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

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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.

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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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Authors and Affiliations

  1. Divisions of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA, 98109, USA

    C. C. Ton, N. Vartanian, M. G. Lin, X. Yuan & P. L. Porter

  2. Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA, 98109, USA

    C. C. Ton, X. Chai, K. E. Malone, C. I. Li, L. Hsu & P. L. Porter

  3. Genomics Shared Resources, Fred Hutchinson Cancer Research Center, Seattle, WA, USA

    A. Dawson, C. Sather & J. Delrow

  4. Department of Pathology, University of Washington, Seattle, WA, USA

    P. L. Porter

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  1. C. C. Ton
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  2. N. Vartanian
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  4. M. G. Lin
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  11. L. Hsu
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  12. P. L. Porter
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Corresponding author

Correspondence to P. L. Porter.

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Ton, C.C., Vartanian, N., Chai, X. et al. Gene expression array testing of FFPE archival breast tumor samples: an optimized protocol for WG-DASL® sample preparation. Breast Cancer Res Treat 125, 879–883 (2011). https://doi.org/10.1007/s10549-010-1159-6

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  • DOI: https://doi.org/10.1007/s10549-010-1159-6

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