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Breast Cancer Research and Treatment

, Volume 125, Issue 3, pp 879–883 | Cite as

Gene expression array testing of FFPE archival breast tumor samples: an optimized protocol for WG-DASL® sample preparation

  • C. C. Ton
  • N. Vartanian
  • X. Chai
  • M. G. Lin
  • X. Yuan
  • K. E. Malone
  • C. I. Li
  • A. Dawson
  • C. Sather
  • J. Delrow
  • L. Hsu
  • P. L. Porter
Brief Report

Abstract

Archived formalin-fixed, paraffin embedded (FFPE) tissues constitute a vast, well-annotated, but underexploited resource for the molecular study of cancer progression, largely because degradation, chemical modification, and cross-linking, render FFPE RNA a suboptimal substrate for conventional analytical methods. We report here a modified protocol for RNA extraction from FFPE tissues which maximized the success rate (with 100% of samples) in the expression profiling of a set of 60 breast cancer samples on the WG-DASL platform; yielding data of sufficient quality such that in hierarchical clustering (a) 12/12 (100%) replicates correctly identified their respective counterparts, with a high self-correlation (r = 0.979), and (b) the overall sample set grouped with high specificity into ER+ (38/40; 95%) and ER− (18/20; 90%) subtypes. These results indicate that a large fraction of decade-old FFPE samples, of diverse institutional origins and processing histories, can yield RNA suitable for gene expression profiling experiments.

Keywords

FFPE RNA extraction WG-DASL Gene expression profiling 

Notes

Acknowledgments

This study was supported by funding: NIH/NCI R01CA098858 (KEM, CIL, PLP, LH); Safeway Foundation (PLP, KEM); NIH/NCI P50 CA148143 (PLP). The authors wish to thank Ryan Basom for assistance with use of Bioconductor lumi package, and in data preprocessing.

Conflict of interest

None.

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Copyright information

© Springer Science+Business Media, LLC. 2010

Authors and Affiliations

  • C. C. Ton
    • 1
    • 2
  • N. Vartanian
    • 1
  • X. Chai
    • 2
  • M. G. Lin
    • 1
  • X. Yuan
    • 1
  • K. E. Malone
    • 2
  • C. I. Li
    • 2
  • A. Dawson
    • 3
  • C. Sather
    • 3
  • J. Delrow
    • 3
  • L. Hsu
    • 2
  • P. L. Porter
    • 1
    • 2
    • 4
  1. 1.Divisions of Human BiologyFred Hutchinson Cancer Research CenterSeattleUSA
  2. 2.Public Health SciencesFred Hutchinson Cancer Research CenterSeattleUSA
  3. 3.Genomics Shared ResourcesFred Hutchinson Cancer Research CenterSeattleUSA
  4. 4.Department of PathologyUniversity of WashingtonSeattleUSA

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