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Updated: Jul 10, 2026
09:16
Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants
Published on: February 21, 2015
Formalin-fixed paraffin-embedded clinical tissues show spurious copy number changes in array-CGH profiles
E A Mc Sherry1, A Mc Goldrick, E W Kay
1UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland.
Clinical Genetics
|October 16, 2007
Summary
Formalin-fixed paraffin-embedded (FFPE) tissues show degraded DNA, leading to more detected genetic alterations in array-CGH studies compared to fresh-frozen samples. This impacts the reliability of genetic profiling from archival specimens.
Area of Science:
- Oncology
- Genomics
- Molecular Pathology
Background:
- Archival formalin-fixed paraffin-embedded (FFPE) clinical specimens are crucial for identifying cancer prognostic and therapeutic targets.
- The utility of FFPE-derived genetic material for array-based comparative genomic hybridization (array-CGH) remains insufficiently explored.
Purpose of the Study:
- To investigate DNA integrity differences between FFPE and fresh-frozen specimens.
- To determine the impact of these differences on genetic profiles obtained via array-CGH.
Main Methods:
- Genomic DNA extraction from matched FFPE and fresh-frozen clinical tissue samples, including T47D breast cancer cell line controls.
- Array-based comparative genomic hybridization (array-CGH) was performed on extracted DNA.
- Comparison of genetic profiles between matched FFPE and fresh-frozen samples.
Main Results:
- Loss of high molecular weight DNA was observed in FFPE tissues and FFPE T47D samples.
- A significant increase in the absolute number of genetic alterations was detected in FFPE tissues compared to their fresh-frozen counterparts.
Conclusions:
- FFPE processing significantly impacts DNA integrity, leading to an increased number of apparent genetic alterations in array-CGH.
- Further research into alternative fixation, processing, DNA extraction, and CGH protocols is needed to reliably analyze genetic changes in archival FFPE specimens for disease progression studies.
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