{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,2]],"date-time":"2026-06-02T13:33:41Z","timestamp":1780407221693,"version":"3.54.1"},"reference-count":57,"publisher":"Frontiers Media SA","funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["0944557"],"award-info":[{"award-number":["0944557"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["1316055"],"award-info":[{"award-number":["1316055"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["1355306"],"award-info":[{"award-number":["1355306"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Genet."],"DOI":"10.3389\/fgene.2016.00191","type":"journal-article","created":{"date-parts":[[2016,11,2]],"date-time":"2016-11-02T09:10:40Z","timestamp":1478077840000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":12,"title":["Epigenetic DNA Methylation Profiling with MSRE: A Quantitative NGS Approach Using a Parkinson's Disease Test Case"],"prefix":"10.3389","volume":"7","author":[{"given":"Adam G.","family":"Marsh","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew T.","family":"Cottrell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Morton F.","family":"Goldman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2016,11,2]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"165","DOI":"10.3109\/00207454.2011.637654","article-title":"DNA methylation as a biomarker for neuropsychiatric diseases","volume":"122","author":"Ai","year":"2012","journal-title":"Int. J. Neurosci."},{"key":"B2","doi-asserted-by":"publisher","first-page":"3554","DOI":"10.1021\/pr401142p","article-title":"Verification of a Parkinson's Disease protein signature in T-lymphocytes by multiple reaction monitoring","volume":"13","author":"Alberio","year":"2014","journal-title":"J. Prot. Res."},{"key":"B3","doi-asserted-by":"publisher","first-page":"1138","DOI":"10.1038\/nmeth.3115","article-title":"Comprehensive analysis of DNA methylation data with RnBeads","volume":"11","author":"Assenov","year":"2014","journal-title":"Nat. Methods"},{"key":"B4","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: A practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J. Roy. Stat. Society. Ser. B"},{"key":"B5","doi-asserted-by":"publisher","first-page":"e0150552","DOI":"10.1371\/journal.pone.0150552","article-title":"Insulin-like growth factor 1 (IGF-1) in Parkinson's Disease: potential as trait-, progression- and prediction marker and confounding factors","volume":"11","author":"Bernhard","year":"2016","journal-title":"PLoS ONE"},{"key":"B6","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/hdy.2010.66","article-title":"From genotype to phenotype. what do epigenetics and epigenomics tell us?","volume":"105","author":"Bi\u00e9mont","year":"2010","journal-title":"Heredity"},{"key":"B7","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1016\/j.taap.2015.12.012","article-title":"Zebrafish embryos as a screen for DNA methylation modifications after compound exposure","volume":"291","author":"Bouwmeester","year":"2016","journal-title":"Toxicol. Appl. Pharmacol."},{"key":"B8","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1002\/mds.26473","article-title":"Alpha-synuclein in gastric and colonic mucosa in Parkinson's disease: limited role as a biomarker","volume":"31","author":"Chung","year":"2016","journal-title":"Move. Disord."},{"key":"B9","doi-asserted-by":"publisher","first-page":"e1265","DOI":"10.1038\/cddis.2014.211","article-title":"Role of alpha-synuclein in autophagy modulation of primary human T lymphocytes","volume":"5","author":"Colasanti","year":"2014","journal-title":"Cell Death Dis."},{"key":"B10","doi-asserted-by":"publisher","first-page":"456479","DOI":"10.1155\/2015\/456479","article-title":"A comparison of variant calling pipelines using genome in a bottle as a reference","volume":"2015","author":"Cornish","year":"2015","journal-title":"Biomed Res. Int."},{"key":"B11","doi-asserted-by":"publisher","first-page":"1946","DOI":"10.1089\/ars.2012.4850","article-title":"Regulation of SOD2 in cancer by histone modifications and CpG methylation: closing the loop between redox biology and epigenetics","volume":"18","author":"Cyr","year":"2013","journal-title":"Antiox. Redox Signal."},{"key":"B12","doi-asserted-by":"publisher","first-page":"9031","DOI":"10.1074\/jbc.C110.212589","article-title":"Alpha-synuclein sequesters Dnmt1 from the nucleus a novel mechanism for epigenetic alterations in lewy body diseases","volume":"286","author":"Desplats","year":"2011","journal-title":"J. Biol. Chem."},{"key":"B13","doi-asserted-by":"publisher","first-page":"1531","DOI":"10.1212\/WNL.0b013e3182a95818","article-title":"Unrecognized vitamin D-3 deficiency is common in Parkinson disease Harvard Biomarker Study","volume":"81","author":"Ding","year":"2013","journal-title":"Neurology"},{"key":"B14","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1016\/j.parkreldis.2015.11.014","article-title":"Identification of a panel of five serum miRNAs as a biomarker for Parkinson's disease","volume":"22","author":"Ding","year":"2016","journal-title":"Parkinson. Relat. Disord."},{"key":"B15","doi-asserted-by":"publisher","first-page":"1582","DOI":"10.1212\/WNL.0000000000000973","article-title":"Skin nerve alpha-synuclein deposits: a biomarker for idiopathic Parkinson Disease response","volume":"83","author":"Donadio","year":"2014","journal-title":"Neurology"},{"key":"B16","doi-asserted-by":"publisher","first-page":"306","DOI":"10.1002\/ana.24567","article-title":"Skin nerve misfolded -synuclein in pure autonomic failure and Parkinson disease","volume":"79","author":"Donadio","year":"2016","journal-title":"Ann. Neurol."},{"key":"B17","doi-asserted-by":"publisher","first-page":"8689","DOI":"10.1073\/pnas.1002720107","article-title":"Conservation and divergence of methylation patterning in plants and animals","volume":"107","author":"Feng","year":"2010","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B18","doi-asserted-by":"publisher","first-page":"651","DOI":"10.1007\/s00401-014-1345-4","article-title":"Inflammatory dysregulation of blood monocytes in Parkinson's disease patients","volume":"128","author":"Grozdanov","year":"2014","journal-title":"Acta Neuropathol."},{"key":"B19","doi-asserted-by":"publisher","first-page":"1359","DOI":"10.1002\/mds.26001","article-title":"Genetic modifiers of Huntington's Disease","volume":"29","author":"Gusella","year":"2014","journal-title":"Move. Disord."},{"key":"B20","doi-asserted-by":"publisher","first-page":"e69815","DOI":"10.1371\/journal.pone.0069815","article-title":"Differential programming of B cells in AID deficient mice","volume":"8","author":"Hogenbirk","year":"2013","journal-title":"PLoS ONE"},{"key":"B21","doi-asserted-by":"publisher","first-page":"325","DOI":"10.1007\/s00401-012-1013-5","article-title":"The genetics and neuropathology of Parkinson's disease","volume":"124","author":"Houlden","year":"2012","journal-title":"Acta Neuropathol."},{"key":"B22","doi-asserted-by":"publisher","first-page":"406","DOI":"10.1016\/j.nut.2014.08.001","article-title":"Lymphocyte vitamin C levels as potential biomarker for progression of Parkinson's disease","volume":"31","author":"Ide","year":"2015","journal-title":"Nutrition"},{"key":"B23","doi-asserted-by":"publisher","first-page":"1368","DOI":"10.4161\/epi.22552","article-title":"Conserved dna methylation patterns in healthy blood cells and extensive changes in leukemia measured by a new quantitative technique","volume":"7","author":"Jelinek","year":"2012","journal-title":"Epigenetics"},{"key":"B24","doi-asserted-by":"publisher","first-page":"9","DOI":"10.2217\/epi.09.47","article-title":"Emerging promise of epigenetics and DNA methylation for the diagnosis and management of women's cancers","volume":"2","author":"Jones","year":"2010","journal-title":"Epigenomics"},{"key":"B25","doi-asserted-by":"publisher","first-page":"4293","DOI":"10.1038\/onc.2008.67","article-title":"Histone H4 lysine 20 monomethylation promotes transcriptional repression by L3MBTL1","volume":"27","author":"Kalakonda","year":"2008","journal-title":"Oncogene"},{"key":"B26","doi-asserted-by":"publisher","first-page":"1413","DOI":"10.1038\/cdd.2015.80","article-title":"Primary cilia and autophagic dysfunction in Huntington's disease","volume":"22","author":"Kaliszewski","year":"2015","journal-title":"Cell Death Different."},{"key":"B27","doi-asserted-by":"publisher","first-page":"1639","DOI":"10.1101\/gr.092759.109","article-title":"Circos: an information aesthetic for comparative genomics","volume":"19","author":"Krzywinski","year":"2009","journal-title":"Gen. Res"},{"key":"B28","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1016\/j.gene.2014.11.022","article-title":"Huntington's disease: an update of therapeutic strategies","volume":"556","author":"Kumar","year":"2015","journal-title":"Gene"},{"key":"B29","doi-asserted-by":"publisher","first-page":"e0141298","DOI":"10.1371\/journal.pone.0141298","article-title":"Evidence of extensive alternative splicing in post mortem human brain HTT transcription by mRNA sequencing","volume":"10","author":"Labadorf","year":"2015","journal-title":"PLoS ONE"},{"key":"B30","doi-asserted-by":"publisher","first-page":"271","DOI":"10.2217\/epi.15.102","article-title":"The role of epigenetics in genetic and environmental epidemiology","volume":"8","author":"Ladd-Acosta","year":"2016","journal-title":"Epigenomics"},{"key":"B31","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1038\/nrg2732","article-title":"Principles and challenges of genome-wide dna methylation analysis","volume":"11","author":"Laird","year":"2010","journal-title":"Nat. Rev. Genet."},{"key":"B32","volume-title":"Numerical Ecology","author":"Legendre","year":"2012","edition":"3rd Edn."},{"key":"B33","doi-asserted-by":"publisher","first-page":"2059","DOI":"10.1128\/MCB.01413-14","article-title":"Histone methyltransferase Setd8 represses Gata2 expression and regulates erythroid maturation","volume":"35","author":"Malik","year":"2015","journal-title":"Mol. Cell. Biol."},{"key":"B34","doi-asserted-by":"publisher","first-page":"173","DOI":"10.3389\/fphys.2014.00173","article-title":"DNA methylation and temperature stress in an Antarctic polychaete, Spiophanes tcherniai","volume":"5","author":"Marsh","year":"2014","journal-title":"Front. Physiol."},{"key":"B35","doi-asserted-by":"publisher","first-page":"1030","DOI":"10.4161\/epi.25865","article-title":"Distinctive patterns of DNA methylation associated with Parkinson disease Identification of concordant epigenetic changes in brain and peripheral blood leukocytes","volume":"8","author":"Masliah","year":"2013","journal-title":"Epigenetics"},{"key":"B36","doi-asserted-by":"publisher","first-page":"291","DOI":"10.1186\/s13059-015-0842-7","article-title":"High density methylation qtl analysis in human blood via next-generation sequencing of the methylated genomic dna fraction","volume":"16","author":"McClay","year":"2015","journal-title":"Gen. Biol."},{"key":"B37","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1007\/s11910-015-0607-4","article-title":"Advances in biomarker research in Parkinson's Disease","volume":"16","author":"Mehta","year":"2016","journal-title":"Curr. Neurol. Neurosci. Rep."},{"key":"B38","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.ymeth.2014.12.011","article-title":"(epi)genomics approaches and their applications","volume":"72","author":"Meissner","year":"2015","journal-title":"Methods"},{"key":"B39","doi-asserted-by":"publisher","first-page":"S40","DOI":"10.1016\/j.metabol.2014.10.030","article-title":"Biomarkers of Parkinson's disease: Present and future","volume":"64","author":"Miller","year":"2015","journal-title":"Metabol. Clin. Exp."},{"key":"B40","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1007\/s00204-014-1426-0","article-title":"DNA methylation alterations in response to prenatal exposure of maternal cigarette smoking: A persistent epigenetic impact on health from maternal lifestyle?","volume":"90","author":"Nielsen","year":"2016","journal-title":"Arch. Toxicol."},{"key":"B41","doi-asserted-by":"publisher","first-page":"e1314","DOI":"10.1371\/journal.pone.0001314","article-title":"Identification of novel high-frequency DNA methylation changes in breast cancer","volume":"2","author":"Ordway","year":"2007","journal-title":"PLoS ONE"},{"key":"B42","doi-asserted-by":"publisher","first-page":"577","DOI":"10.1002\/mds.26073","article-title":"Parkinson's disease correlates with promoter methylation in the alpha-synuclein Gene","volume":"30","author":"Pihlstr\u00f8m","year":"2015","journal-title":"Move. Disord."},{"key":"B43","doi-asserted-by":"publisher","first-page":"831","DOI":"10.1002\/mds.24962","article-title":"The neuropathology of genetic Parkinson's disease","volume":"27","author":"Poulopoulos","year":"2012","journal-title":"Move. Disord."},{"key":"B44","doi-asserted-by":"publisher","first-page":"216.e7","DOI":"10.1016\/j.neurobiolaging.2015.10.033","article-title":"Reduced mitochondrial DNA copy number is a biomarker of Parkinson's disease","volume":"38","author":"Pyle","year":"2016","journal-title":"Neurobiol. Aging"},{"key":"B45","doi-asserted-by":"publisher","first-page":"703","DOI":"10.1007\/s004380050374","article-title":"Differences in dna methylation patterns are detectable during dimorphic transition of fungi by amplification of restriction polymorphisms","volume":"253","author":"Reyna-L\u00f3pez","year":"1997","journal-title":"Mol. Genom. Genet."},{"key":"B46","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"B47","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1002\/acn3.285","article-title":"Parkinson disease and progressive supranuclear palsy: protein expression in skin","volume":"3","author":"Rodr\u00edguez-Leyva","year":"2016","journal-title":"Ann. Clin. Transl. Neurol."},{"key":"B48","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1111\/ene.12753","article-title":"Can we use peripheral tissue biopsies to diagnose Parkinson's disease? a review of the literature","volume":"23","author":"Schneider","year":"2016","journal-title":"Eur. J. Neurol."},{"key":"B49","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1038\/nature15394","article-title":"An integrated map of structural variation in 2,504 human genomes","volume":"526","author":"Sudmant","year":"2015","journal-title":"Nature"},{"key":"B50","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1186\/s40035-016-0052-6","article-title":"Methylation status of DJ-1 in leukocyte DNA of Parkinson's disease patients","volume":"5","author":"Tan","year":"2016","journal-title":"Transl. Neurodegen."},{"key":"B51","doi-asserted-by":"publisher","first-page":"308","DOI":"10.1016\/j.parkreldis.2013.12.002","article-title":"Methylation of alpha-synuclein and leucine-rich repeat kinase 2 in leukocyte DNA of Parkinson's disease patients","volume":"20","author":"Tan","year":"2014","journal-title":"Parkins. Relat. Disord."},{"key":"B52","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1016\/j.toxlet.2014.10.021","article-title":"Liver DNA methylation analysis in adult female C57BL\/6JxFVB mice following perinatal exposure to bisphenol A","volume":"232","author":"van Esterik","year":"2015","journal-title":"Toxicol. Lett."},{"key":"B53","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12920-015-0162-5","article-title":"The IGNITE network: a model for genomic medicine implementation and research","volume":"9","author":"Weitzel","year":"2016","journal-title":"BMC Med. Genom."},{"key":"B54","doi-asserted-by":"publisher","first-page":"37725","DOI":"10.1074\/jbc.M110.139527","article-title":"The MBT repeats of L3MBTL1 link SET8-mediated p53 methylation at lysine 382 to target gene repression","volume":"285","author":"West","year":"2010","journal-title":"J. Biol. Chem."},{"key":"B55","doi-asserted-by":"crossref","DOI":"10.1007\/978-0-387-98141-3","volume-title":"ggplot2: Elegant Graphics for Data Analysis","author":"Wickham","year":"2009"},{"key":"B56","doi-asserted-by":"publisher","first-page":"e91","DOI":"10.1093\/nar\/gku310","article-title":"Robustly detecting differential expression in RNA sequencing data using observation weights","volume":"42","author":"Zhou","year":"2014","journal-title":"Nucl. Acids Res."},{"key":"B57","doi-asserted-by":"publisher","first-page":"N14","DOI":"10.1227\/01.neu.0000438333.49696.12","article-title":"Neuropathology indicates a need for earlier neurorestorative intervention in Parkinson's Disease","volume":"73","author":"Zwagerman","year":"2013","journal-title":"Neurosurgery"}],"container-title":["Frontiers in Genetics"],"original-title":[],"link":[{"URL":"http:\/\/journal.frontiersin.org\/article\/10.3389\/fgene.2016.00191\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,20]],"date-time":"2024-06-20T09:13:54Z","timestamp":1718874834000},"score":1,"resource":{"primary":{"URL":"http:\/\/journal.frontiersin.org\/article\/10.3389\/fgene.2016.00191\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,11,2]]},"references-count":57,"URL":"https:\/\/doi.org\/10.3389\/fgene.2016.00191","relation":{},"ISSN":["1664-8021"],"issn-type":[{"value":"1664-8021","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,11,2]]}}}