Oligonucleotide array outperforms SNP array on formalin-fixed paraffin-embedded clinical samples

Nasri, Soroush, Anjomshoaa, Ahmad, Song, Sarah, Guilford, Parry, McNoe, Les, Black, Michael, Phillips, Vicky, Reeve, Anthony and Humar, Bostjan (2010) Oligonucleotide array outperforms SNP array on formalin-fixed paraffin-embedded clinical samples. Cancer Genetics and Cytogenetics, 198 1: 1-6. doi:10.1016/j.cancergencyto.2009.12.002

Author Nasri, Soroush
Anjomshoaa, Ahmad
Song, Sarah
Guilford, Parry
McNoe, Les
Black, Michael
Phillips, Vicky
Reeve, Anthony
Humar, Bostjan
Title Oligonucleotide array outperforms SNP array on formalin-fixed paraffin-embedded clinical samples
Journal name Cancer Genetics and Cytogenetics   Check publisher's open access policy
ISSN 0165-4608
Publication date 2010-03-17
Sub-type Article (original research)
DOI 10.1016/j.cancergencyto.2009.12.002
Open Access Status
Volume 198
Issue 1
Start page 1
End page 6
Total pages 6
Editor Avery A. Sandberg
Place of publication U. S. A.
Publisher Elsevier
Language eng
Abstract Compromised quality of formalin-fixed paraffin-embedded (FFPE)-derived DNA has compounded the use of archival specimens for array-based genomic studies. Recent technological advances have led to first successes in this field; however, there is currently no general agreement on the most suitable platform for the array-based analysis of FFPE DNA. In this study, FFPE and matched fresh-frozen (FF) specimens were separately analyzed with Affymetrix single nucleotide polymorphism (SNP) 6.0 and Agilent 4x44 K oligonucleotide arrays to compare the genomic profiles from the two tissue sources and to assess the relative performance of the two platforms on FFPE material. Genomic DNA was extracted from matched FFPE–FF pairs of normal intestinal epithelium from four patients and were applied to the SNP and oligonucleotide platforms according to the manufacturer-recommended protocols. On the Affymetrix platform, a substantial increase in apparent copy number alterations was observed in all FFPE tissues relative to their matched FF counterparts. In contrast, FFPE and matched FF genomic profiles obtained via the Agilent platform were very similar. Both the SNP and the oligonucleotide platform performed comparably on FF material. This study demonstrates that Agilent oligonucleotide array comparative genomic hybridization generates reliable results from FFPE extracted DNA, whereas the Affymetrix SNP-based array seems less suitable for the analysis of FFPE material.
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Non HERDC
School of Nursing, Midwifery and Social Work Publications
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 6 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 6 times in Scopus Article | Citations
Google Scholar Search Google Scholar
Created: Mon, 29 Mar 2010, 02:15:14 EST by Dr Sarah Song on behalf of School of Nursing, Midwifery and Social Work