Formalin-Fixed Paraffin-Embedded Tissues: Methods and Protocols (Methods in Molecular Biology)

Presenting an area of research that intersects with and integrates diverse disciplines, including genomics, epigenetics, proteomics, and cellular biology, among others, Formalin-Fixed Paraffin-Embedded Tissues: Methods and Protocols collects contributions from expert researchers in order to provide practical guidelines to this complex study. Compiled in order to provide researchers with up-to-date methodological information pertaining to the utilization of genomic, transcriptomic, and proteomic data in diagnosis, prognosis, and tailored therapy, the ultimate aim of this volume is to decipher diseases at a molecular level. Divided into multiple convenient chapters, this detailed book covers various techniques to construct and utilize tissue arrays, it also provides detailed protocols in immunohistochemistry, immunofluorescence, fluorescent and chromogenic in situ hybridization, and ultimately introduces protocols for FFPET microdissection and nucleic acids extraction for their utilization in advanced techniques such as microarray CGH, DNA methylation and pyrosequencing. The volume also discusses FFPET research from an ethical standpoint and concludes with a chapter on novel tissue fixative. Written in the highly successful Methods in Molecular Biology(TM) series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls.   Authoritative and accessible, Formalin-Fixed Paraffin-Embedded Tissues: Methods and Protocols serves as a practical guide for scientists of all backgrounds and aims to convey the appropriate sense of fascination associated with this vital field of research. 1. Regulatory and Ethical Issues on the Utilization of FFPE Tissues in Research             Catherine M. With, David L. Evers, and Jeffrey T. Mason   2.  Tissue Microarrays: Construction and Uses             Carol B. Fowler, Yan-Gao Man, Shimin Zhang, Timothy J. O'Leary, Jeffrey T. Mason, and Robert E. Cunningham   3. Standardization in Immunohistology             Anthony S-Y Leong and Trishe Y-M Leong   4. Multiple Immunofluorescence Labeling of Formalin-fixed Paraffin-embedded (FFPE) Tissue             David Robertson and Clare M. Isacke   5. Microwaves for Chromogenic-in-situ-hybridization             Anthony S-Y Leong and Zenobia Haffajee   6. Automated Analysis of FISH-stained HER2/neu Samples with Metafer             Christian Schunck and Eiman Mohammad   7. Laser Capture Microdissection (LCM) of FFPE Tissue Sections Bridging the Gap between Microscopy and Molecular Analysis             Renate Burgemeister   8. Nucleic Acids Extraction from Laser Microdissected FFPE Tissue Sections             Renate Burgemeister   9. Microarray-based CGH and Copy Number Analysis of FFPE Samples             Fahd Al-Mulla   10. Microarray Profiling of DNA Extracted from FFPE Tissues using SNP6.0 Affymetrix Platform             Marianne Tuefferd, An de Bondt, Ilse Van den Wyngaert, Willem Talloen, and Hinrich Ghlmann   11. Whole Genome Amplification of DNA Extracted From FFPE Tissues             Mira Bosso and Fahd Al-Mulla   12. Pyrosequencing of DNA Extracted from Formalin-Fixed Paraffin-embedded Tissue                    Brendan Doyle, Ciarn O'Riain, and Kim Appleton   13. Analysis of DNA Methylation in  FFPE Tissues using the MethyLight Technology                        Ashraf Dallol, Waleed Al- Ali, Amina Al-Shaibani, and Fahd Al-Mulla   14. RT-PCR Gene Expression Profiling of RNA from Paraffin-Embedded Tissues Prepared Using a Range of Different Fixatives and Conditions             Mei-Lan Liu, Jennie Jeong, Ranjana Ambannavar, Carl Millward, Frederick Baehner, Chithra Sangli, Debjani Dutta, Mylan Pho, Anhthu Nguyen, and Maureen T. Cronin   15. RT-PCR-Based Gene Expression Profiling for Cancer Biomarker Discovery from Fixed Paraffin Embedded Tissues             Aaron Scott, Ranjana Ambannavar, Jennie Jeong, Mei-Lan Liu and Maureen T. Cronin   16. microRNA Isolation from Formalin-Fixed Paraffin-Embedded Tissues             Aihua Liu and Xiaowei Xu   17. Gene Expression Profiling of RNA Extracted from FFPE tissues:  NuGEN Technologies' Whole-Transcriptome Amplification System             Leah Turner, Joe Don Heath, and Nurith Kurn   18. Protein Mass Spectrometry Applications on FFPE Tissue Sections             Carol B. Fowler, Timothy J. O'Leary, and Jeffrey T. Mason   19. An Alternative Fixative to Formalin Fixation for Molecular Applications: the RCL2-CS100 Approach             Amlie Denoul, Florence Boissire-Michot, Philippe Rochaix, Frdric Bibeau, Nathalie Boulle