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

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 col...

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Autores principales: Kissel, Heather D., Paulson, Thomas G., Liu, Karen, Li, Xiaohong, Swisher, Elizabeth, Garcia, Rochelle, Sanchez, Carissa A., Reid, Brian J., Reed, Susan D., Doherty, Jennifer Anne
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Hindawi Publishing Corporation 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3825122/
https://www.ncbi.nlm.nih.gov/pubmed/24282417
http://dx.doi.org/10.1155/2013/576842
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author Kissel, Heather D.
Paulson, Thomas G.
Liu, Karen
Li, Xiaohong
Swisher, Elizabeth
Garcia, Rochelle
Sanchez, Carissa A.
Reid, Brian J.
Reed, Susan D.
Doherty, Jennifer Anne
author_facet Kissel, Heather D.
Paulson, Thomas G.
Liu, Karen
Li, Xiaohong
Swisher, Elizabeth
Garcia, Rochelle
Sanchez, Carissa A.
Reid, Brian J.
Reed, Susan D.
Doherty, Jennifer Anne
author_sort Kissel, Heather D.
collection PubMed
description 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.
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spelling pubmed-38251222013-11-26 Feasibility of RNA and DNA Extraction from Fresh Pipelle and Archival Endometrial Tissues for Use in Gene Expression and SNP Arrays Kissel, Heather D. Paulson, Thomas G. Liu, Karen Li, Xiaohong Swisher, Elizabeth Garcia, Rochelle Sanchez, Carissa A. Reid, Brian J. Reed, Susan D. Doherty, Jennifer Anne Obstet Gynecol Int Research Article 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. Hindawi Publishing Corporation 2013 2013-10-26 /pmc/articles/PMC3825122/ /pubmed/24282417 http://dx.doi.org/10.1155/2013/576842 Text en Copyright © 2013 Heather D. Kissel et al. https://creativecommons.org/licenses/by/3.0/ 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.
spellingShingle Research Article
Kissel, Heather D.
Paulson, Thomas G.
Liu, Karen
Li, Xiaohong
Swisher, Elizabeth
Garcia, Rochelle
Sanchez, Carissa A.
Reid, Brian J.
Reed, Susan D.
Doherty, Jennifer Anne
Feasibility of RNA and DNA Extraction from Fresh Pipelle and Archival Endometrial Tissues for Use in Gene Expression and SNP Arrays
title Feasibility of RNA and DNA Extraction from Fresh Pipelle and Archival Endometrial Tissues for Use in Gene Expression and SNP Arrays
title_full Feasibility of RNA and DNA Extraction from Fresh Pipelle and Archival Endometrial Tissues for Use in Gene Expression and SNP Arrays
title_fullStr Feasibility of RNA and DNA Extraction from Fresh Pipelle and Archival Endometrial Tissues for Use in Gene Expression and SNP Arrays
title_full_unstemmed Feasibility of RNA and DNA Extraction from Fresh Pipelle and Archival Endometrial Tissues for Use in Gene Expression and SNP Arrays
title_short Feasibility of RNA and DNA Extraction from Fresh Pipelle and Archival Endometrial Tissues for Use in Gene Expression and SNP Arrays
title_sort feasibility of rna and dna extraction from fresh pipelle and archival endometrial tissues for use in gene expression and snp arrays
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3825122/
https://www.ncbi.nlm.nih.gov/pubmed/24282417
http://dx.doi.org/10.1155/2013/576842
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