Virtual histology of an entire mouse brain from formalin fixation to paraffin embedding. Part 1: Data acquisition, anatomical feature segmentation, tracking global volume and density changes

e22142 Background: Analysis of nucleic acids (NA) from formalin fixed paraffin embedded (FFPE) tissue can provide detailed information about gene sequence mutational status, which may be important for oncology treatment decisions. FFPE specimens also have utility for retrospective analyses. Potential degradation of NA during formalin fixation, paraffin embedding processes and possible continued deterioration during subsequent storage may diminish utility of FFPE tissue for these purposes. Using real-time PCR, this study investigated the functional stability of RNA from brain FFPE tissue sections on slides over an extended time period after sectioning. Methods: Brain biopsy specimens obtained from glioblastoma patients with informed consent were used to prepare blocks with standard formalin fixation and paraffin embedding techniques. Slides were made from the FFPE blocks and stored at room temperature until testing. RNA was extracted from sequential slides within one week of sectioning for a zero time and then at 4, 8 and 12 months. Reverse transcription PCR was performed, and real-time PCR was analyzed on the ABI7900 to detect EGFRvIII mutation and cABL gene. RNA Integrity Analysis was performed with an Agilent Bioanalyzer. Results: Consistent qualitative results were obtained with EGFRvIII mutant positive specimens (n =10) and wild type (wt) specimens (n =10) from slides stored up to twelve months at room temperature compared to the initial testing (95% agreement). One wt specimen showed negative results for the first three time points but a low positive result at 12 months, possibly due to tumor content change in the different sections of the FFPE block. Ct values for EGFR (wt and mutant) and cABL genes did not increase during the storage period. RNA integrity number (RIN) indicated the degradation of RNA during FFPE processing, although no further significant degradation occurred during the course of the experiment. Conclusions: The results of this study indicated that although the RNA was impacted by the tissue preparation, fixation, and processing steps, for the brain FFPE slide specimens, target genes with amplicon size up to 124bp could be detected with minimum degradation for up to 12 months when slides were stored at room temperature.

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Breast cancer and melanoma cell line identification by FTIR imaging after formalin-fixation and paraffin-embedding

The Analyst ◽

10.1039/c3an00246b ◽

2013 ◽

Vol 138 (14) ◽

pp. 4083 ◽

Cited By ~ 33

Author(s):

M. Verdonck ◽

N. Wald ◽

J. Janssis ◽

P. Yan ◽

C. Meyer ◽

...

Keyword(s):

Breast Cancer ◽

Cell Line ◽

Melanoma Cell ◽

Melanoma Cell Line ◽

Formalin Fixation ◽

Ftir Imaging ◽

Paraffin Embedding ◽

Line Identification ◽

Cell Line Identification

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Diagnosis of melanoma and fluorescence HMB-45 staining. Malignant melanoma judged in preoperative. Fluorescence HMB-45 immunostaining findings of formalin-fixation paraffin embedding identical slice.

Skin Cancer ◽

10.5227/skincancer.11.203 ◽

1996 ◽

Vol 11 (2) ◽

pp. 203-209

Author(s):

Chizuko MORISHIMA ◽

Takafumi MORISHIMA ◽

Koujin YOSHIZAWA ◽

Hiroyuki HARA ◽

Michio HONJOU ◽

...

Keyword(s):

Malignant Melanoma ◽

Formalin Fixation ◽

Paraffin Embedding ◽

Hmb 45

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A Review of Preanalytical Factors Affecting Molecular, Protein, and Morphological Analysis of Formalin-Fixed, Paraffin-Embedded (FFPE) Tissue: How Well Do You Know Your FFPE Specimen?

Archives of Pathology & Laboratory Medicine ◽

10.5858/arpa.2013-0691-ra ◽

2014 ◽

Vol 138 (11) ◽

pp. 1520-1530 ◽

Cited By ~ 112

Author(s):

B. Paige Bass ◽

Kelly B. Engel ◽

Sarah R. Greytak ◽

Helen M. Moore

Keyword(s):

Formalin Fixation ◽

Research Database ◽

Factors Affecting ◽

Factors Associated ◽

Paraffin Embedding ◽

Formalin Fixed Paraffin ◽

Formalin Fixed Paraffin Embedded ◽

Embedded Blocks ◽

The Impact ◽

Formalin Fixed

Context Formalin fixation and paraffin embedding is a timeless, cost-efficient, and widely adopted method of preserving human tissue biospecimens that has resulted in a substantial reservoir of formalin-fixed, paraffin-embedded blocks that represent both the pathology and preanalytical handling of the biospecimen. This reservoir of specimens is increasingly being used for DNA, RNA, and proteomic analyses. Objective To evaluate the impact of preanalytical factors associated with the formalin fixation and paraffin embedding process on downstream morphological and molecular endpoints. Data Sources We surveyed the existing literature using the National Cancer Institute's Biospecimen Research Database for published reports investigating the potential influence of preanalytical factors associated with the formalin fixation and paraffin embedding process on DNA, RNA, protein, and morphological endpoints. Conclusions Based on the literature evidence, the molecular, proteomic, and morphological endpoints can be altered in formalin-fixed, paraffin-embedded specimens by suboptimal processing conditions. While the direction and magnitude of effects associated with a given preanalytical factor were dependent on the analyte (DNA, RNA, protein, and morphology) and analytical platform, acceptable conditions are highlighted, and a summary of conditions that could preclude analysis is provided.

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