Can you perform HLA typing from FFPE samples?

FFPE (Formalin-Fixed Paraffin-Embedded) is a tissue fixation method used for archival storage of tissue samples in biobanks and clinical repositories.  Both normal and diseased tissue types are stored in FFPE format, often for years or decades.

Unfortunately, FFPE tissue samples often result in significant DNA degradation, DNA fragmentation and reduced DNA yields.  The formalin fixation process induces DNA cross-links with other cellular components, which can inhibit PCR amplification steps commonly used in NGS (next-generation sequencing) library prep protocols.  Long-term tissue storage in FFPE also leads to significant DNA fragmentation.  HLA typing with NGS methods requires fairly long intact DNA fragments (i.e. whole genes, full exons, etc.).  DNA fragmentation in FFPE samples inhibits the proper amplification of HLA targets.  FFPE samples can also result in up to 3X reductions in library yield.  There are minimum DNA mass and concentration requirements for HLA typing by NGS.  Low yields from FFPE samples may prohibit us from even starting the library prep process.

We occasionally get requests from clients about using FFPE samples for NGS HLA typing.  Given the level of DNA degradation and low yields in these samples, we generally do not recommend using them for HLA research.