biostudies-literatureUnknown16(11)Jagannathan V<h4>Background/objectives</h4>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.<h4>Methods</h4>We prepared matched libraries from FF and FFPE samples of three dogs affected by an inherited disease, <i>EFNB3</i>-related congenital mirror movement disorder 1 (CMM1). Paired-end short-read sequencing data were obtained on an IlluminGenes1371https://www.ebi.ac.uk/biostudies/studies/S-EPMC12652997biostudies-literatureGermline Variant Call Accuracy in Whole Genome Sequence Data from Canine Formalin-Fixed Paraffin-Embedded Tissue Samples.PMC12652997Jagannathan VLeeb TfalseGermline Variant Call Accuracy in Whole Genome Sequence Data from Canine Formalin-Fixed Paraffin-Embedded Tissue Samples.<h4>Background/objectives</h4>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.<h4>Methods</h4>We prepared matched libraries from FF and FFPE samples of three dogs affected by an inherited disease, <i>EFNB3</i>-related congenital mirror movement disorder 1 (CMM1). Paired-end short-read sequencing data were obtained on an Illumin2025-01-01T00:00:00Z2025 Nov2026-05-20T03:09:53.778Z2026-05-20T03:08:46.49ZS-EPMC126529974130082110.3390/genes16111371