 2018.

Reference

Cole A, Flake DD II, Rajamani S, et al. Evaluation of microarrays for measuring CCP gene expression. Presented at the 2018 annual meeting of the Large Urology Group Practice Association in Chicago, Nov. 1-3.

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