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Obstetrics and Gynecology International
Volume 2013 (2013), Article ID 576842, 9 pages
http://dx.doi.org/10.1155/2013/576842
Research Article

Feasibility of RNA and DNA Extraction from Fresh Pipelle and Archival Endometrial Tissues for Use in Gene Expression and SNP Arrays

1Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
2Division of Vaccine and Infectious Disease, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
3Department of Obstetrics and Gynecology, University of Washington School of Medicine, Seattle, WA 98105, USA
4Department of Pathology, University of Washington Medical School, Seattle, WA 98105, USA
5Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
6Department of Medicine, University of Washington, Seattle, WA 98105, USA
7Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
8The Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
9The Norris Cotton Cancer Center, Lebanon, NH 03756, USA

Received 8 May 2013; Accepted 22 August 2013

Academic Editor: Eric Prossnitz

Copyright © 2013 Heather D. Kissel et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Identifying molecular markers of endometrial hyperplasia (neoplasia) progression is critical to cancer prevention. To assess RNA and DNA quantity and quality from routinely collected endometrial samples and evaluate the performance of RNA- and DNA-based arrays across endometrial tissue types, we collected fresh frozen (FF) Pipelle, FF curettage, and formalin-fixed paraffin-embedded (FFPE) hysterectomy specimens (benign indications) from eight women. Additionally, neoplastic and uninvolved tissues from 24 FFPE archival hysterectomy specimens with endometrial hyperplasias and carcinomas were assessed. RNA was extracted from 15 of 16 FF and 51 of 51 FFPE samples, with yields >1.2 μg for 13/15 (87%) FF and 50/51 (98%) FFPE samples. Extracted RNA was of high quality; all samples performed successfully on the Illumina whole-genome cDNA-mediated annealing, selection, extension, and ligation (WG-DASL) array and performance did not vary by tissue type. While DNA quantity from FFPE samples was excellent, quality was not sufficient for successful performance on the Affymetrix SNP Array 6.0. In conclusion, FF Pipelle samples, which are minimally invasive, yielded excellent quantity and quality of RNA for gene expression arrays (similar to FF curettage) and should be considered for use in genomic studies. FFPE-derived DNA should be evaluated on new rapidly evolving sequencing platforms.