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A Predictive Factor of the Quality of Microarray Comparative Genomic Hybridization Analysis for Formalin-fixed Paraffin-embedded Archival Tissue


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Title: A Predictive Factor of the Quality of Microarray Comparative Genomic Hybridization Analysis for Formalin-fixed Paraffin-embedded Archival Tissue
Authors: Nakao, Kenjiro / Oikawa, Masahiro / Arai, Junichi / Mussazhanova, Zhanna / Kondo, Hisayoshi / Shichijo, Kazuko / Nakashima, Masahiro / Hayashi, Tomayoshi / Yoshiura, Koh-ichiro / Hatachi, Toshiko / Nagayasu, Takeshi
Issue Date: Sep-2013
Publisher: Lippincott Williams and Wilkins
Citation: Diagnostic Molecular Pathology, 22(3), pp.174-180; 2013
Abstract: Utilizing formalin-fixed paraffin-embedded (FFPE) archival tissue, the most common form of tissue preservation in routine practice, for cytogenetic analysis using microarray comparative genomic hybridization (aCGH) remains challenging. We searched for a predictive factor of the performance of FFPE DNA in aCGH analysis. DNA was extracted from 63 FFPE archival tissue samples of various tissue types (31 breast cancers, 24 lung cancers, and 8 thyroid tumors), followed by aCGH analysis using high-density oligonucleotide microarrays. Tumor DNA from matched frozen samples and from FFPE samples after whole-genome amplification were also analyzed in 2 and 4 case, respectively. The derivative log ratio spread (DLRSpread) was used to assess the overall quality of each aCGH result. The DLRSpread correlated significantly with the double-stranded DNA ratio of tumor DNA, storage time, and the degree of labeling with Cy5 (P<0.0001; correlation coefficients=-0.796, 0.551, -0.481, respectively). Stepwise multiple linear regression analysis revealed that the double-stranded DNA ratio of tumor DNA is the most significant predictive factor of DLRSpread (regression coefficient=-0.4798; P=<0.0001). The cytogenetic profiles of FFPE and matched frozen samples showed good concordance. Although the double-stranded DNA ratios were increased after whole-genome amplification, the DLRSpread was not improved. The double-stranded DNA ratio can be used to predict the performance of aCGH analysis for DNA from FFPE samples. Using this quality metric, valuable FFPE archival tissue samples can be utilized for aCGH analysis.
Keywords: cancer / comparative genomic hybridization / cytogenetics / Formalin-fixed paraffin-embedded / microarray
URI: http://hdl.handle.net/10069/34082
ISSN: 10529551
DOI: 10.1097/PDM.0b013e31828191de
Rights: © 2013 by Lippincott Williams & Wilkins. / This is a non-final version of an article published in final form in Diagnostic Molecular Pathology, 22(3), pp.174-180;2013
Type: Journal Article
Text Version: author
Appears in Collections:Articles in academic journal

Citable URI : http://hdl.handle.net/10069/34082

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