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

Area of Science:

• Veterinary Genetics
• Genomic Sequencing
• Molecular Diagnostics

Background:

• Fresh frozen (FF) samples are standard for high-molecular-weight DNA isolation.
• Archived formalin-fixed paraffin-embedded (FFPE) tissues are often the only source for genetic studies.
• Formaldehyde fixation causes nucleic acid degradation, posing challenges for genetic analysis.

Purpose of the Study:

• To compare whole-genome sequencing (WGS) results from FF and FFPE canine DNA.
• To assess the feasibility of using FFPE samples for genetic investigations in dogs.
• To evaluate FFPE sample suitability for identifying causative variants in inherited diseases.

Main Methods:

• Matched FF and FFPE DNA libraries were prepared from three dogs with EFNB3-related congenital mirror movement disorder 1 (CMM1).
• Paired-end short-read sequencing was performed using an Illumina platform.
• Data analysis employed adapted workflows for both FF and FFPE datasets.

Main Results:

• Whole-genome sequencing data from FF and FFPE samples showed substantial consistency.
• FFPE samples yielded sufficient data quality to accurately identify the causal EFNB3 variant.
• While FF data offered superior variant call accuracy, FFPE data proved effective for variant detection.

Conclusions:

• This pilot study confirms the viability of FFPE samples for canine WGS and germline variant detection.
• Utilizing FFPE samples is a valuable strategy in veterinary genetics for investigating suspected inherited diseases when FF samples are absent.
• FFPE-based WGS offers a promising avenue for genetic research in domestic animals, particularly for rare or historical cases.