osteosarcoma is a relatively uncommon malignancy however, it is the most common form of primary malignant bone tumors in human. diagnosis and prognosis of patients with osteosarcoma is limited to clinico-radiopathological parameters, whereas molecular markers of tumor aggression have been poorly identified. survivin, an inhibitor of apoptosis (iap), is unique for its expression in human tumors ...

A formalin-fixed paraffin-embedded (FFPE) sample usually yields highly degraded DNA, which limits the use of techniques requiring high-quality DNA, such as Infinium Methylation microarrays. To overcome this restriction, we have applied an FFPE restoration procedure consisting of DNA repair and ligation processes in a set of paired fresh-frozen (FF) and FFPE samples. We validated the FFPE result...

micrornas (mirnas) are a group of short non-coding rnas implicated in numerous fundamental cellular processes, and their disregulations have been linked to several pathologic conditions, mainly cancers. determining tissue distribution of mirnas is a prerequisite for understanding their exact functions during development, tissue homeostasis and abnormality. in situ hybridization is a powerful te...

Formalin-fixed, paraffin-embedded (FFPE) material tends to yield degraded DNA and is thus suboptimal for use in many downstream applications. We describe an integrated analysis of genotype, loss of heterozygosity (LOH), and copy number for DNA derived from FFPE tissues using oligonucleotide microarrays containing over 500K single nucleotide polymorphisms. A prequalifying PCR test predicted the ...

In preclinical studies, heregulin (HRG) expression was shown to be the most relevant predictive biomarker for response to patritumab, a fully human anti-epidermal growth factor receptor 3 monoclonal antibody. In support of a phase 2 study of erlotinib ± patritumab in non-small cell lung cancer (NSCLC), a reverse-transcription quantitative polymerase chain reaction (RT-qPCR) assay for relative q...

The Whole Genome Sampling Analysis (WGSA) assay in combination with Affymetrix GeneChip Mapping Arrays is used for copy number analysis of high-quality DNA samples (i.e., samples that have been collected from blood, fresh or frozen tissue, or cell lines). Formalin-fixed, paraffin-embedded (FFPE) samples, however, represent the most prevalent form of archived clinical samples, but they provide a...

Matrix-Assisted Laser Desorption Ionization (MALDI) Mass Spectrometry Imaging (MSI) is fast becoming an industry leading technique as a means of investigating the distributions of protein and peptide molecules directly from sections of tissue. Developing protocols for the analysis of FFPE tissue opens up numerous opportunities for novel biomarker discovery, due to the large number of tissue ban...

Formalin-fixed paraffin-embedded (FFPE) tissue specimens comprise a potentially valuable resource for both prospective and retrospective biomarker discovery. Unlocking the proteomic profile of clinicopathological FFPE tissues is a critically essential step for annotating clinical findings and predicting biomarkers for ultimate disease prognosis and therapeutic follow-up.

Formalin-fixed paraffin-embedded (FFPE) samples represent a valuable resource for clinical researches. However, FFPE samples are usually considered an unreliable source for gene expression analysis due to the partial RNA degradation. In this study, through comparing gene expression profiles between FFPE samples and paired fresh-frozen (FF) samples for three cancer types, we firstly showed that ...

The Transplex Complete Whole Transcriptome Amplification (WTA2) Kit has been enhanced to effectively amplify damaged RNA. Total RNA samples isolated from matched FFPE (formalin-fixed paraffin-embedded) and frozen prostate tissues (malignant and normal) were amplified with the Transplex WTA2 Kit and analyzed on Agilent Whole Genome expression microarrays. A call rate of >65% was observed for com...