161P - Utilization of formalin-fixed, paraffin-embedded archival tissue for cytogenetic analysis of microarray-comparative genomic hybridization

Date 30 September 2012
Event ESMO Congress 2012
Session Poster presentation II
Topics Translational Research
Presenter Masahiro Oikawa
Authors M. Oikawa1, J. Arai1, H. Kondo2, M. Nakashima3, T. Hayashi4, K. Yoshiura5, H. Yano1, T. Nagayasu1
  • 1Surgical Oncology, Nagaski University Hospital, 852-8501 - Nagasaki/JP
  • 2Biostatistics Section, Division Of Scientific Data Registry, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki - Nagasaki/JP
  • 3Tumor And Diagnostic Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki - Nagasaki/JP
  • 4Pathology, Nagasaki University Hospital, Nagasaki - Nagasaki/JP
  • 5Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki - Nagasaki/JP

Abstract

Background

Utilization of formalin-fixed, paraffin-embedded (FFPE) archival tissue, which is the most common form of tissue preservation in routine practice, for cytogenetic analysis of microarray comparative genomic hybridization (aCGH) remains challenging. We searched for predictive factors of FFPE DNA performance on aCGH analysis.

Materials and methods

Tumor DNA was extracted from 63 various types of FFPE archival tissues (31 of breast cancer, 24 of lung cancer, and 8 of thyroid tumor) followed by aCGH analysis using high-density oligonucleotide microarray. In two cases, tumor DNA from a matched frozen sample and tumor DNA after whole-genome amplification (WGA) from an FFPE sample were also analyzed. The derivative log ratio spread (DLRSpread) was used as a metric to assess the overall quality of each aCGH result.

Results

The DLRSpread was significantly correlated with the double-stranded DNA ratio of tumor DNA, storage time, and degree of Cy5 labeling (P < 0.0001; correlation coefficients = -0.796, 0.551, and -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 the DLRSpread (regression coefficient = -0.4798; P < 0.0001). Cytogenetic profiles of FFPE samples and matched frozen samples were well concordant. Although the double-stranded DNA ratios were increased after WGA, the DLRSpreads were not improved.

Conclusions

The double-stranded DNA ratio of tumor DNA predicted the performance of DNA from FFPE samples on aCGH analysis. Quality control by these metrics can utilize valuable FFPE archival tissue on aCGH analysis.

Disclosure

All authors have declared no conflicts of interest.