Faculty Opinions recommendation of Comparison of Accuracy of Whole-Exome Sequencing with Formalin-Fixed Paraffin-Embedded and Fresh Frozen Tissue Samples.

2017 ◽  
Author(s):  
Alexandre Alanio
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Tissue Samples ◽  
Whole Exome ◽  
Formalin Fixed Paraffin ◽  
Frozen Tissue ◽  
Formalin Fixed Paraffin Embedded ◽  
Fresh Frozen ◽  
Formalin Fixed

scholarly journals Whole-Exome Sequencing (WES) Using Formalin-Fixed Paraffin Embedded (FFPE) Tissue

2013 ◽  
Vol 24 ◽  
pp. ix93
Author(s):  
K. Ouchi ◽  
S. Takahashi ◽  
K. Tatsuno ◽  
A. Hayashi ◽  
S. Yamamoto ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Ffpe Tissue ◽  
Whole Exome ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Formalin Fixed

scholarly journals Caveolin-3 Null Mutation in Family with Barretts Esophagus and Esophageal Adenocarcinoma

2021 ◽  
Author(s):  
Katherine S Garman ◽  
Richard von Furstenberg ◽  
Thomas C Becker ◽  
Gary W Falk ◽  
Joseph E Willis ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Myoepithelial Cells ◽  
Null Mutation ◽  
High Grade ◽  
Whole Exome ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Barretts Esophagus ◽  
Formalin Fixed

INTRODUCTION: Aggregation of Barretts esophagus (BE) and esophageal adenocarcinoma (EAC) in families has been termed familial Barretts esophagus (FBE). Analysis of single, large FBE families can enable the identification of genetic susceptibility to complex diseases such as BE and EAC. METHODS: Phenotypes of BE and EAC were ascertained in a large FBE family with 7 affected members: 4 men with EAC, 1 man with BE and high grade dysplasia, and 2 women with non-dysplastic BE by review of endoscopy and surgical pathology reports. Whole exome sequencing was performed on germline DNA from 3 affected members to identify variants in coding genes that segregated with disease. Formalin fixed paraffin embedded tissue from an affected family member as well as non-familial subjects with BE and EAC was examined with regular histology and immunohistochemistry. The CAV3 gene with a variant segregating in the family was further characterized in a porcine model of esophageal injury using immunofluorescence. RESULTS: Using a whole exome sequencing approach on an exceptional FBE family we identified a segregating nonsense mutation in the gene Caveolin-3 (CAV3). Histologic examination of a formalin fixed paraffin embedded (FFPE) esophagectomy specimen from an individual carrying the CAV3 null mutation revealed esophageal submucosal glands (ESMG) that showed acinar metaplasia with marked atypia and absence of myoepithelial cells, distinctly different from acinar metaplasia seen in ESMG of non-familial subjects with BE and high grade dysplasia. Immunofluorescence studies of ESMG in porcine esophagus revealed the presence of CAV3 in selected cells in a distribution that was consistent with myoepithelial cells. Experimental injury of the porcine esophagus using radiofrequency ablation revealed that CAV3 expression increased markedly within ESMGs, ESMG ductal epithelium, and overlying healing neosquamous epithelium 10 days after injury. CONCLUSIONS: We theorize that CAV3 expression, perhaps through myoepithelial cells within ESMGs, controls the differentiation and proliferation of squamous epithelial precursor cells in response to injury. Furthermore, the truncating nonsense CAV3 mutation discovered in a family disrupts normal squamous healing and the organization of ESMGs, making affected family members susceptible to the proliferation and development of metaplastic columnar BE and EAC.

scholarly journals Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine

2014 ◽  
Vol 20 (6) ◽  
pp. 682-688 ◽  
Author(s):  
Eliezer M Van Allen ◽  
Nikhil Wagle ◽  
Petar Stojanov ◽  
Danielle L Perrin ◽  
Kristian Cibulskis ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Clinical Interpretation ◽  
Whole Exome ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Cancer Medicine ◽  
Formalin Fixed
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