Deep clonal profiling of formalin fixed paraffin embedded clinical samples.

Area of Science:

• Genomics
• Cancer Research
• Molecular Pathology

Background:

• Formalin-fixed paraffin-embedded (FFPE) tissues are a rich source of annotated clinical samples valuable for personalized medicine and therapeutic development.
• Challenges with FFPE tissues include variable DNA quality and the presence of non-tumor cells, complicating genomic analysis.
• Pure tumor cell populations are crucial for accurate cancer genome definition.

Purpose of the Study:

• To develop a methodology for isolating pure tumor cell nuclei from FFPE tissues.
• To enable high-definition genomic analyses, including oligonucleotide array comparative genomic hybridization (aCGH) and whole exome sequencing (WES), on FFPE samples.
• To profile various tumor types and compare FFPE-derived genomic data with fresh-frozen samples.

Main Methods:

• Utilized flow cytometry to isolate pure tumor cell nuclei from FFPE tissue samples.
• Developed a DNA extraction and processing methodology compatible with downstream genomic analyses.
• Applied oligonucleotide array CGH and whole exome sequencing to profile tumor genomes and exomes.

Main Results:

• Successfully isolated pure tumor cell nuclei from FFPE tissues across multiple cancer types (breast, brain, bladder, ovarian, pancreas).
• Demonstrated the compatibility of the developed methodology with both aCGH and WES.
• Generated genomic and exomic profiles from FFPE samples, including direct comparison with matching fresh-frozen pancreatic adenocarcinoma samples.

Conclusions:

• Flow cytometry-based isolation of tumor cell nuclei from FFPE tissues is a viable method for high-definition genomic studies.
• This approach overcomes limitations of DNA quality and cellular heterogeneity in FFPE samples.
• Enables deeper understanding of cancer genomes for improved patient management and personalized therapeutics.