{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T10:45:06Z","timestamp":1785408306534,"version":"3.56.0"},"posted":{"date-parts":[[2025,6,30]]},"group-title":"Genomics","reference-count":78,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,6,30]],"date-time":"2025-06-30T00:00:00Z","timestamp":1751241600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"award":["R35 GM133415"],"award-info":[{"award-number":["R35 GM133415"]}],"id":[{"id":"https:\/\/ror.org\/04q48ey07","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,6,30]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>\n                  Approximately 2.6% of live births in the United States are conceived using assisted reproductive technologies (ARTs). While some ART procedures, including in vitro fertilization (IVF) and intracytoplasmic sperm injection, are known to alter the epigenetic landscape of early embryonic development, their impact on DNA sequence stability is unclear. Here, we leverage the strengths of the laboratory mouse model system to investigate whether a standard ART regimen\u2014ovarian hyperstimulation, gamete isolation, IVF, embryo culture, and embryo transfer\u2014affects genome stability. Age-matched cohorts of ART-derived and naturally conceived C57BL\/6J inbred mice were reared in a controlled setting and whole genome sequenced to \u223c50x coverage. Using a rigorous pipeline for\n                  <jats:italic>de novo<\/jats:italic>\n                  single nucleotide variant (dnSNV) discovery, we observe a \u223c30% increase in the dnSNV rate in ART-compared to naturally-conceived mice. Analysis of the dnSNV mutation spectrum identified signature contributions related to germline DNA repair activity, affirming expectations and evidencing the quality of our dnSNV calls. We observed no enrichment of dnSNVs in specific genomic contexts, suggesting that the observed rate increase in ART-derived mice is a general genome-wide phenomenon. Similarly, we show that the developmental timing of dnSNVs is similar in ART- and natural-born cohorts. Together, our findings show that ART is moderately mutagenic in house mice and motivate future work to define the precise procedure(s) associated with this increased mutational vulnerability. While we caution that our findings cannot be immediately translated to humans, they nonetheless emphasize a pressing need for investigations on the potential mutagenicity of ART in our species.\n                <\/jats:p>\n                <jats:sec>\n                  <jats:title>SIGNIFICANCE STATEMENT<\/jats:title>\n                  <jats:p>This study investigates whether assisted reproductive technologies (ARTs) increase the risk of inherited genetic mutations in offspring. Using a well-controlled mouse model system, we compared the de novo mutation burden in genomes of mice conceived through ART to a naturally conceived cohort. We find a \u223c30% increase in new DNA mutations in ART-conceived mice, suggesting that ART procedures have a genome destabilizing effect. This increase in mutation rate appears to be uniform across the genome, rather than attributable to specific genomic contexts. While we caution against the direct translation of our findings to humans, our work nonetheless highlights the need for further research into the genetic safety of ART in people.<\/jats:p>\n                <\/jats:sec>","DOI":"10.1101\/2025.06.27.662069","type":"posted-content","created":{"date-parts":[[2025,6,30]],"date-time":"2025-06-30T23:55:11Z","timestamp":1751327711000},"source":"Crossref","is-referenced-by-count":0,"title":["Increased rate of\n                  <i>de novo<\/i>\n                  single nucleotide mutation in house mice born through assisted reproduction"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-2679-9933","authenticated-orcid":false,"given":"Laura","family":"Blanco-Berdugo","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7260-0131","authenticated-orcid":false,"given":"Alexis","family":"Garretson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0918-0389","authenticated-orcid":false,"given":"Beth L.","family":"Dumont","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2025070219451147000_2025.06.27.662069v1.1","unstructured":"ESHRE ART Fact Sheet. (2025). Available at: https:\/\/www.eshre.eu\/Press-Room\/Resources\/Fact-sheets [Accessed 20 June 2025]."},{"key":"2025070219451147000_2025.06.27.662069v1.2","unstructured":"CDC, State-Specific ART Surveillance. Assisted Reproductive Technology (ART) (2024). Available at: https:\/\/www.cdc.gov\/art\/php\/surveillance-state-specific\/index.html [Accessed 20 June 2025]."},{"key":"2025070219451147000_2025.06.27.662069v1.3","doi-asserted-by":"publisher","DOI":"10.1093\/humrep\/dead197"},{"key":"2025070219451147000_2025.06.27.662069v1.4","first-page":"e12552","article-title":"Assisted reproductive technology in Japan: A summary report for 2021 by the Ethics Committee of the Japan Society of Obstetrics and Gynecology","volume":"23","year":"2023","journal-title":"Reproductive Medicine and Biology"},{"key":"2025070219451147000_2025.06.27.662069v1.5","unstructured":"CDC, National ART Summary. Assisted Reproductive Technology (ART) (2024). Available at: https:\/\/www.cdc.gov\/art\/php\/national-summary\/index.html [Accessed 20 June 2025]."},{"key":"2025070219451147000_2025.06.27.662069v1.6","first-page":"1","article-title":"Infertility and Impaired Fecundity in Women and Men in the United States, 2015\u20132019","volume":"202","year":"2024","journal-title":"National Health Statistics Report"},{"key":"2025070219451147000_2025.06.27.662069v1.7","doi-asserted-by":"crossref","unstructured":"M. J. Osterman , B. E. Hamilton , J. A. Martin , A. K. Driscoll , C. P. Valenzuela , Births: Final Data for 2023. National Vital Statistics Reports 74 (2025).","DOI":"10.15620\/cdc\/175204"},{"key":"2025070219451147000_2025.06.27.662069v1.8","doi-asserted-by":"publisher","DOI":"10.1093\/hmg\/ddv400"},{"key":"2025070219451147000_2025.06.27.662069v1.9","doi-asserted-by":"publisher","DOI":"10.1016\/j.apjr.2016.06.015"},{"key":"2025070219451147000_2025.06.27.662069v1.10","doi-asserted-by":"publisher","DOI":"10.1080\/15592294.2019.1615353"},{"key":"2025070219451147000_2025.06.27.662069v1.11","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbrc.2023.09.020"},{"key":"2025070219451147000_2025.06.27.662069v1.12","doi-asserted-by":"publisher","DOI":"10.1093\/humrep\/deaa310"},{"key":"2025070219451147000_2025.06.27.662069v1.13","doi-asserted-by":"publisher","DOI":"10.1093\/humrep\/dex366"},{"key":"2025070219451147000_2025.06.27.662069v1.14","doi-asserted-by":"crossref","unstructured":"J. Ghosh , C. Coutifaris , C. Sapienza , M. Mainigi , Global DNA methylation levels are altered by modifiable clinical manipulations in assisted reproductive technologies. Clinical Epigenetics 9, 14 (2017).","DOI":"10.1186\/s13148-017-0318-6"},{"key":"2025070219451147000_2025.06.27.662069v1.15","doi-asserted-by":"crossref","unstructured":"S. Mani , J. Ghosh , C. Coutifaris , C. Sapienza , M. Mainigi , Epigenetic changes and assisted reproductive technologies. Epigenetics 15, 12 (2019).","DOI":"10.1080\/15592294.2019.1646572"},{"key":"2025070219451147000_2025.06.27.662069v1.16","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-29540-w"},{"key":"2025070219451147000_2025.06.27.662069v1.17","doi-asserted-by":"crossref","unstructured":"S. Song , et al., DNA methylation differences between in vitro- and in vivo-conceived children are associated with ART procedures rather than infertility. Clin Epigenetics 7, 41 (2015).","DOI":"10.1186\/s13148-015-0071-7"},{"key":"2025070219451147000_2025.06.27.662069v1.18","doi-asserted-by":"publisher","DOI":"10.1093\/hmg\/ddm280"},{"key":"2025070219451147000_2025.06.27.662069v1.19","doi-asserted-by":"publisher","DOI":"10.1530\/REP-06-0247"},{"key":"2025070219451147000_2025.06.27.662069v1.20","doi-asserted-by":"publisher","DOI":"10.1095\/biolreprod.103.016832"},{"key":"2025070219451147000_2025.06.27.662069v1.21","doi-asserted-by":"publisher","DOI":"10.1038\/jhg.2013.61"},{"key":"2025070219451147000_2025.06.27.662069v1.22","doi-asserted-by":"publisher","DOI":"10.1093\/molehr\/gaw028"},{"key":"2025070219451147000_2025.06.27.662069v1.23","doi-asserted-by":"crossref","unstructured":"V. K. Cortessis , et al., Comprehensive meta-analysis reveals association between multiple imprinting disorders and conception by assisted reproductive technology. Journal of Assisted Reproduction and Genetics 35, 943 (2018).","DOI":"10.1007\/s10815-018-1173-x"},{"key":"2025070219451147000_2025.06.27.662069v1.24","doi-asserted-by":"crossref","unstructured":"H. Hattori , et al., Association of four imprinting disorders and ART. Clinical Epigenetics 11, 21 (2019).","DOI":"10.1186\/s13148-019-0623-3"},{"key":"2025070219451147000_2025.06.27.662069v1.25","doi-asserted-by":"publisher","DOI":"10.1016\/j.ejogrb.2009.05.035"},{"key":"2025070219451147000_2025.06.27.662069v1.26","doi-asserted-by":"crossref","unstructured":"S. Palomba , R. Homburg , S. Santagni , G. B. La Sala , R. Orvieto , Risk of adverse pregnancy and perinatal outcomes after high technology infertility treatment: a comprehensive systematic review. Reprod Biol Endocrinol 14, 76 (2016).","DOI":"10.1186\/s12958-016-0211-8"},{"key":"2025070219451147000_2025.06.27.662069v1.27","doi-asserted-by":"publisher","DOI":"10.1093\/humrep\/deaa272"},{"key":"2025070219451147000_2025.06.27.662069v1.28","doi-asserted-by":"crossref","unstructured":"R. J. Hart , L. A. Wijs , The longer-term effects of IVF on offspring from childhood to adolescence. Frontiers in Reproductive Health 4, 1045762 (2022).","DOI":"10.3389\/frph.2022.1045762"},{"key":"2025070219451147000_2025.06.27.662069v1.29","doi-asserted-by":"publisher","DOI":"10.1093\/humrep\/17.9.2362"},{"key":"2025070219451147000_2025.06.27.662069v1.30","doi-asserted-by":"publisher","DOI":"10.1093\/humrep\/17.10.2600"},{"key":"2025070219451147000_2025.06.27.662069v1.31","doi-asserted-by":"publisher","DOI":"10.1101\/gr.277884.123"},{"key":"2025070219451147000_2025.06.27.662069v1.32","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-019-0620-2"},{"key":"2025070219451147000_2025.06.27.662069v1.33","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0611642104"},{"key":"2025070219451147000_2025.06.27.662069v1.34","doi-asserted-by":"publisher","DOI":"10.1038\/s41422-021-00521-w"},{"key":"2025070219451147000_2025.06.27.662069v1.35","doi-asserted-by":"publisher","DOI":"10.1038\/S41586-021-03779-7"},{"key":"2025070219451147000_2025.06.27.662069v1.36","doi-asserted-by":"publisher","DOI":"10.1038\/nrg3890"},{"key":"2025070219451147000_2025.06.27.662069v1.37","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.117.1114"},{"key":"2025070219451147000_2025.06.27.662069v1.38","doi-asserted-by":"publisher","DOI":"10.1038\/nm.1924"},{"key":"2025070219451147000_2025.06.27.662069v1.39","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-34294-6"},{"key":"2025070219451147000_2025.06.27.662069v1.40","doi-asserted-by":"publisher","DOI":"10.3390\/jcm13082222"},{"key":"2025070219451147000_2025.06.27.662069v1.41","doi-asserted-by":"publisher","DOI":"10.1093\/carcin\/15.12.2695"},{"key":"2025070219451147000_2025.06.27.662069v1.42","doi-asserted-by":"publisher","DOI":"10.1038\/nrc2344"},{"key":"2025070219451147000_2025.06.27.662069v1.43","doi-asserted-by":"publisher","DOI":"10.1101\/gr.276665.122"},{"key":"2025070219451147000_2025.06.27.662069v1.44","doi-asserted-by":"crossref","unstructured":"A. Garretson , L. Blanco-Berdugo , A. Roberts , B. L. Dumont , Benchmarking Genomic Variant Calling Tools in Inbred Mouse Strains: Recommendations and Considerations. [Preprint] (2025). Available at: https:\/\/www.biorxiv.org\/content\/10.1101\/2025.05.28.656711v1 [Accessed 20 June 2025].","DOI":"10.1101\/2025.05.28.656711"},{"key":"2025070219451147000_2025.06.27.662069v1.45","doi-asserted-by":"publisher","DOI":"10.1101\/gr.186148.114"},{"key":"2025070219451147000_2025.06.27.662069v1.46","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-12023-w"},{"key":"2025070219451147000_2025.06.27.662069v1.47","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-023-05752-y"},{"key":"2025070219451147000_2025.06.27.662069v1.48","doi-asserted-by":"publisher","DOI":"10.1101\/gr.279982.124"},{"key":"2025070219451147000_2025.06.27.662069v1.49","doi-asserted-by":"publisher","DOI":"10.1038\/nature08658"},{"key":"2025070219451147000_2025.06.27.662069v1.50","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-1943-3"},{"key":"2025070219451147000_2025.06.27.662069v1.51","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msae163"},{"key":"2025070219451147000_2025.06.27.662069v1.52","doi-asserted-by":"publisher","DOI":"10.1126\/science.1063443"},{"key":"2025070219451147000_2025.06.27.662069v1.53","doi-asserted-by":"publisher","DOI":"10.1038\/nature13992"},{"key":"2025070219451147000_2025.06.27.662069v1.54","doi-asserted-by":"publisher","DOI":"10.1038\/nature19362"},{"key":"2025070219451147000_2025.06.27.662069v1.55","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-03822-7"},{"key":"2025070219451147000_2025.06.27.662069v1.56","doi-asserted-by":"publisher","DOI":"10.1038\/ng.363"},{"key":"2025070219451147000_2025.06.27.662069v1.57","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2021.06.025"},{"key":"2025070219451147000_2025.06.27.662069v1.58","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3129"},{"key":"2025070219451147000_2025.06.27.662069v1.59","doi-asserted-by":"publisher","DOI":"10.1016\/J.AJHG.2021.02.012"},{"key":"2025070219451147000_2025.06.27.662069v1.60","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-025-59750-x"},{"key":"2025070219451147000_2025.06.27.662069v1.61","doi-asserted-by":"publisher","DOI":"10.1038\/35066065"},{"key":"2025070219451147000_2025.06.27.662069v1.62","doi-asserted-by":"publisher","DOI":"10.1093\/humupd\/dmt006"},{"key":"2025070219451147000_2025.06.27.662069v1.63","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa1008095"},{"key":"2025070219451147000_2025.06.27.662069v1.64","doi-asserted-by":"publisher","DOI":"10.1093\/biolre\/ioac057"},{"key":"2025070219451147000_2025.06.27.662069v1.65","doi-asserted-by":"publisher","DOI":"10.1016\/j.tig.2006.09.010"},{"key":"2025070219451147000_2025.06.27.662069v1.66","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-31872-6"},{"key":"2025070219451147000_2025.06.27.662069v1.67","doi-asserted-by":"publisher","DOI":"10.1002\/imt2.107"},{"key":"2025070219451147000_2025.06.27.662069v1.68","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btaa1081"},{"key":"2025070219451147000_2025.06.27.662069v1.69","doi-asserted-by":"publisher","DOI":"10.1101\/gr.229102. Article published online before print in May 2002"},{"key":"2025070219451147000_2025.06.27.662069v1.70","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr330"},{"key":"2025070219451147000_2025.06.27.662069v1.71","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btad756"},{"key":"2025070219451147000_2025.06.27.662069v1.72","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","volume":"6","year":"2012","journal-title":"SnpEff. Fly (Austin"},{"key":"2025070219451147000_2025.06.27.662069v1.73","unstructured":"J. A. Stamatoyannopoulos , et al., An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biology 13, 418 (2012)."},{"key":"2025070219451147000_2025.06.27.662069v1.74","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts378"},{"key":"2025070219451147000_2025.06.27.662069v1.75","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv710"},{"key":"2025070219451147000_2025.06.27.662069v1.76","doi-asserted-by":"crossref","unstructured":"A. C. English , V. K. Menon , R. A. Gibbs , G. A. Metcalf , F. J. Sedlazeck , Truvari: refined structural variant comparison preserves allelic diversity. Genome Biology 23, 271 (2022).","DOI":"10.1186\/s13059-022-02840-6"},{"key":"2025070219451147000_2025.06.27.662069v1.77","doi-asserted-by":"crossref","unstructured":"J. R. Belyeu , et al., Samplot: a platform for structural variant visual validation and automated filtering. Genome Biology 22, 161 (2021).","DOI":"10.1186\/s13059-021-02380-5"},{"key":"2025070219451147000_2025.06.27.662069v1.78","doi-asserted-by":"crossref","unstructured":"W. McLaren , et al., The Ensembl Variant Effect Predictor. Genome Biology 17, 122 (2016).","DOI":"10.1186\/s13059-016-0974-4"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2025.06.27.662069","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T09:02:09Z","timestamp":1768467729000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2025.06.27.662069"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,6,30]]},"references-count":78,"URL":"https:\/\/doi.org\/10.1101\/2025.06.27.662069","relation":{},"subject":[],"published":{"date-parts":[[2025,6,30]]},"subtype":"preprint"}}