Analytical validation of a prognostic prostate cancer gene expression assay using formalin fixed paraffin embedded tissue

Autor: Viktor Berge, Olaide Raji, R.W. Watson, Katherine M. Sheehan, Denis Paul Harkin, Wesley Reardon, Christopher Steele, Felipe Augusto Andre Ishiy, Elaine W. Kay, Andrena McCavigan, Steven Walker, Laura A. Knight, Christopher Michael Brown, Shauna Lambe, Paul Wallace Medlow, Richard D. Kennedy, Betina Katz, Gemma E Logan
Rok vydání: 2018
Předmět:
Male
Oncology
Analytical validation
Microarray
medicine.medical_treatment
01 natural sciences
010104 statistics & probability
Prostate cancer
0302 clinical medicine
Recurrence
Genetics(clinical)
Genetics (clinical)
Oligonucleotide Array Sequence Analysis
Paraffin Embedding
medicine.diagnostic_test
Prostatectomy
Repeatability
Prognosis
Gene Expression Regulation
Neoplastic
030220 oncology & carcinogenesis
Metastatic
DNA microarray
Research Article
Quality Control
lcsh:Internal medicine
medicine.medical_specialty
Analyte
lcsh:QH426-470
Prognostic
03 medical and health sciences
SDG 3 - Good Health and Well-being
Internal medicine
Biopsy
Genetics
medicine
Humans
0101 mathematics
lcsh:RC31-1245
Reproducibility
business.industry
Gene Expression Profiling
Prostatic Neoplasms
Reproducibility of Results
medicine.disease
lcsh:Genetics
business
Zdroj: BMC Medical Genomics
Medlow, P W, Steele, C J, McCavigan, A M, Reardon, W, Brown, C M, Lambe, S M, Ishiy, F A A, Walker, S M, Logan, G E, Raji, O Y, Berge, V, Katz, B, Kay, E W, Sheehan, K, Watson, R W, Harkin, D P, Kennedy, R D & Knight, L A 2018, ' Analytical validation of a prognostic prostate cancer gene expression assay using formalin fixed paraffin embedded tissue ', BMC Medical Genomics, vol. 11, no. 1, 125 . https://doi.org/10.1186/s12920-018-0442-y
BMC Medical Genomics, Vol 11, Iss 1, Pp 1-11 (2018)
ISSN: 1755-8794
DOI: 10.1186/s12920-018-0442-y
Popis: Background There is a clear need for assays that can predict the risk of metastatic prostate cancer following curative procedures. Importantly these assays must be analytically robust in order to provide quality data for important clinical decisions. DNA microarray based gene expression assays measure several analytes simultaneously and can present specific challenges to analytical validation. This study describes the analytical validation of one such assay designed to predict metastatic recurrence in prostate cancer using primary formalin fixed paraffin embedded tumour material. Methods Accuracy was evaluated with a method comparison study between the assay development platform (Prostate Disease Specific Array) and an alternative platform (Xcel™ microarray) using 50 formalin-fixed, paraffin-embedded prostate cancer patient samples. An additional 70 samples were used to establish the assay reportable range. Determination of assay precision and sensitivity was performed on multiple technical replicates of three prostate cancer samples across multiple variables (operators, days, runs, reagent lots, and equipment) and RNA/cDNA inputs respectively using the appropriate linear mixed model. Results The overall agreement between the development and alternative platform was 94.7% (95% confidence interval, 86.9–98.5%). The reportable range was determined to be 0.150 to 1.107 for core needle biopsy samples and − 0.214 to 0.844 for radical prostatectomy samples. From the precision study, the standard deviations for assay repeatability and reproducibility were 0.032 and 0.040 respectively. The sensitivity study demonstrated that a total RNA input and cDNA input of 50 ng and 3.5 μg respectively was conservative. Conclusion The Metastatic Assay was found to be highly reproducible and precise. In conclusion the studies demonstrated an acceptable analytical performance for the assay and support its potential use in the clinic. Electronic supplementary material The online version of this article (10.1186/s12920-018-0442-y) contains supplementary material, which is available to authorized users.
Databáze: OpenAIRE
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