Germline Variant Call Accuracy in Whole Genome Sequence Data from Canine Formalin-Fixed Paraffin-Embedded Tissue Samples.

Background/objectives
Fresh frozen (FF) samples are routinely used to isolate high-molecular-weight intact genomic DNA. However, when FF samples are not available, archived formalin-fixed paraffin-embedded (FFPE) tissue samples often represent the only available material in clinical research. Due to formaldehyde-induced degradation of nucleic acids they pose special challenges for genetic investigations. In this study we compare whole-genome sequencing results on intact DNA versus fragmented DNA derived from FFPE samples of three dogs.Methods
We prepared matched libraries from FF and FFPE samples of three dogs affected by an inherited disease, EFNB3-related congenital mirror movement disorder 1 (CMM1). Paired-end short-read sequencing data were obtained on an Illumina sequencer and analyzed with adapted workflows for FF or FFPE data, respectively.Results
The data between FF and FFPE samples were largely consistent. FF data showed a superior variant call accuracy, as expected. However, the data quality from the FFPE samples was sufficient to correctly identify the causal variant in EFNB3.Conclusions
This pilot study demonstrates the feasibility of using FFPE samples from dogs for whole-genome sequencing and the detection of germline variants. Using FFPE samples in the analysis of suspected inherited diseases in domestic animals may represent a valuable approach in veterinary genetics if no other samples are available.