{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T11:12:55Z","timestamp":1762859575201,"version":"build-2065373602"},"reference-count":22,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T00:00:00Z","timestamp":1762819200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>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.<\/jats:p>","DOI":"10.3390\/genes16111371","type":"journal-article","created":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T10:56:27Z","timestamp":1762858587000},"page":"1371","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Germline Variant Call Accuracy in Whole Genome Sequence Data from Canine Formalin-Fixed Paraffin-Embedded Tissue Samples"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8155-0041","authenticated-orcid":false,"given":"Vidhya","family":"Jagannathan","sequence":"first","affiliation":[{"name":"Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0553-4880","authenticated-orcid":false,"given":"Tosso","family":"Leeb","sequence":"additional","affiliation":[{"name":"Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,11,11]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Fortunato, A., Mallo, D., Rupp, S.M., King, L.M., Hardman, T., Lo, J.Y., Hall, A., Marks, J.R., Hwang, E.S., and Maley, C.C. (2021). A New Method to Accurately Identify Single Nucleotide Variants Using Small FFPE Breast Samples. Brief. Bioinform., 22.","DOI":"10.1093\/bib\/bbab221"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"7731","DOI":"10.1038\/s41467-024-51577-2","article-title":"Large-Scale Analysis of Whole Genome Sequencing Data from Formalin-Fixed Paraffin-Embedded Cancer Specimens Demonstrates Preservation of Clinical Utility","volume":"15","author":"Basyuni","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Chong, I.Y., Starling, N., Rust, A., Alexander, J., Aronson, L., Llorca-Cardenosa, M., Chauhan, R., Chaudry, A., Kumar, S., and Fenwick, K. (2021). The Mutational Concordance of Fixed Formalin Paraffin Embedded and Fresh Frozen Gastro-Oesophageal Tumours Using Whole Exome Sequencing. J. Clin. Med., 10.","DOI":"10.3390\/jcm10020215"},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Gao, X.H., Li, J., Gong, H.F., Yu, G.Y., Liu, P., Hao, L.Q., Liu, L.J., Bai, C.G., and Zhang, W. (2020). Comparison of Fresh Frozen Tissue with Formalin-Fixed Paraffin-Embedded Tissue for Mutation Analysis Using a Multi-Gene Panel in Patients With Colorectal Cancer. Front. Oncol., 10.","DOI":"10.3389\/fonc.2020.00310"},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Bhagwate, A.V., Liu, Y., Winham, S.J., McDonough, S.J., Stallings-Mann, M.L., Heinzen, E.P., Davila, J.I., Vierkant, R.A., Hoskin, T.L., and Frost, M. (2019). Bioinformatics and DNA-Extraction Strategies to Reliably Detect Genetic Variants from FFPE Breast Tissue Samples. BMC Genom., 20.","DOI":"10.1186\/s12864-019-6056-8"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"De Schaetzen Van Brienen, L., Larmuseau, M., Van Der Eecken, K., De Ryck, F., Robbe, P., Schuh, A., Fostier, J., Ost, P., and Marchal, K. (2020). Comparative Analysis of Somatic Variant Calling on Matched FF and FFPE WGS Samples. BMC Med. Genom., 13.","DOI":"10.1186\/s12920-020-00746-5"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"2718","DOI":"10.1093\/bioinformatics\/btaa053","article-title":"UMI-VarCal: A New UMI-Based Variant Caller That Efficiently Improves Low-Frequency Variant Detection in Paired-End Sequencing NGS Libraries","volume":"36","author":"Sater","year":"2020","journal-title":"Bioinformatics"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"2270","DOI":"10.1016\/j.csbj.2020.08.011","article-title":"UMI-Gen: A UMI-Based Read Simulator for Variant Calling Evaluation in Paired-End Sequencing NGS Libraries","volume":"18","author":"Sater","year":"2020","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Heo, D., Kim, I., Seo, H., Kim, S.G., Kim, M., Park, J., Park, H., Kang, S., Kim, J., and Paik, S. (2024). DEEPOMICS FFPE, a Deep Neural Network Model, Identifies DNA Sequencing Artifacts from Formalin Fixed Paraffin Embedded Tissue with High Accuracy. Sci. Rep., 14.","DOI":"10.1038\/s41598-024-53167-0"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Trevarton, A.J., Chang, J.T., and Symmans, W.F. (2023). Simple Combination of Multiple Somatic Variant Callers to Increase Accuracy. Sci. Rep., 13.","DOI":"10.1038\/s41598-023-34925-y"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Dodani, D.D., Nguyen, M.H., Morin, R.D., Marra, M.A., and Corbett, R.D. (2022). Combinatorial and Machine Learning Approaches for Improved Somatic Variant Calling From Formalin-Fixed Paraffin-Embedded Genome Sequence Data. Front. Genet., 13.","DOI":"10.3389\/fgene.2022.834764"},{"key":"ref_12","first-page":"11.10.1","article-title":"From FastQ Data to High-Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline","volume":"43","author":"Carneiro","year":"2013","journal-title":"Curr. Protoc. Bioinform."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Diossy, M., Sztupinszki, Z., Krzystanek, M., Borcsok, J., Eklund, A.C., Csabai, I., Pedersen, A.G., and Szallasi, Z. (2021). Strand Orientation Bias Detector to Determine the Probability of FFPE Sequencing Artifacts. Brief. Bioinform., 22.","DOI":"10.1093\/bib\/bbab186"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"983","DOI":"10.1038\/nbt.4235","article-title":"A Universal SNP and Small-Indel Variant Caller Using Deep Neural Networks","volume":"36","author":"Poplin","year":"2018","journal-title":"Nat. Biotechnol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1883","DOI":"10.1002\/mds.30243","article-title":"EFNB3 Frameshift Variant in Weimaraner Dogs with a Condition Resembling a Congenital Mirror Movement Disorder","volume":"40","author":"Schwarz","year":"2025","journal-title":"Mov. Disord."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"e70078","DOI":"10.1002\/imt2.70078","article-title":"fastp 1.0: An ultra-fast all-round tool for FASTQ data quality control and preprocessing","volume":"4","author":"Chen","year":"2025","journal-title":"iMeta"},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Vasimuddin, M., Misra, S., Li, H., and Aluru, S. (2019, January 20\u201324). Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. Proceedings of the 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS), Rio de Janeiro, Brazil.","DOI":"10.1109\/IPDPS.2019.00041"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"giab008","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"Gigascience"},{"key":"ref_19","unstructured":"fgbio. Available online: https:\/\/github.com\/fulcrumgenomics\/fgbio."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"80","DOI":"10.4161\/fly.19695","article-title":"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3","volume":"6","author":"Cingolani","year":"2012","journal-title":"Fly"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"7143","DOI":"10.1093\/nar\/gkad519","article-title":"A Critical Spotlight on the Paradigms of FFPE-DNA Sequencing","volume":"51","author":"Steiert","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1196","DOI":"10.1038\/gim.2017.241","article-title":"Clinical Whole-Genome Sequencing from Routine Formalin-Fixed, Paraffin-Embedded Specimens: Pilot Study for the 100,000 Genomes Project","volume":"20","author":"Robbe","year":"2018","journal-title":"Genet. Med."}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/16\/11\/1371\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T11:09:33Z","timestamp":1762859373000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/16\/11\/1371"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11,11]]},"references-count":22,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2025,11]]}},"alternative-id":["genes16111371"],"URL":"https:\/\/doi.org\/10.3390\/genes16111371","relation":{},"ISSN":["2073-4425"],"issn-type":[{"value":"2073-4425","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,11,11]]}}}