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

Abstract

The use of whole genome amplification (WGA) and whole transcriptome amplification (WTA) techniques enables the enrichment of DNA and RNA from very small amounts of tissue. Here, we tested the suitability of WGA and WTA for tumor tissue biobanking. DNA and RNA from 13 standardized and seven non-standardized frozen and 12 formalin-fixed, paraffin-embedded (FFPE) clear cell renal cell carcinoma specimens (>9 years old) served to test the robustness of the WGA and WTA products by reidentifying von Hippel-Lindau (VHL) gene mutations known to exist in these samples. The enrichment of DNA and RNA from frozen tissue was up to 1,291-fold and 423-fold, respectively. The sizes and yields (10- to 73-fold) of the amplified DNA obtained from the 12 FFPE samples were generally lower. The quality of the RNA from the FFPE samples was too low to reliably perform WTA. Our results demonstrate that frozen tumor tissue is very suitable for WGA and WTA. All 20 VHL mutations were verified with WGA. Notably, we were able to show that 18 of the 20 (90 %) VHL mutations are also transcribed. In FFPE tumor tissue, 8 of 12 cases (67 %) showed the expected mutations after the first WGA. Accurate WTA with FFPE material is sophisticated and strongly depends on the modification and degradation status of the fixed tissue. We conclude that for sustainable tissue biobanking, the use of WGA and WTA is a unique opportunity to provide researchers with sufficient amounts of nucleic acids, preferably from limited frozen tissue material.