At age 9, the methylome of assisted reproductive technology children that underwent embryo culture in different media is not significantly different on a genome-wide scale.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36206092", "kind": "science-record", "revision": 3, "content_hash": "sha256:a5f66772d90c951c66fbe150d605db2d0beadd66d7d48929ff2e93710c3a6426", "created_at": "2026-11-01T18:15:31Z", "updated_at": "2026-11-01T21:29:06Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "At age 9, the methylome of assisted reproductive technology children that underwent embryo culture in different media is not significantly different on a genome-wide scale.", "doi": "10.1093/humrep/deac213", "pmid": "36206092", "authors": ["Rebekka M Koeck", "Florence Busato", "Jorg Tost", "Heleen Zandstra", "Sylvie Remy", "Sabine Langie", "Marij Gielen", "Ron van Golde", "John C M Dumoulin", "Han Brunner", "Masoud Zamani Esteki", "Aafke P A van Montfoort"], "journal": "Human reproduction (Oxford, England)", "year": 2022, "abstract": "STUDY QUESTION: Can we detect DNA methylation differences between ART children that underwent embryo culture in different media?\nSUMMARY ANSWER: We identified no significant differences in site-specific or regional DNA methylation between the different culture medium groups.\nWHAT IS KNOWN ALREADY: Embryo culture in G3 or K-SICM medium leads to differences in embryonic, neonatal and childhood outcomes, including growth and weight. The methylome may mediate this association as the period of in vitro culture of ART treatments coincides with epigenetic reprogramming.\nSTUDY DESIGN, SIZE, DURATION: This study was conducted as a follow-up to a previous culture medium comparison study in which couples were pseudo-randomized to embryo culture in G3 or K-SICM medium. Of the resultant singletons, 120 (n = 65 G3, n = 55 K-SICM), were recruited at age 9.\nPARTICIPANTS/MATERIALS, SETTING, METHODS: The ART children provided a saliva sample from which the methylome was analysed using the Infinium MethylationEPIC array. After quality and context filtering, 106 (n = 57 G3, n = 49 K-SICM) samples and 659 708 sites were retained for the analyses. Differential methylation analyses were conducted using mixed effects linear models corrected for age, sex, sample plate and cell composition. These were applied to all cytosine-guanine dinucleotide (CpG) sites, various genomic regions (genes, promoters, CpG Islands (CGIs)) and as a targeted analysis of imprinted genes and birth weight-associated CpG sites. Differential variance was assessed using the improved epigenetic variable outliers for risk prediction analysis (iEVORA) algorithm and methylation outliers were identified using a previously defined threshold (upper or lower quartile plus or minus three times the interquartile range, respectively).\nMAIN RESULTS AND THE ROLE OF CHANCE: After correcting for multiple testing, we did not identify any significantly differentially methylated CpG sites, genes, promoters or CGIs between G3 and K-SICM children despite a lenient corrected P-value threshold of 0.1. Targeted analyses of (sites within) imprinted genes and birth weight-associated sites also did not identify any significant differences. The number of DNA methylation outliers per sample was comparable between the culture medium groups. iEVORA identified 101 differentially variable CpG sites of which 94 were more variable in the G3 group.\nLARGE SCALE DATA: Gene Expression Omnibus (GEO) GSE196432.\nLIMITATIONS, REASONS FOR CAUTION: To detect significant methylation differences with a magnitude of <10% between the groups many more participants would be necessary; however, the clinical relevance of such small differences is unclear.\nWIDER IMPLICATIONS OF THE FINDINGS: The results of this study are reassuring, suggesting that if there is an effect of the culture medium on DNA methylation (and methylation-mediated diseases risk), it does not differ between the two media investigated here. The findings concur with other methylome studies of ART neonates and children that underwent embryo culture in different media, which also found no significant methylome differences.\nSTUDY FUNDING/COMPETING INTEREST(S): Study funded by March of Dimes (6-FY13-153), EVA (Erfelijkheid Voortplanting & Aanleg) specialty programme (grant no. KP111513) of Maastricht University Medical Centre (MUMC+) and the Horizon 2020 innovation (ERIN) (grant no. EU952516) of the European Commission. The authors do not report any conflicts of interest relevant to this study.\nTRIAL REGISTRATION NUMBER: Dutch Trial register-NL4083.", "claims": [{"id": "claim-method", "statement": "Methylation M-values, representing the log2 ratio of the methylated probe intensity compared to the unmethylated probe intensity (Du et al., 2010), were used to test for associations between DNA methylation and culture medium using mixed effects linear models implemented with the variancePartition package (Hoffman and Schadt, 2016).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36206092", "locator": "sections[11] \"Comparison of G3 and K-SICM children\" paragraph 3", "quote": "Methylation M-values, representing the log2 ratio of the methylated probe intensity compared to the unmethylated probe intensity (Du et al., 2010), were used to test for associations between DNA methylation and culture medium using mixed effects linear models implemented with the variancePartition package (Hoffman and Schadt, 2016)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw and processed array data from this study have been uploaded to the Gene Expression Omnibus (GEO) database and are available under the accession number GSE196432 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE196432). The raw array data from the FLEHS study are available within the GEO database under the accession number GSE110128.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36206092", "locator": "sections[22] \"Data Availability\" paragraph 2", "quote": "The raw and processed array data from this study have been uploaded to the Gene Expression Omnibus (GEO) database and are available under the accession number GSE196432 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE196432). The raw array data from the FLEHS study are available within the GEO database under the accession number GSE110128."}], "state": "complete"}, {"id": "claim-target-result", "statement": "No significant differences in site-specific or regional DNA methylation were identified between the G3 and K-SICM culture-medium groups.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36206092", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "We identified no significant differences in site-specific or regional DNA methylation between the different culture medium groups."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "No significant differences in site-specific or regional DNA methylation were identified between the G3 and K-SICM culture-medium groups.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:36206092"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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