{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T17:41:55Z","timestamp":1740159715643,"version":"3.37.3"},"reference-count":29,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,9,16]],"date-time":"2024-09-16T00:00:00Z","timestamp":1726444800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2024,9,16]],"date-time":"2024-09-16T00:00:00Z","timestamp":1726444800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/100009633","name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","doi-asserted-by":"publisher","award":["T32HD098066","T32HD098066","T32HD098066"],"award-info":[{"award-number":["T32HD098066","T32HD098066","T32HD098066"]}],"id":[{"id":"10.13039\/100009633","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006108","name":"National Center for Advancing Translational Sciences","doi-asserted-by":"publisher","award":["UL1TR001876","UL1TR001876","UL1TR001876"],"award-info":[{"award-number":["UL1TR001876","UL1TR001876","UL1TR001876"]}],"id":[{"id":"10.13039\/100006108","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100020056","name":"A. James and Alice B. Clark Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100020056","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Clin Epigenet"],"DOI":"10.1186\/s13148-024-01741-8","type":"journal-article","created":{"date-parts":[[2024,9,16]],"date-time":"2024-09-16T05:01:52Z","timestamp":1726462912000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Technical considerations for placental tissue processing and the subsequent impact on genome-wide DNA methylation analysis"],"prefix":"10.1186","volume":"16","author":[{"given":"Kristen M.","family":"Kocher","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Julius","family":"Ngwa","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kushal J.","family":"Kapse","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Surajit","family":"Bhattacharya","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christopher","family":"Rossi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Emmanuele","family":"Delot","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adre","family":"duPlessis","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Catherine","family":"Limperopoulos","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nickie","family":"Andescavage","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2024,9,16]]},"reference":[{"doi-asserted-by":"crossref","unstructured":"Nelissen ECM, van Montfoort APA, Dumoulin JCM, Evers JLH. Epigenetics and the placenta. Hum Reprod Update. 2011;17(3).","key":"1741_CR1","DOI":"10.1093\/humupd\/dmq052"},{"unstructured":"Baergen RN, Burton GJ, Kaplan CG. Benirschke\u2019s Pathology of the Human Placenta: Seventh Edition. Benirschke\u2019s Pathology of the Human Placenta: Seventh Edition. 2021.","key":"1741_CR2"},{"doi-asserted-by":"crossref","unstructured":"Rosenfeld CS. The placenta-brain-axis. Vol. 99, Journal of Neuroscience Research. 2021.","key":"1741_CR3","DOI":"10.1002\/jnr.24603"},{"doi-asserted-by":"crossref","unstructured":"Gon\u00e7alves BM, Graceli JB, da Rocha PB, Tilli HP, Vieira EM, de Sibio MT, et al. Placental model as an important tool to study maternal-fetal interface. Reproductive Toxicology. 2022;112.","key":"1741_CR4","DOI":"10.1016\/j.reprotox.2022.06.005"},{"doi-asserted-by":"crossref","unstructured":"Harary D, Akinyemi A, Charron MJ, Fuloria M. Fetal growth and intrauterine epigenetic programming of obesity and cardiometabolic disease. Vol. 23, NeoReviews. 2022.","key":"1741_CR5","DOI":"10.1542\/neo.23-6-e363"},{"doi-asserted-by":"crossref","unstructured":"Zhu Z, Cao F, Li X. Epigenetic programming and fetal metabolic programming. Vol. 10, Frontiers in Endocrinology. 2019.","key":"1741_CR6","DOI":"10.3389\/fendo.2019.00764"},{"unstructured":"Buss C, Entringer S, Wadhwa PD. Fetal programming of brain development: Intrauterine stress and susceptibility to psychopathology. In: Science Signaling. 2012.","key":"1741_CR7"},{"doi-asserted-by":"crossref","unstructured":"Moore LD, Le T, Fan G. DNA methylation and its basic function. Vol. 38, Neuropsychopharmacology. 2013.","key":"1741_CR8","DOI":"10.1038\/npp.2012.112"},{"doi-asserted-by":"crossref","unstructured":"Gomaa N, Konwar C, Gladish N, Au-Young SH, Guo T, Sheng M, et al. Association of pediatric buccal epigenetic age acceleration with adverse neonatal brain growth and neurodevelopmental outcomes among children born very preterm with a neonatal infection. JAMA Netw Open. 2022;5(11).","key":"1741_CR9","DOI":"10.1001\/jamanetworkopen.2022.39796"},{"doi-asserted-by":"crossref","unstructured":"Provenzi L, Mambretti F, Villa M, Grumi S, Citterio A, Bertazzoli E, et al. Hidden pandemic: COVID-19-related stress, SLC6A4 methylation, and infants\u2019 temperament at 3\u00a0months. Sci Rep. 2021;11(1).","key":"1741_CR10","DOI":"10.1038\/s41598-021-95053-z"},{"doi-asserted-by":"crossref","unstructured":"Kocher K, Bhattacharya S, Niforatos-Andescavage N, Almalvez M, Henderson D, Vilain E, et al. Genome-wide neonatal epigenetic changes associated with maternal exposure to the COVID-19 pandemic. BMC Med Genomics. 2023;16(1).","key":"1741_CR11","DOI":"10.1186\/s12920-023-01707-4"},{"doi-asserted-by":"crossref","unstructured":"Cardenas A, Faleschini S, Cortes Hidalgo A, Rifas-Shiman SL, Baccarelli AA, Demeo DL, et al. Prenatal maternal antidepressants, anxiety, and depression and offspring DNA methylation: Epigenome-wide associations at birth and persistence into early childhood. Clin Epigenetics. 2019;11(1).","key":"1741_CR12","DOI":"10.1186\/s13148-019-0653-x"},{"doi-asserted-by":"crossref","unstructured":"Oberlander TF, Weinberg J, Papsdorf M, Grunau R, Misri S, Devlin AM. Prenatal exposure to maternal depression, neonatal methylation of human glucocorticoid receptor gene (NR3C1) and infant cortisol stress responses. Epigenetics. 2008;3(2).","key":"1741_CR13","DOI":"10.4161\/epi.3.2.6034"},{"doi-asserted-by":"crossref","unstructured":"Snijders C, Maihofer AX, Ratanatharathorn A, Baker DG, Boks MP, Geuze E, et al. Longitudinal epigenome-wide association studies of three male military cohorts reveal multiple CpG sites associated with post-traumatic stress disorder. Clin Epigenetics. 2020;12(1).","key":"1741_CR14","DOI":"10.1186\/s13148-019-0798-7"},{"doi-asserted-by":"crossref","unstructured":"McGill MG, Pokhvisneva I, Clappison AS, McEwen LM, Beijers R, Tollenaar MS, et al. Maternal prenatal anxiety and the fetal origins of epigenetic aging. Biol Psychiatry. 2022;91(3).","key":"1741_CR15","DOI":"10.1016\/j.biopsych.2021.07.025"},{"doi-asserted-by":"crossref","unstructured":"Lee Y, Choufani S, Weksberg R, Wilson SL, Yuan V, Burt A, et al. Placental epigenetic clocks: estimating gestational age using placental DNA methylation levels. Aging. 2019;11(12).","key":"1741_CR16","DOI":"10.18632\/aging.102049"},{"doi-asserted-by":"crossref","unstructured":"Mayne BT, Leemaqz SY, Smith AK, Breen J, Roberts CT, Bianco-Miotto T. Accelerated placental aging in early onset preeclampsia pregnancies identified by DNA methylation. Epigenomics. 2017;9(3).","key":"1741_CR17","DOI":"10.2217\/epi-2016-0103"},{"doi-asserted-by":"crossref","unstructured":"Moran S, Vizoso M, Martinez-Card\u00fas A, Gomez A, Mat\u00edas-Guiu X, Chiavenna SM, et al. Validation of DNA methylation profiling in formalin-fixed paraffin-embedded samples using the infinium human Methylation450 Microarray. Epigenetics. 2014;9(6).","key":"1741_CR18","DOI":"10.4161\/epi.28790"},{"doi-asserted-by":"crossref","unstructured":"Oliveira DVNP, Hentze J, O\u2019Rourke CJ, Andersen JB, H\u00f8gdall C, H\u00f8gdall E V. DNA methylation in ovarian tumors\u2014a comparison between fresh tissue and FFPE samples. Reproductive Sciences. 2021;28(11).","key":"1741_CR19","DOI":"10.1007\/s43032-021-00589-0"},{"issue":"1","key":"1741_CR20","doi-asserted-by":"publisher","first-page":"16381","DOI":"10.1038\/s41598-023-43788-2","volume":"13","author":"ME Dupont","year":"2023","unstructured":"Dupont ME, Jacobsen SB, Christiansen SNN, Tfelt-Hansen J, Smerup MH, Andersen JD, et al. Fresh and frozen cardiac tissue are comparable in DNA methylation array \u03b2-values, but formalin-fixed, paraffin-embedded tissue may overestimate DNA methylation levels. Sci Rep. 2023;13(1):16381.","journal-title":"Sci Rep"},{"doi-asserted-by":"crossref","unstructured":"Dupont ME, Christiansen SN, Jacobsen SB, Kampmann ML, Olsen KB, Tfelt-Hansen J, et al. DNA quality evaluation of formalin-fixed paraffin-embedded heart tissue for DNA methylation array analysis. Sci Rep. 2023;13(1).","key":"1741_CR21","DOI":"10.1038\/s41598-023-29120-y"},{"doi-asserted-by":"crossref","unstructured":"Yuan V, Price EM, Del Gobbo G, Mostafavi S, Cox B, Binder AM, et al. Accurate ethnicity prediction from placental DNA methylation data. Epigenetics Chromatin. 2019;12(1).","key":"1741_CR22","DOI":"10.1186\/s13072-019-0296-3"},{"doi-asserted-by":"crossref","unstructured":"Maksimovic J, Gordon L, Oshlack A. SWAN: Subset-quantile within array normalization for illumina infinium HumanMethylation450 BeadChips. Genome Biol. 2012;13(6).","key":"1741_CR23","DOI":"10.1186\/gb-2012-13-6-r44"},{"doi-asserted-by":"crossref","unstructured":"Kocher K, Bhattacharya S, Bramble MS, Okitundu-Luwa D, Ngoyi DM, Tshala-Katumbay D, et al. DNA methylation patterns associated with konzo in Sub-Saharan Africa. Clin Epigenetics. 2022;14(1).","key":"1741_CR24","DOI":"10.1186\/s13148-022-01372-x"},{"doi-asserted-by":"crossref","unstructured":"Wilhelm-Benartzi CS, Koestler DC, Karagas MR, Flanagan JM, Christensen BC, Kelsey KT, et al. Review of processing and analysis methods for DNA methylation array data. Vol. 109, Br J Cancer. 2013.","key":"1741_CR25","DOI":"10.1038\/bjc.2013.496"},{"doi-asserted-by":"crossref","unstructured":"Mansell G, Gorrie-Stone TJ, Bao Y, Kumari M, Schalkwyk LS, Mill J, et al. Guidance for DNA methylation studies: statistical insights from the Illumina EPIC array. BMC Genomics. 2019;20(1).","key":"1741_CR26","DOI":"10.1186\/s12864-019-5761-7"},{"doi-asserted-by":"crossref","unstructured":"Pelegi-Siso D, De Prado P, Ronkainen J, Bustamante M, Gonzalez JR. Methylclock: A Bioconductor package to estimate DNA methylation age methylclock: A Bioconductor package to estimate DNA methylation age. Bioinformatics. 2021;37(12).","key":"1741_CR27","DOI":"10.1093\/bioinformatics\/btaa825"},{"doi-asserted-by":"crossref","unstructured":"Cohen MC, Peres LC, Al-Adnani M, Zapata-V\u00e1zquez R. Increased number of fetal nucleated red blood cells in the placentas of term or near-term stillborn and neonates correlates with the presence of diffuse intradural hemorrhage in the perinatal period. Pediatric and Dev Pathol. 2014;17(1).","key":"1741_CR28","DOI":"10.2350\/12-02-1157-OA.1"},{"doi-asserted-by":"crossref","unstructured":"Haftorn KL, Denault WRP, Lee Y, Page CM, Romanowska J, Lyle R, et al. Nucleated red blood cells explain most of the association between DNA methylation and gestational age. Commun Biol. 2023;6(1).","key":"1741_CR29","DOI":"10.1038\/s42003-023-04584-w"}],"container-title":["Clinical Epigenetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13148-024-01741-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s13148-024-01741-8\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13148-024-01741-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,9,16]],"date-time":"2024-09-16T17:03:05Z","timestamp":1726506185000},"score":1,"resource":{"primary":{"URL":"https:\/\/clinicalepigeneticsjournal.biomedcentral.com\/articles\/10.1186\/s13148-024-01741-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,9,16]]},"references-count":29,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["1741"],"URL":"https:\/\/doi.org\/10.1186\/s13148-024-01741-8","relation":{},"ISSN":["1868-7083"],"issn-type":[{"type":"electronic","value":"1868-7083"}],"subject":[],"published":{"date-parts":[[2024,9,16]]},"assertion":[{"value":"26 March 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 September 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 September 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"This study was approved by Children's National Hospital Institutional Review Board (approval: Pro00014257). Informed written consent was acquired prior to study enrollment by all study participants or their legal guardian.","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":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"128"}}