FFPE specimens
Targeted DNA and RNA sequencing of fine-needle biopsy FFPE specimens in patients with unresectable hepatocellular carcinoma treated with sorafenib
... collected FFPE specimens underwent a histological review, and only those containing sufficient tumor cells as revealed by hematoxylin-eosin staining were subjected to nucleic acid ...DNA/RNA FFPE kit ...
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DNA Methylation Signatures Predicting Bevacizumab Efficacy in Metastatic Breast Cancer
... archival FFPE specimens of 36 patients with HER2-negative metastatic breast cancer treated with chemotherapy in combination with bevacizumab as first-line therapy (learning ...
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Comparison of RNA isolation from FFPE tissue on two different platforms
... archival FFPE tissue for identifying new molecular will not only aid diagnosis, but also guide treatment of ...from FFPE was shown as a prognostic factor in ovarian carcinoma (Darb-Esfahani et ...in ...
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Original Article Rates of MAGE-A3 and PRAME expressing tumors in FFPE tissue specimens from bladder cancer patients: potential targets for antigen-specific cancer immunotherapeutics
... tissue specimens (N = 156) from blad- der cancer patients were selected from the pathology archive of a single center (University Hospitals Leuven, Belgium) and tested by means of quantitative reverse ...
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Reliable gene expression profiling of formalin-fixed paraffin-embedded breast cancer tissue (FFPE) using cDNA-mediated annealing, extension, selection, and ligation whole-genome (DASL WG) assay
... in FFPE samples compared to matched FF specimens were 88 % and 95 %, ...in FFPE specimens and produced high self-correlation between replicates (r 2 > ...from FFPE samples; however ...
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Levels of human replication factor C4, a clamp loader, correlate with tumor progression and predict the prognosis for colorectal cancer
... frozen specimens and 49 paired formalin-fixed, paraffin-embedded (FFPE) specimens from primary CRC tissues and patient-matched normal colonic tissues were obtained from the 6 th Affiliated Hospital ...
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Detection of HPV DNA in paraffin embedded cervical samples: a comparison of four genotyping methods
... Genotyping agreement for 60 paired cytology- and formalin-fixed and paraffin embedded FFPE specimens in the SUCCEED study; Onclarity, The BD Onclarity™ HPV Assay; Inno-LiPA, The Inno-LiP[r] ...
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Performances of two different panfungal PCRs to detect mould DNA in formalin fixed paraffin embedded tissue: what are the limiting factors?
... in FFPE tis- sue specimens compared with conventional techniques have been reported in previous studies to be 51% to ...the FFPE specimens was not specified in many of the studies mentioned ...
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Comparison of quantitative real time PCR with Sequencing and ribosomal RNA FISH for the identification of fungi in Formalin fixed, paraffin embedded tissue specimens
... of FFPE tissue ...of FFPE tissue samples using two nested PCR assays targeting the 18S rRNA gene of the mucorales and the mitochondrial DNA of Aspergil- lus ...of FFPE tissue samples, sug- gesting a ...
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Original Article Quantitative RT-PCR assay of HER2 mRNA expression in formalin-fixed and paraffin-embedded breast cancer tissues
... the FFPE samples was analyzed using a quantitative RT-PCR (RT-qPCR) method and the obtained HER2 expression levels were compared with those from IHC/FISH ...
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A methodology for utilization of predictive genomic signatures in FFPE samples
... We have previously described methods to generate gene expression signatures reflecting the activity of a number of oncogenic signaling pathways [10,11]. These pathway gene expression signatures have been used to predict ...
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Multiplex bisulfite PCR resequencing of clinical FFPE DNA
... Results: We report here for the first time on comparison studies between the Fluidigm Access Array system and multiplex assays for multiplex bisulfite PCR resequencing. The requirement of the Fluidigm Access Array system ...
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Original Article Over-expression of miR-98 in FFPE tissues might serve as a valuable source for biomarker discovery in breast cancer patients
... using FFPE tissues. In order to explore diagnostic ability of miR-98 in FFPE for breast cancer patients, we performed ROC curve ...in FFPE tissues of breast cancer produced an AUC of ...
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Endometrial beta3 Integrin profile reflects endometrial receptivity defects in women with unexplained recurrent pregnancy loss
... The conflicting data on β3 integrin subunit expression in endometrium of women with RPL led us to conduct the present study. Our data indicate that women with unexplained RPL have significantly reduced integrin ex- ...
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Original Article Development of a new real-time PCR system for simultaneous detection of bacteria and fungi in pathological samples
... A total of 68 bacteria and 9 fungi were chosen as targets (Table 1). The choice of bacterial strains was made based on associations with human diseases and prevalence among humans. Probe-primer sets for each target were ...
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Integrative analysis of copy number and gene expression in breast cancer using formalin fixed paraffin embedded core biopsy tissue: a feasibility study
... The genes assessed as part of the DASL cancer panel assay consisted of 502 genes derived from various pub- lished data sets where gene selection is biased towards haematological malignancies. This is not an ideal setting ...
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Modified SureSelectQXT Target Enrichment Protocol for Illumina Multiplexed Sequencing of FFPE Samples
... 2 x reagent volumes. As expected, impact on the concentration for high-quality DNA samples (NA12892 and NT1) was low, while the impact was remarkable for T1. We also tested the impact of using a quarter of the originally ...
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Adaptation of a RAS pathway activation signature from FF to FFPE tissues in colorectal cancer
... of FFPE samples [21], we used the mean signal scores for the probes coupled with their fold-change information, to filter out 2 genes that were insufficiently expressed across the 39 ...to FFPE translation ...
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Epigenomic profiling of archived FFPE tissues by enhanced PAT-ChIP (EPAT-ChIP) technology
... archival FFPE samples cannot be controlled by definition, we focused on the improve- ment of chromatin extraction efficiency by (i) modify- ing sonication steps in terms of times and amplitudes relative to the ...
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PTPRO promoter methylation is predictive of poorer outcome for HER2 positive breast cancer: indication for personalized therapy
... tissue specimens were harvested and preserved from patients between June 1998 and December 2010 at the Affiliated Cancer Hospital of Shantou University Medical ...
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