scholarly journals Targeted or whole genome sequencing of formalin fixed tissue samples: potential applications in cancer genomics

Oncotarget ◽  
2015 ◽  
Vol 6 (28) ◽  
pp. 25943-25961 ◽  
Author(s):  
Sarah Munchel ◽  
Yen Hoang ◽  
Yue Zhao ◽  
Joseph Cottrell ◽  
Brandy Klotzle ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Cancer Genomics ◽  
Whole Genome ◽  
Fixed Tissue ◽  
Tissue Samples ◽  
Formalin Fixed Tissue ◽  
Potential Applications ◽  
Formalin Fixed

Abstract 4281: Targeted or whole genome sequencing of formalin-fixed tissue samples

2014 ◽  
Author(s):  
Sarah Munchel ◽  
Yen Hoang ◽  
Yue Zhao ◽  
Joseph Cottrell ◽  
Brandy Klotzle ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Fixed Tissue ◽  
Tissue Samples ◽  
Formalin Fixed Tissue ◽  
Formalin Fixed

scholarly journals Specific Detection of Lawsonia intracellularis in Porcine Proliferative Enteropathy Inferred from Fluorescent rRNA In Situ Hybridization

1998 ◽  
Vol 35 (2) ◽  
pp. 153-156 ◽  
Author(s):  
M. Boye ◽  
T. K. Jensen ◽  
K. Møller ◽  
T. D. Leser ◽  
S. E. Jorsal
Keyword(s):  
In Situ Hybridization ◽  
Fluorescent In Situ Hybridization ◽  
Lawsonia Intracellularis ◽  
Specific Detection ◽  
Fixed Tissue ◽  
Tissue Samples ◽  
Formalin Fixed Tissue ◽  
Proliferative Enteropathy ◽  
Formalin Fixed

Fluorescent in situ hybridization targeting 16S ribosomal RNA was used for specific detection of the obligate intracellular bacterium Lawsonia intracellularis in enterocytes from pigs affected by proliferative enteropathy. A specific oligonucleotide probe was designed and the specificity of the probe was determined by simultaneous comparison with indirect immunofluorescence assay for detection of L. intracellularis in formalin-fixed tissue samples from 15 pigs affected by porcine proliferative enteropathy. We used 10 tissue samples from pigs without proliferative mucosal changes as negative controls. The results showed that the oligonucleotide probe is specific for L. intracellularis and that fluorescent in situ hybridization targeting ribosomal RNA is a suitable and fast method for specific detection and histological recognition of L. intracellularis in formalin-fixed tissue.

Effect of formalin fixation on thermal conductivity of the biological tissue

2014 ◽  
Author(s):  
Steven C. Bauserman ◽  
Jonathan W. Valvano
Keyword(s):  
Thermal Conductivity ◽  
Biological Tissues ◽  
Formalin Fixation ◽  
Fatty Tissue ◽  
Fresh Tissue ◽  
Fixed Tissue ◽  
Tissue Samples ◽  
Formalin Fixed Tissue ◽  
Formalin Fixed

Effect of formalin fixation on thermal conductivity of the biological tissues is presented. A self-heated thermistor probe was used to measure the tissue thermal conductivity. The thermal conductivity of muscle and fatty tissue samples was measured before the formalin fixation and then 27 hours after formalin fixation. The results indicate that the formalin fixation does not cause a significant change in the tissue thermal conductivity of muscle and fatty tissues. In the clinical setting, tissues removed surgically are often fixed in formalin for subsequent pathological analysis. These results suggest that, in terms of thermal properties, it is equally appropriate to perform in vitro studies in either fresh tissue or formalin-fixed tissue.

scholarly journals Shallow whole genome sequencing for robust copy number profiling of formalin-fixed paraffin-embedded breast cancers

2018 ◽  
Vol 104 (3) ◽  
pp. 161-169 ◽  
Author(s):  
Suet-Feung Chin ◽  
Angela Santonja ◽  
Marta Grzelak ◽  
Soomin Ahn ◽  
Stephen-John Sammut ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Copy Number ◽  
Whole Genome ◽  
Breast Cancers ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Formalin Fixed

scholarly journals Biochemical Subtyping of Amyloid in Formalin-Fixed Tissue Samples Confirms and Supplements Immunohistologic Data

2004 ◽  
Vol 121 (6) ◽  
pp. 794-800 ◽  
Author(s):  
Batia Kaplan ◽  
Brian M. Martin ◽  
Avi Livneh ◽  
Mordechai Pras ◽  
Gloria R. Gallo
Keyword(s):  
Fixed Tissue ◽  
Tissue Samples ◽  
Formalin Fixed Tissue ◽  
Formalin Fixed

scholarly journals Resin Tissue Microarrays: a Universal Format for Immunohistochemistry

2005 ◽  
Vol 53 (10) ◽  
pp. 1189-1197 ◽  
Author(s):  
William J. Howat ◽  
Anthony Warford ◽  
Joanne N. Mitchell ◽  
Kay F. Clarke ◽  
Jen S. Conquer ◽  
...  
Keyword(s):  
Polyclonal Antibodies ◽  
Tissue Microarrays ◽  
Single Chain ◽  
Fixed Tissue ◽  
Tissue Samples ◽  
Glycol Methacrylate ◽  
Formalin Fixed Tissue ◽  
Single Chain Fv ◽  
Nuclear Antigens ◽  
Formalin Fixed

Tissue microarray (TMA) technology allows the miniaturization and characterization of multiple tissue samples on a single slide and commonly uses formalin-fixed paraffin-embedded (FFPE) tissue or acetone-fixed frozen tissue. The former provides good morphology but can compromise antigenicity, whereas the latter provides compromised morphology with good antigenicity. Here, we report the development of TMAs in glycol methacrylate resin, which combine the advantages of both methods in one embedding format. Freshly collected tissue fixed in -20C acetone or 10% neutral buffered formaldehyde were cored and arrayed into an intermediary medium of 2% agarose before infiltration of the agarose array with glycol methacrylate resin. Acetone-fixed resin TMA demonstrated improved morphology over acetone-fixed frozen TMA, with no loss of antigenicity. Staining for extracellular, cell surface, and nuclear antigens could be realized with monoclonal and polyclonal antibodies as well as with monomeric single-chain Fv preparations. In addition, when compared with FFPE TMA, formalin-fixed tissue in a resin TMA gave enhanced morphology and subcellular detail. Therefore, resin provides a universal format for the construction of TMAs, providing improved tissue morphology while retaining antigenicity, allows thin-section preparation, and could be used to replace preparation of frozen and FFPE TMAs for freshly collected tissue.

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