FFPE Tissue DNA Extraction and VDJ Analysis

Genomic DNA was extracted from 5 to 10 μm of FFPE tissue using a DNA extractor (MagCore NucleicAcid Extractor, RBC Bioscience, Taiwan) and MagCore Genomic DNA FFPE One-Step Kit, following the manufacturer’s recommendations. Genomic DNA quality was assessed using BIOMED-2 control gene PCR protocol and samples with a DNA product size of ≥ 300 base pairs (bp) were analyzed [11 (link)]. Before initiating VDJ gene rearrangement analysis by HTS, all cases were analyzed to evaluate clonality according to the BIOMED-2 protocol [11 (link)]. NGS analysis was performed on 454 GS Junior system (Roche) previously described [12 (link)]. Data analysis was performed using the Roche (Basel, Switzerland) proprietary software package for the 454 GS Junior system (Roche). Image acquisition, image processing, and signal processing were performed during the run.

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Granai M., Amato T., Di Napoli A., Santi R., Vergoni F., Di Stefano G., Mancini V., Kovalchuk S., Cencini E., Carta A.G., Aversa S., Ziepert M., Cevenini G., Lazzi S., Leoncini L, & Bellan C. (2019). IGHV mutational status of nodal marginal zone lymphoma by NGS reveals distinct pathogenic pathways with different prognostic implications. Virchows Archiv, 477(1), 143-150.

Publication 2019

MagCore NucleicAcid Extractor MagCore Genomic DNA FFPE One-Step Kit 454 GS Junior system

A dna Gene Gene rearrangement Genomic Tissue

Corresponding Organization : University of Siena

Other organizations : Sapienza University of Rome, Azienda Ospedaliero-Universitaria Careggi, University of Florence, Leipzig University

Top 5 similar protocols

Variable analysis

independent variables

DNA extraction method (MagCore NucleicAcid Extractor, RBC Bioscience, Taiwan)
DNA extraction kit (MagCore Genomic DNA FFPE One-Step Kit)

dependent variables

Genomic DNA quality (assessed using BIOMED-2 control gene PCR protocol)
Clonality (evaluated according to the BIOMED-2 protocol)
VDJ gene rearrangement analysis by HTS

control variables

FFPE tissue sample size (5 to 10 μm)
Manufacturer's recommendations for DNA extraction

controls

Positive control: BIOMED-2 control gene PCR protocol
Negative control: Not explicitly mentioned

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