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, G.; Gehrmann, Mathias; Stropp, Udo; Brauch, Hiltrud; Fritz, Péter; Eichelbaum, Michel; Schwab, Matthias; Schroth, Werner

doi:10.1373/clinchem.2010.151233

Cited by 78 publications

(55 citation statements)

References 16 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Total RNA was extracted from one 5-or 10-mm whole FFPE tissue section with a silica bead-based, fully automated isolation method (Tissue Preparation System, VERSANT Tissue Preparation Reagents, Siemens Healthcare Diagnostics) as described in Supplementary Appendix (13). All samples were analyzed with quantitative one-step reverse transcriptase PCR (qRT-PCR) on an ABI PRISM 7900HT (Applied Biosystems) using SuperScript III PLATINUM One-Step Quantitative RT-PCR System with ROX (Invitrogen).…”

Section: Rna Extraction and Gene Expression Analysis With Quantitativmentioning

confidence: 99%

A New Molecular Predictor of Distant Recurrence in ER-Positive, HER2-Negative Breast Cancer Adds Independent Information to Conventional Clinical Risk Factors

Filipits

Rudas

Jakesz

et al. 2011

Clinical Cancer Research

Self Cite

623

610

View full text Add to dashboard Cite

Purpose: According to current guidelines, molecular tests predicting the outcome of breast cancer patients can be used to assist in making treatment decisions after consideration of conventional markers. We developed and validated a gene expression signature predicting the likelihood of distant recurrence in patients with estrogen receptor (ER)-positive, HER2-negative breast cancer treated with adjuvant endocrine therapy.Experimental Design: RNA levels assessed by quantitative reverse transcriptase PCR in formalinfixed, paraffin-embedded tumor tissue were used to calculate a risk score (Endopredict, EP) consisting of eight cancer-related and three reference genes. EP was combined with nodal status and tumor size into a comprehensive risk score, EPclin. Both prespecified risk scores including cutoff values to determine a risk group for each patient (low and high) were validated independently in patients from two large randomized phase III trials [Austrian Breast and Colorectal Cancer Study Group (ABCSG)-6: n ¼ 378, ABCSG-8: n ¼ 1,324].Results: In both validation cohorts, continuous EP was an independent predictor of distant recurrence in multivariate analysis (ABCSG-6: P ¼ 0.010, ABCSG-8: P < 0.001). Combining Adjuvant!Online, quantitative ER, Ki67, and treatment with EP yielded a prognostic power significantly superior to the clinicopathologic factors alone [c-indices: 0.764 vs. 0.750, P ¼ 0.024 (ABCSG-6) and 0.726 vs. 0.701, P ¼ 0.003 (ABCSG-8)]. EPclin had c-indices of 0.788 and 0.732 and resulted in 10-year distant recurrence rates of 4% and 4% in EPclin low-risk and 28% and 22% in EPclin high-risk patients in ABCSG-6 (P < 0.001) and ABCSG-8 (P < 0.001), respectively.Conclusions: The multigene EP risk score provided additional prognostic information to the risk of distant recurrence of breast cancer patients, independent from clinicopathologic parameters. The EPclin score outperformed all conventional clinicopathologic risk factors.

show abstract

Section: Rna Extraction and Gene Expression Analysis With Quantitativmentioning

confidence: 99%

A New Molecular Predictor of Distant Recurrence in ER-Positive, HER2-Negative Breast Cancer Adds Independent Information to Conventional Clinical Risk Factors

Filipits

Rudas

Jakesz

et al. 2011

Clinical Cancer Research

Self Cite

623

610

View full text Add to dashboard Cite

show abstract

“…Reactions were carried out on an ABI Prism 7900 Sequence Detector (ABI) and in duplicate. Seven potential reference genes were analyzed: ACTR3, CHCHD1, NDFIP1, SPCS2, and TMEM85 were selected on the basis of our previous in vitro results (27); RPL37A and TFRC have previously been described (35,36). The geNORM application available in RealTime Statminer (Intergromics) was used on the training set of 58 HNSCC samples, and 3 optimal reference genes (RPL37A, ACTR3, and NDFIP1) were selected for normalization.…”

Section: Hypoxia Tracer and Isolation Of Hypoxic Xenograft Tissuementioning

confidence: 99%

Development of a Hypoxia Gene Expression Classifier with Predictive Impact for Hypoxic Modification of Radiotherapy in Head and Neck Cancer

et al. 2011

View full text Add to dashboard Cite

Hypoxia, a common feature of the microenvironment in solid tumors, is associated with resistance to radiotherapy, reduced therapeutic response, and a poorer clinical outcome. In head and neck squamous cell carcinomas (HNSCC), the negative effect of hypoxia on radiotherapy can be counteracted via addition of hypoxic modification to the radiotherapy. To predict which patients harbor hypoxic tumors and would therefore benefit from hypoxic modification, clinically applicable methods for pretherapeutic hypoxic evaluation and categorization are needed. In this study, we developed a hypoxia classifier based on gene expression. Through study of xenograft tumors from human squamous cell carcinoma cell lines, we verified the in vivo relevance of previously identified in vitro derived hypoxia-induced genes. We then evaluated a training set of 58 hypoxia-evaluated HNSCCs to generate a gene expression classifier containing 15 genes. This 15-gene hypoxia classifier was validated in 323 patients with HNSCC randomized for hypoxic modification or placebo in combination with radiotherapy. Tumors categorized as hypoxic on the basis of the classifier were associated with a significantly poorer clinical outcome than nonhypoxic tumors. This outcome was improved and equalized to the nonhypoxic tumors by addition of hypoxic modification. Thus, findings show that the classifier attained both prognostic and predictive impact, and its pretherapeutic use may provide a method to identify those patients who will benefit from hypoxic modification of radiotherapy. Cancer Res; 71(17); 5923-31. Ó2011 AACR.

show abstract

“…A study of peripheral blood mononuclear cells (PBMCs) from lung cancer patients identified a signature of 29 genes that distinguished patients from controls (46). Panels of mRNA biomarkers for early detection have also been identified in bladder, breast and renal carcinomas (47)(48)(49). These studies suggest that blood-based mRNA signatures may be potentially useful tools for the early detection of lung cancer.…”

Section: Lung Cancer Biomarkers On the Basis Of Biomoleculesmentioning

confidence: 99%

Potential molecular approaches for the early diagnosis of lung cancer (Review)

Oak

Wilson

Lee

et al. 2012

Molecular Medicine Reports

View full text Add to dashboard Cite

Abstract. Lung cancer is the leading cause of mortality from cancer among men and women worldwide. More individuals die each year of lung cancer than of colon, breast and prostate cancer combined. Despite new diagnostic techniques, the overall 5-year survival rate remains at approximately 15% and the majority of patients still present with advanced disease. Therefore, lung cancer is the most lethal cancer at present. Diagnosing and treating cancer at its early stages, ideally during the precancerous stages, could increase the 5-year survival rate by 3-4-fold, with the possibility of cure. To date, no screening method has been shown to decrease the disease-specific mortality rate. This review describes issues related to early lung cancer screening and their rationale, the management of primary cancers detected by screening and the different approaches that have been tested for cancer screening; these include imaging techniques, bronchoscopies and molecular screening, such as analysis of epigenomics using different noninvasive or invasive sources, such as blood, sputum, bronchoscopic samples and exhaled breath.

show abstract

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

Cited by 78 publications

References 16 publications

A New Molecular Predictor of Distant Recurrence in ER-Positive, HER2-Negative Breast Cancer Adds Independent Information to Conventional Clinical Risk Factors

A New Molecular Predictor of Distant Recurrence in ER-Positive, HER2-Negative Breast Cancer Adds Independent Information to Conventional Clinical Risk Factors

Development of a Hypoxia Gene Expression Classifier with Predictive Impact for Hypoxic Modification of Radiotherapy in Head and Neck Cancer

Potential molecular approaches for the early diagnosis of lung cancer (Review)

Contact Info

Product

Resources

About