Detection of copy number alterations using shallow whole genome sequencing on formalin-fixed paraffin-embedded tumor tissue

In routine clinical practice, tumor tissue is stored as formalin-fixed paraffin-embedded (FFPE) blocks. However, the use of DNA purified from FFPE tissue for cancer genome analysis is challenged by poorer DNA quality and quantity. Whilst several studies have reported genome-wide massive parallel sequencing applied on FFPE samples, copy number analysis on FFPE material is not yet commonly executed. In this study, we evaluated the use of FFPE tumor tissue for DNA copy number alteration (CNA) detection by shallow whole genome sequencing (sWGS). Very comparable CNA profiles were obtained across paired fresh and FFPE samples. Although the variance in the profiles of FFPE material is often higher, we believe this has no impact on the performance of statistically calling an aberration. There is a high concordance in CNA detection, with slightly more alterations being detected in FFPE material. Higher amplitudes are observed in FFPE samples, which compensate for the increased variance. Moreover, we expect a higher tumor fraction in FFPE material, as we are able to select the section and/or area with the highest tumor content, thereby increasing the observed amplitudes. In conclusion, CNAs can be just as reliably detected in FFPE tumor tissue as in fresh material by sWGS. This opens up the possibility to analyze tumor tissue which has been collected during routine clinical work by sWGS in a more controlled manner. Moreover, archival FFPE material is available for each tumor of individual patients in every laboratory for surgical pathology and represents a large biobank for future clinical research