Supporting References for TPS


Peer-reviewed Publications with Siemens Authors and Co-authors*


RNA extraction from archival formalin-fixed paraffin-embedded tissue: a comparison of manual, semiautomated, and fully automated purification methods. Bohmann, et al. Clin Chem. 2009;55(9):1719-1727.

 

Summary
This article compares different RNA extraction technologies (Siemens manual, Qiagen, semi-automated, and Siemens fully automated TPS methods) from formalin-fixed paraffin-embedded (FFPE) tissue sections. In this method comparison study, TPS showed the best reproducibility and least hands-on and total times when extracted RNA from 90 FFPE tissue samples was used for expression analysis.


A high-sensitivity, medium-density and target amplification-free planar waveguide microarray system for gene expression analysis of formalin-fixed and paraffin-embedded tissue. Schwers, et al. Clin Chem. 2009;55(11):1995-2003.

 

Summary
TPS was used to extract RNA from FFPE tissue samples. The extracted RNA was applied to an amplification-free, planar waveguide microarray system for gene expression analysis.


Automated extraction of DNA and RNA from a single formalin-fixed paraffin-embedded tissue section for analysis of both single-nucleotide polymorphisms and mRNA expression. Hennig, et al. Clin Chem. 2010;56(12):1845-1853.

 

Summary
A total of 210 FFPE samples that had been stored for up to 25 years were processed with TPS using the split protocol (delivering both DNA and RNA in separate eluates from a single sample). TPS provided extracts with a success rate of 99% for combined analysis in normal and paired cancer tissue of RNA expression profiles with real-time, one-step RT-PCR and SNP genotypes with mass spectroscopy analysis from Luminex. Success rates were measured by the number of analyzable specimens for both RNA normalization and DNA control genes.


Tumor-associated lymphocytes as an independent predictor of response to neoadjuvant chemotherapy in breast cancer. Denkert, et al. JCO. 2010;28:105-113.

 

Summary
RNA was extracted from 1058 breast cancer needle biopsy FFPE samples that had been stored for up to 10 years. TPS eluates had a success rate of 100% for both extraction and RNA expression analysis with real-time, one-step RT-PCR. Success rates were measured by the number of analyzable specimens for both normalization and target genes.


Quantitative determination of estrogen receptor, progesterone receptor, and HER2 in formalin-fixed paraffin-embedded tissue - a new option for predictive biomarker assessment in breast cancer. Müller, et al. Diagn Mol Path. 2011;20:1-10.

 

Summary
TPS successfully extracted RNA with low section-to-section variability from 501 FFPE breast cancer samples that had been stored for up to 21 years. TPS proved to be a “reliable high-throughput instrument for standardized testing of biomarkers in clinical routine and for research studies on archived FFPE material up to 21 years old.” The quantitative mRNA assessments of ESR1, PGR, and HER2 are comparable to the results obtained with immunohistochemical analysis, which is the current gold standard.


Comparison of different approaches for assessment of HER2 expression on protein and mRNA level: prediction of chemotherapy response in the neoadjuvant GeparTrio trial (NCT00544765). Noske, et al. Breast Cancer Res Treat. 2011;126:109-117.

 

Summary
TPS was used to extract RNA from 278 individual FFPE breast cancer needle biopsies that had been stored up to 10 years. All eluates had a 100% success rate for RNA expression analysis studies with real-time, one-step RT-PCR.


A new molecular predictor of distant recurrence in ER-positive, HER2-negative breast cancer adds independent information to conventional clinical risk factors. Filipits, et al. Clin Cancer Res. 2011;17(18):6012-6020.

 

Summary
TPS was used to extract RNA from 1702 individual 5 or 10 µm whole FFPE breast cancer tissue sections that had been stored for up to 20 years as part of two multicentric breast cancer trials. 98% of eluates were used successfully for real-time, one-step RT-PCR.


Applicability of a system for fully automated nucleic acid extraction from formalin-fixed paraffin-embedded sections for routine KRAS mutation testing. Lehmann, et al. Diag Mol Path. 2012;21:114-119.

 

Summary
“Automated extraction of both DNA and RNA was successful in 339 of 340 FFPE samples representing 5 different tissue types [breast, colon, lymph node, liver, and lung]. In comparison with a conventional manual extraction protocol [Qiagen], the method [TPS] showed an overall agreement of 97.7% (95% confidence interval, 88.2%-99.9%) for the subsequent mutational analysis of the KRAS gene in colorectal cancer samples. It ensures standardization of sample processing and can be applied to samples in routine pathology.” TPS was nearly twice as fast as manual method.


Prognostic utility of β-tubulin isotype III and correlations with other molecular and clinicopathological variables in patients with early breast cancer: a translational Hellenic Cooperative Oncology Group (HeCOG) study. Pentheroudakis, et al. BCRT. 2011;127:179-193.


Summary
Sufficient yields of RNA were isolated using TPS from individual 10 µm FFPE tissue sections from 314 breast cancer samples that had been stored for up to 20 years.


RNA-based determination of ESR1 and HER2 expression and response to neoadjuvant chemotherapy. Denkert, et al. Annals of Oncology. 2013;24(3):632-639.

 

Summary
TPS was used to extract RNA from individual FFPE tissue sections in a cohort of 1093 FFPE breast cancer core biopsies. “96.1% of those samples contained sufficient RNA and were included in the study” and were used for RNA expression analysis with real-time, one-step RT-PCR.


CDK10 is not a target for aberrant DNA methylation in breast cancer. Heller, et al. Anticancer Res. 2009;29:3939-3944.

 

Summary
TPS was used to extract RNA from 96 FFPE cancer tissue sections. All eluates were analyzed with real-time, one-step RT-PCR.


Abbreviations

RT = reverse transcription
FFPE = formalin-fixed paraffin-embedded



Independent Peer-reviewed Publications


Gene expression classifier predicts for hypoxic modification of radiotherapy with nimorazole in squamous cell carcinomas of the head and neck. Toustrup, et al. Radiotherapy and Oncology. 2012;102(1):122-129.

 

Summary
TPS was used to extract RNA from 323 individual head/neck squamous cell carcinoma (HNSCC) FFPE tissue samples that had been stored for up to 25 years. Extracted RNA was used with real-time, two-step RT-PCR.


Gene expression classifier predicts for hypoxic modification of radiotherapy with nimorazole in squamous cell carcinomas of the head and neck. Toustrup, et al. Radiotherapy and Oncology. 2012;102(1):122-129.

 

Summary
TPS was used to extract RNA from 323 individual head/neck squamous cell carcinoma (HNSCC) FFPE tissue samples that had been stored for up to 25 years. Extracted RNA was used with real-time, two-step RT-PCR.


Development of a hypoxia gene expression classifier with predictive impact for hypoxic modification of radiotherapy in head and neck cancer. Toustrup, et al. Cancer Res. 2011;71(17):5923-5931.

Summary
RNA was extracted from a cohort of 323 head/neck squamous cell carcinoma (HNSCC) FFPE tissue samples using TPS. The investigators applied a 15-gene RNA expression classifier with real-time, two-step RT-PCR.


Comparison of the RNA-based EndoPredict multigene test between core biopsies and corresponding surgical breast cancer sections. Müller, et al. J Clin Path. 2012;65 (7):660-662.

Summary
RNA was extracted from 40 FFPE tumor sections and 40 corresponding core biopsies using TPS. Eluates were analyzed for RNA expression analysis with real-time, one-step RT-PCR.


Assessment of a fully automated high-throughput DNA extraction method from formalin-fixed, paraffin-embedded tissue for KRAS and BRAF somatic mutation analysis. van Eijk, et al. Exp and Mol Path. 2013;121-125.

Summary
DNA was extracted from approximately 150 routine FFPE tissue cores or micro-dissected tissue. According to this study, the authors found that TPS “delivers high quality DNA from both small FFPE tissue cores and micro-dissected tissue material. In comparison to classical methods [manual in-house method], less than 50% of starting tissue was sufficient as input for micro-dissection. Turnaround times decreased significantly, and 50% less hands-on time was needed.”


Endothelial CCR2 signaling induced by colon carcinoma cells enables extravasation via the JAK2-Stat5 and p38MAPK pathway. Wolf, et al. Cancer Cell. 2012;22:91-105.

Summary
TPS eluates obtained from mouse FFPE tissue samples were used for RNA expression analysis of cancer genes.


Nucleic acid extraction methods from fixed and paraffin-embedded tissues for cancer diagnostics. Bonin and Stanta. Expert Rev Mol Diagn. 2013;13(3):271-282.

Summary
This review, authored by leading experts in the field of molecular pathology, summarizes workflows, challenges, and available extraction methods for DNA and RNA from fixed paraffin-embedded tissues for cancer diagnostics. The authors highlighted that the only fully automated system to extract both DNA and RNA was the Siemens Tissue Preparation System.


Abbreviations

RT = reverse transcription
FFPE = formalin-fixed paraffin-embedded



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Article summaries include statements that refer to article results, and are only direct quotes where indicated. Siemens has not validated these claims.

Success rate is defined as percentage of extracted samples with generated RNA or DNA signal with real-time RT-PCR or PCR respectively on the TPS eluates.

*Siemens provided financial support for the research and/or publication of these articles.