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Phi29-based amplification of fresh-frozen and FFPE tumor DNA

ABSTRACT: Corresponds to Bredel et al 2005 Figure 1 Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

ORGANISM(S): Homo sapiens

PROVIDER: GSE4078 | GEO | 2006/01/21

SECONDARY ACCESSION(S): PRJNA104575

REPOSITORIES: GEO

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Phi29-based amplification of fresh-frozen and FFPE tumor DNA

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The 31 pairs of FF (fresh frozen) andFFPE (Formalin-fixed paraffin-embedded) data for the application of 95GC to FFPE in 2019.

Project description:The study aimed to apply 95GC, originally developed using fresh‑frozen (FF) tissues, to formalin‑fixed paraffin‑embedded (FFPE) tissues, because FFPE tissues are routinely prepared and are readily available. Although we previously reported the applicability of 72GC to FFPE tissues (DOI: 10.1016/j.clbc.2013.11.006), the present study aimed to improve the accuracy of 95GC for FFPE tissues using the reference robust multiarray average (refRMA) method, optimized for FFPE tissues. Therefore, a 95GC RS (Recurrence Score) was first developed and then the accuracy of the newly developed 95GC algorithm for FFPE tissues was evaluated using the 95GC RS. These 31 pairs of FF and FFPE data are included in the concordance analysis of 95GC high/low results between FF and FFPE (Figure 3B). A long time passed, and now it is unclear how these 31 cases were distributed among the analysis. *Note: This old data has been updated multiple times by the other members. Then, there are some differences from the original paper and unclear points still remain. Therefore, do not use it for formal analysis aimed at public insurance coverage etc. This is for research purposes only. Please cite this paper when writing a new paper. PMID: 31638234 DOI: 10.3892/or.2019.7358

2023-06-16 | GSE234686 | GEO

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