Ontology type: schema:ScholarlyArticle Open Access: True
2016-12
AUTHORSHeidi D Pharo, Hilde Honne, Hege M Vedeld, Christina Dahl, Kim Andresen, Knut Liestøl, Marine Jeanmougin, Per Guldberg, Guro E Lind
ABSTRACTDiverging methylation frequencies are often reported for the same locus in the same disease, underscoring the need for limiting technical variability in DNA methylation analyses. We have investigated seven likely sources of variability at different steps of bisulfite PCR-based DNA methylation analyses using a fully automated quantitative methylation-specific PCR setup of six gene promoters across 20 colon cancer cell lines. Based on >15,000 individual PCRs, all tested parameters affected the normalized percent of methylated reference (PMR) differences, with a fourfold varying magnitude. Additionally, large variations were observed across the six genes analyzed. The highest variation was seen using single-copy genes as reference for normalization, followed by different amounts of template in the PCR, different amounts of DNA in the bisulfite reaction, and storage of bisulfite converted samples. Finally, when a highly standardized pipeline was repeated, the difference in PMR value for the same assay in the same cell line was on average limited to five (on a 0-100 scale). In conclusion, a standardized pipeline is essential for consistent methylation results, where parameters are kept constant for all samples. Nevertheless, a certain level of variation in methylation values must be expected, underscoring the need for careful interpretation of data. More... »
PAGES33936
http://scigraph.springernature.com/pub.10.1038/srep33936
DOIhttp://dx.doi.org/10.1038/srep33936
DIMENSIONShttps://app.dimensions.ai/details/publication/pub.1006258605
PUBMEDhttps://www.ncbi.nlm.nih.gov/pubmed/27671843
JSON-LD is the canonical representation for SciGraph data.
TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT
[
{
"@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json",
"about": [
{
"id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Genetics",
"type": "DefinedTerm"
},
{
"id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Biological Sciences",
"type": "DefinedTerm"
}
],
"author": [
{
"affiliation": {
"alternateName": "University of Oslo",
"id": "https://www.grid.ac/institutes/grid.5510.1",
"name": [
"Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, the Norwegian Radium Hospital, Oslo, Norway.",
"KG Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.",
"Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway.",
"Department of Biosciences, The Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway."
],
"type": "Organization"
},
"familyName": "Pharo",
"givenName": "Heidi D",
"id": "sg:person.07666575241.04",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.07666575241.04"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "University of Oslo",
"id": "https://www.grid.ac/institutes/grid.5510.1",
"name": [
"Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, the Norwegian Radium Hospital, Oslo, Norway.",
"KG Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.",
"Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway."
],
"type": "Organization"
},
"familyName": "Honne",
"givenName": "Hilde",
"id": "sg:person.0765524576.66",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0765524576.66"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "University of Oslo",
"id": "https://www.grid.ac/institutes/grid.5510.1",
"name": [
"Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, the Norwegian Radium Hospital, Oslo, Norway.",
"KG Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.",
"Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway."
],
"type": "Organization"
},
"familyName": "Vedeld",
"givenName": "Hege M",
"id": "sg:person.01004740536.22",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01004740536.22"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Danish Cancer Society",
"id": "https://www.grid.ac/institutes/grid.417390.8",
"name": [
"Danish Cancer Society Research Center, Copenhagen, Denmark."
],
"type": "Organization"
},
"familyName": "Dahl",
"givenName": "Christina",
"id": "sg:person.01011250102.01",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01011250102.01"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "University of Oslo",
"id": "https://www.grid.ac/institutes/grid.5510.1",
"name": [
"Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, the Norwegian Radium Hospital, Oslo, Norway.",
"KG Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.",
"Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway."
],
"type": "Organization"
},
"familyName": "Andresen",
"givenName": "Kim",
"id": "sg:person.0670512136.45",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0670512136.45"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "University of Oslo",
"id": "https://www.grid.ac/institutes/grid.5510.1",
"name": [
"Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway.",
"Department of Informatics, University of Oslo, Oslo, Norway."
],
"type": "Organization"
},
"familyName": "Liest\u00f8l",
"givenName": "Knut",
"id": "sg:person.01013101321.80",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01013101321.80"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "University of Oslo",
"id": "https://www.grid.ac/institutes/grid.5510.1",
"name": [
"Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, the Norwegian Radium Hospital, Oslo, Norway.",
"KG Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.",
"Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway."
],
"type": "Organization"
},
"familyName": "Jeanmougin",
"givenName": "Marine",
"id": "sg:person.014247440241.18",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014247440241.18"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Danish Cancer Society",
"id": "https://www.grid.ac/institutes/grid.417390.8",
"name": [
"Danish Cancer Society Research Center, Copenhagen, Denmark."
],
"type": "Organization"
},
"familyName": "Guldberg",
"givenName": "Per",
"id": "sg:person.0760021664.46",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0760021664.46"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "University of Oslo",
"id": "https://www.grid.ac/institutes/grid.5510.1",
"name": [
"Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, the Norwegian Radium Hospital, Oslo, Norway.",
"KG Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.",
"Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway.",
"Department of Biosciences, The Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway."
],
"type": "Organization"
},
"familyName": "Lind",
"givenName": "Guro E",
"id": "sg:person.01227551572.62",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01227551572.62"
],
"type": "Person"
}
],
"citation": [
{
"id": "sg:pub.10.1186/s12885-016-2135-2",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1000738953",
"https://doi.org/10.1186/s12885-016-2135-2"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1073/pnas.89.5.1827",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1007596846"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nbt.1685",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1011479792",
"https://doi.org/10.1038/nbt.1685"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/s13277-014-2300-7",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1011767386",
"https://doi.org/10.1007/s13277-014-2300-7"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/j.cancergencyto.2004.03.014",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1012512942"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/nar/gki987",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1013244220"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/nar/28.8.e32",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1014093221"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/j.biochi.2012.07.014",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1018741253"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/1479-5876-10-36",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1022264975",
"https://doi.org/10.1186/1479-5876-10-36"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/j.cell.2011.02.013",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1023540354"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/nar/gki901",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1024763851"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.7150/jca.12174",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1029997752"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1073/pnas.93.18.9821",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1030175469"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1371/journal.pone.0107272",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1032648165"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/1471-2164-15-1174",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1033774002",
"https://doi.org/10.1186/1471-2164-15-1174"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.2353/jmoldx.2006.050135",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1033835302"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/s12885-015-1962-x",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1035064688",
"https://doi.org/10.1186/s12885-015-1962-x"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/s13148-016-0196-3",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1038299145",
"https://doi.org/10.1186/s13148-016-0196-3"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1146/annurev.genom.9.081307.164217",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1040316789"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1158/1940-6207.capr-15-0180",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1041820019"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1371/journal.pone.0122302",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1045441715"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1371/journal.pone.0122302",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1045441715"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/oncsis.2013.35",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1047315575",
"https://doi.org/10.1038/oncsis.2013.35"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/nar/gkn455",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1051564385"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1126/science.281.5375.363",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1062561814"
],
"type": "CreativeWork"
},
{
"id": "https://app.dimensions.ai/details/publication/pub.1074801138",
"type": "CreativeWork"
}
],
"datePublished": "2016-12",
"datePublishedReg": "2016-12-01",
"description": "Diverging methylation frequencies are often reported for the same locus in the same disease, underscoring the need for limiting technical variability in DNA methylation analyses. We have investigated seven likely sources of variability at different steps of bisulfite PCR-based DNA methylation analyses using a fully automated quantitative methylation-specific PCR setup of six gene promoters across 20 colon cancer cell lines. Based on >15,000 individual PCRs, all tested parameters affected the normalized percent of methylated reference (PMR) differences, with a fourfold varying magnitude. Additionally, large variations were observed across the six genes analyzed. The highest variation was seen using single-copy genes as reference for normalization, followed by different amounts of template in the PCR, different amounts of DNA in the bisulfite reaction, and storage of bisulfite converted samples. Finally, when a highly standardized pipeline was repeated, the difference in PMR value for the same assay in the same cell line was on average limited to five (on a 0-100 scale). In conclusion, a standardized pipeline is essential for consistent methylation results, where parameters are kept constant for all samples. Nevertheless, a certain level of variation in methylation values must be expected, underscoring the need for careful interpretation of data.",
"genre": "research_article",
"id": "sg:pub.10.1038/srep33936",
"inLanguage": [
"en"
],
"isAccessibleForFree": true,
"isFundedItemOf": [
{
"id": "sg:grant.4646688",
"type": "MonetaryGrant"
},
{
"id": "sg:grant.4667014",
"type": "MonetaryGrant"
}
],
"isPartOf": [
{
"id": "sg:journal.1045337",
"issn": [
"2045-2322"
],
"name": "Scientific Reports",
"type": "Periodical"
},
{
"issueNumber": "1",
"type": "PublicationIssue"
},
{
"type": "PublicationVolume",
"volumeNumber": "6"
}
],
"name": "Experimental factors affecting the robustness of DNA methylation analysis",
"pagination": "33936",
"productId": [
{
"name": "readcube_id",
"type": "PropertyValue",
"value": [
"1dcfe0532a390b1ad22edb46bc9e33f7432a67a43932003756a82721ffb2c30c"
]
},
{
"name": "pubmed_id",
"type": "PropertyValue",
"value": [
"27671843"
]
},
{
"name": "nlm_unique_id",
"type": "PropertyValue",
"value": [
"101563288"
]
},
{
"name": "doi",
"type": "PropertyValue",
"value": [
"10.1038/srep33936"
]
},
{
"name": "dimensions_id",
"type": "PropertyValue",
"value": [
"pub.1006258605"
]
}
],
"sameAs": [
"https://doi.org/10.1038/srep33936",
"https://app.dimensions.ai/details/publication/pub.1006258605"
],
"sdDataset": "articles",
"sdDatePublished": "2019-04-10T22:39",
"sdLicense": "https://scigraph.springernature.com/explorer/license/",
"sdPublisher": {
"name": "Springer Nature - SN SciGraph project",
"type": "Organization"
},
"sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000001_0000000264/records_8690_00000549.jsonl",
"type": "ScholarlyArticle",
"url": "http://www.nature.com/srep/2016/160927/srep33936/full/srep33936.html"
}
]Download the RDF metadata as: json-ld nt turtle xml License info
JSON-LD is a popular format for linked data which is fully compatible with JSON.
curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1038/srep33936'
N-Triples is a line-based linked data format ideal for batch operations.
curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/srep33936'
Turtle is a human-readable linked data format.
curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/srep33936'
RDF/XML is a standard XML format for linked data.
curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/srep33936'
This table displays all metadata directly associated to this object as RDF triples.
217 TRIPLES
21 PREDICATES
54 URIs
21 LITERALS
9 BLANK NODES