Whole genome and transcriptome amplification: practicable tools for sustainable tissue biobanking?

Area of Science:

• Oncology
• Molecular Biology
• Biobanking

Background:

• Whole genome amplification (WGA) and whole transcriptome amplification (WTA) enable nucleic acid enrichment from limited tissue samples.
• Tumor tissue biobanking is crucial for research but often involves limited or degraded material.

Purpose of the Study:

• To evaluate the suitability of WGA and WTA for tumor tissue biobanking using aged clear cell renal cell carcinoma (ccRCC) specimens.
• To assess the robustness and reliability of WGA and WTA for analyzing genetic mutations in biobanked tissues.

Main Methods:

• DNA and RNA were extracted from frozen and formalin-fixed, paraffin-embedded (FFPE) ccRCC specimens (>9 years old).
• WGA and WTA were performed to amplify nucleic acids.
• The presence of known von Hippel-Lindau (VHL) gene mutations was reidentified to validate WGA and WTA products.

Main Results:

• WGA and WTA showed high enrichment factors for frozen tissues (DNA up to 1,291-fold, RNA up to 423-fold).
• All 20 known VHL mutations were successfully verified using WGA in frozen samples, with 90% also detected in transcripts via WTA.
• WGA yielded lower quality and quantity from FFPE samples, and WTA was unreliable due to RNA degradation; 67% of VHL mutations were detected by WGA in FFPE.
• WTA from FFPE tissues proved challenging and highly dependent on sample fixation and degradation status.

Conclusions:

• WGA and WTA are highly suitable for biobanking frozen tumor tissues, providing sufficient nucleic acids for mutation analysis.
• While WGA shows promise for FFPE tissues, WTA is less reliable due to RNA degradation.
• These amplification techniques offer a valuable approach for sustainable tissue biobanking, particularly from limited frozen material.