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In this study, the high efficacy of a whole exome sequencing kit was demonstrated for the improved pig reference genome (<jats:italic>Sus scrofa<\/jats:italic> 11.1) to profile biomedically relevant swine breeds and enable high-depth sequencing required for intratumor heterogeneity profiling.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We identify a total of 751,624 single nucleotide variants (SNVs) and 113,597 insertions and deletions (INDELs) across 93 samples from 12 porcine breeds. The identified mutations and affected pathways are correlated to muscle-to-fat ratios between different porcine breeds and further inform their utility as models of obesity and cardiovascular disease. Finally, 7935 SNVs and 358 INDELs are present in an Oncopig hepatocellular carcinoma (HCC) cell line and samples from a single Oncopig HCC tumor, with pathways related to hepatic fibrosis, WNT\/B-catenin, ATM signaling, and p53 signaling enriched.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>These results demonstrate the kit\u2019s high efficacy and utility for identifying mutations in the context of obesity, cardiovascular disease, and cancer across a range of pig models used in biomedical research.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/s13059-025-03589-4","type":"journal-article","created":{"date-parts":[[2025,5,8]],"date-time":"2025-05-08T10:30:46Z","timestamp":1746700246000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Development of a whole-exome sequencing kit to facilitate porcine biomedical research"],"prefix":"10.1186","volume":"26","author":[{"given":"Vishwaarth","family":"Vijayakumar","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tanvi","family":"Joshi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lobna","family":"Elkhadragy","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lawrence B.","family":"Schook","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ron C.","family":"Gaba","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mohammed","family":"El-Kebir","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kyle M.","family":"Schachtschneider","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2025,5,8]]},"reference":[{"issue":"1","key":"3589_CR1","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1093\/ilar\/ilv016","volume":"56","author":"M Seaton","year":"2015","unstructured":"Seaton M, Hocking A, Gibran NS. 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Humane care was provided to all animals under the criteria described in the Guide for the Care and Use of Laboratory Animals.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"L.B.S. and K.M.S. works for Sus Clinicals, which provides the Oncopig and other pig-based preclinical testing services to customers. L. B. S., L. E., and K.M.S. also reports funding support from the NIH\/NCI. L.B.S. reports grants from Guerbet USA LLC, Janssen Research & Development LLC, TriSalus Life Sciences, and Early Inc. L. E. and L.B.S. also reports funding support from the Society of Interventional Radiology. R.C.G. reports funding support from the NIH, Guerbet USA LLC, Janssen Research & Development LLC, NeoTherma Oncology, TriSalus Life Sciences, and Sus Clinicals. R.C.G. also reports consulting fees from the Boston Consulting Group, a provisional patent, and stock options from Sus Clinicals. R.C.G. reports being on the advisory boards of Sus Clinicals and Clinical Events Committee.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"118"}}