NIH, National Cancer Institute, Division of Cancer Treatment and Diagnosis (DCTD) NIH - National Institutes of Health National Cancer Institute DCTD - Division of Cancer Treatment and Diagnosis
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Single nucleotide polymorphism array analysis of flow-sorted epithelial cells from frozen versus fixed tissues for whole genome analysis of allelic loss in breast cancer.

Author(s): Schubert EL, Hsu L, Cousens LA, Glogovac J, Self S, Reid BJ, Rabinovitch PS, Porter PL

Publication: Am J Pathol, 2002, Vol. 160, Page 73

PubMed ID: 11786401 PubMed Review Paper? No

Purpose of Paper

To validate the detection of single nucleotide polymorphisms (SNP), specifically allelic loss, in formalin-fixed paraffin embedded (FFPE) and frozen breast cancer tissue specimens using the Affymetrix HuSNP array before and after whole genome amplification (WGA).

Conclusion of Paper

SNP analysis using the HuSNP array resulted in a high degree of concordance among paired FFPE and frozen tissue. Although analysis of WGA produced results that varied slightly from those obtained using extracted genomic DNA, paired FFPE and frozen tissue yielded similar results within the assay. Further microsatellite analysis of short tandem repeats (STR) confirmed array based results.

Studies

  1. Study Purpose

    To validate the detection of single nucleotide polymorphisms (SNP), specifically allelic loss, in formalin-fixed paraffin embedded (FFPE) and frozen breast cancer tissue specimens using the Affymetrix HuSNP array before and after whole genome amplification (WGA).

    Summary of Findings:

    Both of the cases examined yielded similar genotype results among paired FFPE and frozen specimens using HuSNP array technology. WGA amplification also yielded reproducible and similar results among paired FFPE and frozen tissue, although results differed slightly from those obtained with extracted genomic DNA.

    Biospecimens
    Preservative Types
    • Formalin
    • OCT
    Diagnoses:
    • Neoplastic - Carcinoma
    • Neoplastic - Normal Adjacent
    Platform:
    AnalyteTechnology Platform
    DNA SNP assay
    Pre-analytical Factors:
    ClassificationPre-analytical FactorValue(s)
    Biospecimen Preservation Type of fixation/preservation OCT
    Formalin (buffered)
    View more
  2. Study Purpose

    To compare results of SNP array-based analysis with those obtained via targeted analysis of polymorphic repeat loci, specifically STR.

    Summary of Findings:

    Resultant data of the HuSNP analysis agreed well with microsatellite analysis of STR. Specifically, 24 STR markers on chromosomes 11 and 17 that correspond to 69 informative sites were analyzed, 60 of which correlated with HuSNP marker data.

    Biospecimens
    Preservative Types
    • Formalin
    • Frozen
    Diagnoses:
    • Neoplastic - Carcinoma
    • Neoplastic - Normal Adjacent
    Platform:
    AnalyteTechnology Platform
    DNA SNP assay
    Pre-analytical Factors:
    ClassificationPre-analytical FactorValue(s)
    Biospecimen Preservation Type of fixation/preservation Formalin (buffered)
    Snap frozen
    View more

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