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Real-Time PCR Assays on Formalin-Fixed, Paraffin-Embedded Medulloblastomas

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Medulloblastoma

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2423))

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Abstract

Real-time PCR technology has been instrumental in contributing toward biomarker discovery, classification of tumors as well as risk stratification of patients. However, much of its success depends on the quality and quantity of the starting material used for RNA extraction. Clinical samples are most often provided as formalin-fixed and paraffin-embedded, wherein the RNA is extensively degraded, affecting sensitivity. Here, we describe a real-time PCR based assay developed for molecular subgrouping of medulloblastomas that is particularly useful for formalin-fixed, paraffin-embedded (FFPE) samples.

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References

  1. Chung JY, Braunschweig T, Williams R et al (2008) Factors in tissue handling and processing that impact RNA obtained from formalin-fixed, paraffin-embedded tissue. J Histochem Cytochem 56(11):1033–1042

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. von Ahlfen S, Missel A, Bendrat K et al (2007) Determinants of RNA quality from FFPE samples. PLoS One 2(12):e1261

    Article  CAS  Google Scholar 

  3. Specht K, Richter T, Muller U et al (2001) Quantitative gene expression analysis in microdissected archival formalin-fixed and paraffin-embedded tumor tissue. Am J Pathol 158(2):419–429

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Hall JS, Taylor J, Valentine HR et al (2012) Enhanced stability of microRNA expression facilitates classification of FFPE tumour samples exhibiting near total mRNA degradation. Br J Cancer 107(4):684–694

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Kunder R, Jalali R, Sridhar E et al (2013) Real-time PCR assay based on the differential expression of microRNAs and protein-coding genes for molecular classification of formalin-fixed paraffin embedded medulloblastomas. Neuro-Oncology 15(12):1644–1651

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Korbler T, Grskovic M, Dominis M et al (2003) A simple method for RNA isolation from formalin-fixed and paraffin-embedded lymphatic tissues. Exp Mol Pathol 74(3):336–340

    Article  CAS  PubMed  Google Scholar 

  7. Chomczynski P, Sacchi N (1987) Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162(1):156–159

    Article  CAS  PubMed  Google Scholar 

  8. Tibshirani R, Hastie T, Narasimhan B et al (2002) Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci U S A 99(10):6567–6572

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Kunder, R., Shirsat, N.V. (2022). Real-Time PCR Assays on Formalin-Fixed, Paraffin-Embedded Medulloblastomas. In: Dey, A., Malhotra, A., Garg, N. (eds) Medulloblastoma. Methods in Molecular Biology, vol 2423. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1952-0_2

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  • DOI: https://doi.org/10.1007/978-1-0716-1952-0_2

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1951-3

  • Online ISBN: 978-1-0716-1952-0

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