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Detect Genetic Variants From FFPE Breast Tissue Samples

Detect Genetic Variants From FFPE Breast Tissue Samples

Archived FFPE samples are invaluable clinical resources for studying clinically relevant morphology features as well as genetic changes. However, FFPE DNA quality and quantity are often not optimal, so NGS-based genetics variant detections can be inclined to false negatives. To optimize variant detection from the FFPE sample, bioinformatics and wet-lab approaches must be evaluated.

Research and clinical care have moved into the new era of molecular medicine and genomic/molecular characterizations of human tissue. This is especially true in breast cancer care. Mainstream use of molecular tests is a common practice for clinical research and application. Research efforts to create molecular panels can be best done with nucleic acid derived from fresh tissue or formalin-fixed paraffin-embedded block repository. This ensures that the nucleic acid quality is high. 

Comparing Quality Between Frozen and FFPE Breast Cancer Samples

Image Source: Google

For clinical research cohorts, however, it is not always possible to obtain fresh or frozen tissues. When molecular predictors for long-term outcomes are required, archived formalin-fixed paraffin-embedded (FFPE), tissues are often available. FFPE tissues are not suitable for molecular or genomics measurements. This is due to poor-quality DNA and RNA from FFPE tissue blocks. 

Nucleic acids taken from FFPE tissue blocks are of poor quality, which raises questions about the validity of next-generation sequencing (NGS), from FFPE tissues. The research goal is, for example, to identify genetic and molecular markers of future breast carcinoma from benign breast biopsy tissue that was archived years before the event. 

There are so many research centers exploring methodologic methods to optimize DNA sequencing using FFPE tissues in order to assist this effort. This report describes a method to simultaneously evaluate paired FFPE DNA and frozen DNA to verify the validity of sequencing results from FFPE tissue.