Genotype instability during long-term subculture of lymphoblastoid cell lines View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2013-01

AUTHORS

Ji Hee Oh, Young Jin Kim, Sanghoon Moon, Hye-Young Nam, Jae-Pil Jeon, Jong Ho Lee, Jong-Young Lee, Yoon Shin Cho

ABSTRACT

Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines (LCLs) promise to address the challenge posed by the limited availability of primary cells needed as a source of genomic DNA for genetic studies. However, the genetic stability of LCLs following prolonged culture has never been rigorously investigated. To evaluate genotypic errors caused by EBV integration into human chromosomes, we isolated genomic DNA from human peripheral blood mononuclear cells and LCLs collected from 20 individuals and genotyped the DNA samples using the Affymetrix 500K SNP array set. Genotype concordance measurements between two sources of DNA from the same individual indicated that genotypic discordance is negligible in early-passage LCLs (<20 passages) but substantial in late-passage LCLs (>50 passages). Analysis of concordance on a chromosome-by-chromosome basis identified genomic regions with a high frequency of genotypic errors resulting from the loss of heterozygosity observed in late-passage LCLs. Our findings suggest that, although LCLs harvested during early stages of propagation are a reliable source of genomic DNA for genetic studies, investigations that involve genotyping of the entire genome should not use DNA from late-passage LCLs. More... »

PAGES

16

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/jhg.2012.123

DOI

http://dx.doi.org/10.1038/jhg.2012.123

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1036184253

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/23171997


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

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"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Adult", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Aged", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Cell Line, Transformed", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Cell Transformation, Viral", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Cells, Cultured", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genetic Variation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genotype", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Herpesvirus 4, Human", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Humans", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Leukocytes, Mononuclear", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Middle Aged", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Polymorphism, Single Nucleotide", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Virus Integration", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Yonsei University", 
          "id": "https://www.grid.ac/institutes/grid.15444.30", 
          "name": [
            "Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, Republic of Korea", 
            "Yonsei University Research Institute of Science for Ageing, Yonsei University, Seoul, Republic of Korea"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Oh", 
        "givenName": "Ji Hee", 
        "id": "sg:person.0761452454.04", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0761452454.04"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Seoul National University", 
          "id": "https://www.grid.ac/institutes/grid.31501.36", 
          "name": [
            "Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, Republic of Korea", 
            "Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Kim", 
        "givenName": "Young Jin", 
        "id": "sg:person.01173172106.42", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01173172106.42"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Korea National Institute of Health", 
          "id": "https://www.grid.ac/institutes/grid.415482.e", 
          "name": [
            "Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, Republic of Korea"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Moon", 
        "givenName": "Sanghoon", 
        "id": "sg:person.0772303416.18", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0772303416.18"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "National Biobank of Korea, Chungcheongbuk-do, Republic of Korea"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Nam", 
        "givenName": "Hye-Young", 
        "id": "sg:person.0622103172.05", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0622103172.05"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "National Biobank of Korea, Chungcheongbuk-do, Republic of Korea"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Jeon", 
        "givenName": "Jae-Pil", 
        "id": "sg:person.01361061630.78", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01361061630.78"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Yonsei University", 
          "id": "https://www.grid.ac/institutes/grid.15444.30", 
          "name": [
            "Yonsei University Research Institute of Science for Ageing, Yonsei University, Seoul, Republic of Korea"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Lee", 
        "givenName": "Jong Ho", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Korea National Institute of Health", 
          "id": "https://www.grid.ac/institutes/grid.415482.e", 
          "name": [
            "Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, Republic of Korea"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Lee", 
        "givenName": "Jong-Young", 
        "id": "sg:person.01176761116.47", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01176761116.47"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Hallym University", 
          "id": "https://www.grid.ac/institutes/grid.256753.0", 
          "name": [
            "Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, Republic of Korea", 
            "Department of Biomedical Science, Hallym University, Gangwon-do, Republic of Korea"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Cho", 
        "givenName": "Yoon Shin", 
        "id": "sg:person.016331315467.33", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016331315467.33"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "sg:pub.10.1186/1471-2164-10-106", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1001678851", 
          "https://doi.org/10.1186/1471-2164-10-106"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/bth034", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1002445505"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature08979", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1003788883", 
          "https://doi.org/10.1038/nature08979"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature08979", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1003788883", 
          "https://doi.org/10.1038/nature08979"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1158/0008-5472.can-04-0079", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005835469"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.bbagen.2003.10.014", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007688444"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1365-2184.2010.00717.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1011451994"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1365-2184.2010.00717.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1011451994"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/sj.ejhg.5201164", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017348559", 
          "https://doi.org/10.1038/sj.ejhg.5201164"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/sj.ejhg.5201164", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017348559", 
          "https://doi.org/10.1038/sj.ejhg.5201164"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1086/519795", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1019061180"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/labinvest.3700593", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1019231500", 
          "https://doi.org/10.1038/labinvest.3700593"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1365-2184.2010.00687.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1021846538"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1365-2184.2010.00687.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1021846538"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.94.17.8988", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025475250"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng.357", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025919373", 
          "https://doi.org/10.1038/ng.357"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng.357", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025919373", 
          "https://doi.org/10.1038/ng.357"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature02168", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033654326", 
          "https://doi.org/10.1038/nature02168"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature02168", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033654326", 
          "https://doi.org/10.1038/nature02168"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2156-10-15", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1039230383", 
          "https://doi.org/10.1186/1471-2156-10-15"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/bti741", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1040127778"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/gbe/evr014", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045727474"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s10059-009-0018-y", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047224152", 
          "https://doi.org/10.1007/s10059-009-0018-y"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s10059-009-0018-y", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047224152", 
          "https://doi.org/10.1007/s10059-009-0018-y"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s10059-009-0018-y", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047224152", 
          "https://doi.org/10.1007/s10059-009-0018-y"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng.238", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047420273", 
          "https://doi.org/10.1038/ng.238"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pgen.1000287", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1049217674"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cancergencyto.2006.10.010", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1049954226"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/hmg/ddl436", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1050878215"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pone.0006915", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051679823"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature05329", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1052925490", 
          "https://doi.org/10.1038/nature05329"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature05329", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1052925490", 
          "https://doi.org/10.1038/nature05329"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature05329", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1052925490", 
          "https://doi.org/10.1038/nature05329"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1074555905", 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2013-01", 
    "datePublishedReg": "2013-01-01", 
    "description": "Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines (LCLs) promise to address the challenge posed by the limited availability of primary cells needed as a source of genomic DNA for genetic studies. However, the genetic stability of LCLs following prolonged culture has never been rigorously investigated. To evaluate genotypic errors caused by EBV integration into human chromosomes, we isolated genomic DNA from human peripheral blood mononuclear cells and LCLs collected from 20 individuals and genotyped the DNA samples using the Affymetrix 500K SNP array set. Genotype concordance measurements between two sources of DNA from the same individual indicated that genotypic discordance is negligible in early-passage LCLs (<20 passages) but substantial in late-passage LCLs (>50 passages). Analysis of concordance on a chromosome-by-chromosome basis identified genomic regions with a high frequency of genotypic errors resulting from the loss of heterozygosity observed in late-passage LCLs. Our findings suggest that, although LCLs harvested during early stages of propagation are a reliable source of genomic DNA for genetic studies, investigations that involve genotyping of the entire genome should not use DNA from late-passage LCLs.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1038/jhg.2012.123", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.7467793", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1294984", 
        "issn": [
          "1434-5161", 
          "1435-232X"
        ], 
        "name": "Journal of Human Genetics", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "58"
      }
    ], 
    "name": "Genotype instability during long-term subculture of lymphoblastoid cell lines", 
    "pagination": "16", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "ac5e069b15490843225aee9a46335d5b9a7bf402ccd2f791508ebdb4e9d1472f"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "23171997"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "9808008"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1038/jhg.2012.123"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1036184253"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1038/jhg.2012.123", 
      "https://app.dimensions.ai/details/publication/pub.1036184253"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-10T17:20", 
    "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_8672_00000435.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://www.nature.com/articles/jhg2012123"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

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/jhg.2012.123'

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/jhg.2012.123'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/jhg.2012.123'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/jhg.2012.123'


 

This table displays all metadata directly associated to this object as RDF triples.

268 TRIPLES      21 PREDICATES      66 URIs      34 LITERALS      22 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1038/jhg.2012.123 schema:about N04c425f37d4f4c9e92e7628b46b0503d
2 N087be044aab14c80af64e54246f54c26
3 N20c57c7011c14c09bf38b03a1c7a4c97
4 N210c47337fa6421e9ffd28a20ce57335
5 N26951d7f45684eaf9bdbec765b431ae4
6 N356ad34da5484a18acf0556c1c6ac70c
7 N3e6141b3446f4159b5c307dd11fae028
8 N5d2441e239544ac7b130ec15f9777493
9 N6043c3c5f66a49cb92848d2f44394f8b
10 N6d34e784f42544219281030615dae2c0
11 N771d7ef78fc745e29b6fb32b605b2550
12 Ncb20591965114174af5f0112c9451352
13 Nfed4ca6a812c4cf4955f0368ad51e3e2
14 anzsrc-for:06
15 anzsrc-for:0604
16 schema:author Ndc4964e86df749cab89495e3a80f448a
17 schema:citation sg:pub.10.1007/s10059-009-0018-y
18 sg:pub.10.1038/labinvest.3700593
19 sg:pub.10.1038/nature02168
20 sg:pub.10.1038/nature05329
21 sg:pub.10.1038/nature08979
22 sg:pub.10.1038/ng.238
23 sg:pub.10.1038/ng.357
24 sg:pub.10.1038/sj.ejhg.5201164
25 sg:pub.10.1186/1471-2156-10-15
26 sg:pub.10.1186/1471-2164-10-106
27 https://app.dimensions.ai/details/publication/pub.1074555905
28 https://doi.org/10.1016/j.bbagen.2003.10.014
29 https://doi.org/10.1016/j.cancergencyto.2006.10.010
30 https://doi.org/10.1073/pnas.94.17.8988
31 https://doi.org/10.1086/519795
32 https://doi.org/10.1093/bioinformatics/bth034
33 https://doi.org/10.1093/bioinformatics/bti741
34 https://doi.org/10.1093/gbe/evr014
35 https://doi.org/10.1093/hmg/ddl436
36 https://doi.org/10.1111/j.1365-2184.2010.00687.x
37 https://doi.org/10.1111/j.1365-2184.2010.00717.x
38 https://doi.org/10.1158/0008-5472.can-04-0079
39 https://doi.org/10.1371/journal.pgen.1000287
40 https://doi.org/10.1371/journal.pone.0006915
41 schema:datePublished 2013-01
42 schema:datePublishedReg 2013-01-01
43 schema:description Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines (LCLs) promise to address the challenge posed by the limited availability of primary cells needed as a source of genomic DNA for genetic studies. However, the genetic stability of LCLs following prolonged culture has never been rigorously investigated. To evaluate genotypic errors caused by EBV integration into human chromosomes, we isolated genomic DNA from human peripheral blood mononuclear cells and LCLs collected from 20 individuals and genotyped the DNA samples using the Affymetrix 500K SNP array set. Genotype concordance measurements between two sources of DNA from the same individual indicated that genotypic discordance is negligible in early-passage LCLs (<20 passages) but substantial in late-passage LCLs (>50 passages). Analysis of concordance on a chromosome-by-chromosome basis identified genomic regions with a high frequency of genotypic errors resulting from the loss of heterozygosity observed in late-passage LCLs. Our findings suggest that, although LCLs harvested during early stages of propagation are a reliable source of genomic DNA for genetic studies, investigations that involve genotyping of the entire genome should not use DNA from late-passage LCLs.
44 schema:genre research_article
45 schema:inLanguage en
46 schema:isAccessibleForFree true
47 schema:isPartOf N166aa06f01b84dc1aeceab874a338fba
48 N367192ff5d7345079def6ca4c25c477d
49 sg:journal.1294984
50 schema:name Genotype instability during long-term subculture of lymphoblastoid cell lines
51 schema:pagination 16
52 schema:productId N19c330e9279048ee8cb4af176ce1fcbe
53 N76ff7bf181614126b001d6cec4b2ca68
54 N8ccff71405ec4cdaa3ee394669297e4a
55 Ncafbd4a6a30344078456b3e9344f113a
56 Ne1de262ac47b4076b295fb54088bbc84
57 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036184253
58 https://doi.org/10.1038/jhg.2012.123
59 schema:sdDatePublished 2019-04-10T17:20
60 schema:sdLicense https://scigraph.springernature.com/explorer/license/
61 schema:sdPublisher N7bd7c80a1006491dbc22b8b30b6ec7da
62 schema:url https://www.nature.com/articles/jhg2012123
63 sgo:license sg:explorer/license/
64 sgo:sdDataset articles
65 rdf:type schema:ScholarlyArticle
66 N0288c85e2c174430bb298cf6b1f8aaaf rdf:first sg:person.0772303416.18
67 rdf:rest Nde55982ad21f4c2da5d6705fef69e968
68 N04c425f37d4f4c9e92e7628b46b0503d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
69 schema:name Herpesvirus 4, Human
70 rdf:type schema:DefinedTerm
71 N087be044aab14c80af64e54246f54c26 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
72 schema:name Polymorphism, Single Nucleotide
73 rdf:type schema:DefinedTerm
74 N166aa06f01b84dc1aeceab874a338fba schema:volumeNumber 58
75 rdf:type schema:PublicationVolume
76 N19c330e9279048ee8cb4af176ce1fcbe schema:name pubmed_id
77 schema:value 23171997
78 rdf:type schema:PropertyValue
79 N20c57c7011c14c09bf38b03a1c7a4c97 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
80 schema:name Cell Line, Transformed
81 rdf:type schema:DefinedTerm
82 N210c47337fa6421e9ffd28a20ce57335 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
83 schema:name Adult
84 rdf:type schema:DefinedTerm
85 N26951d7f45684eaf9bdbec765b431ae4 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
86 schema:name Genotype
87 rdf:type schema:DefinedTerm
88 N2bb708726bfa4ec086c9234925a501f1 schema:affiliation https://www.grid.ac/institutes/grid.15444.30
89 schema:familyName Lee
90 schema:givenName Jong Ho
91 rdf:type schema:Person
92 N356ad34da5484a18acf0556c1c6ac70c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
93 schema:name Humans
94 rdf:type schema:DefinedTerm
95 N367192ff5d7345079def6ca4c25c477d schema:issueNumber 1
96 rdf:type schema:PublicationIssue
97 N3e6141b3446f4159b5c307dd11fae028 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
98 schema:name Aged
99 rdf:type schema:DefinedTerm
100 N4617d47e9d894a2280703d39a6086664 rdf:first sg:person.01361061630.78
101 rdf:rest Nbca498311b0e42e8b0b28142d231e541
102 N5d2441e239544ac7b130ec15f9777493 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
103 schema:name Virus Integration
104 rdf:type schema:DefinedTerm
105 N6043c3c5f66a49cb92848d2f44394f8b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
106 schema:name Genetic Variation
107 rdf:type schema:DefinedTerm
108 N6d34e784f42544219281030615dae2c0 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
109 schema:name Middle Aged
110 rdf:type schema:DefinedTerm
111 N76ff7bf181614126b001d6cec4b2ca68 schema:name nlm_unique_id
112 schema:value 9808008
113 rdf:type schema:PropertyValue
114 N771d7ef78fc745e29b6fb32b605b2550 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
115 schema:name Cells, Cultured
116 rdf:type schema:DefinedTerm
117 N7bd7c80a1006491dbc22b8b30b6ec7da schema:name Springer Nature - SN SciGraph project
118 rdf:type schema:Organization
119 N8b0e86762e80468581d015a1137776db schema:name National Biobank of Korea, Chungcheongbuk-do, Republic of Korea
120 rdf:type schema:Organization
121 N8ccff71405ec4cdaa3ee394669297e4a schema:name dimensions_id
122 schema:value pub.1036184253
123 rdf:type schema:PropertyValue
124 N9803e84e2e624860a290f38842a14403 rdf:first sg:person.01176761116.47
125 rdf:rest Ncef7fdb137884de1991130b7b7d9ee1b
126 Nb56096baa3d94b0d855e596c0e71b77b rdf:first sg:person.01173172106.42
127 rdf:rest N0288c85e2c174430bb298cf6b1f8aaaf
128 Nbca498311b0e42e8b0b28142d231e541 rdf:first N2bb708726bfa4ec086c9234925a501f1
129 rdf:rest N9803e84e2e624860a290f38842a14403
130 Ncafbd4a6a30344078456b3e9344f113a schema:name readcube_id
131 schema:value ac5e069b15490843225aee9a46335d5b9a7bf402ccd2f791508ebdb4e9d1472f
132 rdf:type schema:PropertyValue
133 Ncb20591965114174af5f0112c9451352 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
134 schema:name Leukocytes, Mononuclear
135 rdf:type schema:DefinedTerm
136 Ncef7fdb137884de1991130b7b7d9ee1b rdf:first sg:person.016331315467.33
137 rdf:rest rdf:nil
138 Ndc4964e86df749cab89495e3a80f448a rdf:first sg:person.0761452454.04
139 rdf:rest Nb56096baa3d94b0d855e596c0e71b77b
140 Nde55982ad21f4c2da5d6705fef69e968 rdf:first sg:person.0622103172.05
141 rdf:rest N4617d47e9d894a2280703d39a6086664
142 Ne1de262ac47b4076b295fb54088bbc84 schema:name doi
143 schema:value 10.1038/jhg.2012.123
144 rdf:type schema:PropertyValue
145 Ne93bd55de0134151bab1530138c0fe87 schema:name National Biobank of Korea, Chungcheongbuk-do, Republic of Korea
146 rdf:type schema:Organization
147 Nfed4ca6a812c4cf4955f0368ad51e3e2 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
148 schema:name Cell Transformation, Viral
149 rdf:type schema:DefinedTerm
150 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
151 schema:name Biological Sciences
152 rdf:type schema:DefinedTerm
153 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
154 schema:name Genetics
155 rdf:type schema:DefinedTerm
156 sg:grant.7467793 http://pending.schema.org/fundedItem sg:pub.10.1038/jhg.2012.123
157 rdf:type schema:MonetaryGrant
158 sg:journal.1294984 schema:issn 1434-5161
159 1435-232X
160 schema:name Journal of Human Genetics
161 rdf:type schema:Periodical
162 sg:person.01173172106.42 schema:affiliation https://www.grid.ac/institutes/grid.31501.36
163 schema:familyName Kim
164 schema:givenName Young Jin
165 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01173172106.42
166 rdf:type schema:Person
167 sg:person.01176761116.47 schema:affiliation https://www.grid.ac/institutes/grid.415482.e
168 schema:familyName Lee
169 schema:givenName Jong-Young
170 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01176761116.47
171 rdf:type schema:Person
172 sg:person.01361061630.78 schema:affiliation N8b0e86762e80468581d015a1137776db
173 schema:familyName Jeon
174 schema:givenName Jae-Pil
175 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01361061630.78
176 rdf:type schema:Person
177 sg:person.016331315467.33 schema:affiliation https://www.grid.ac/institutes/grid.256753.0
178 schema:familyName Cho
179 schema:givenName Yoon Shin
180 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016331315467.33
181 rdf:type schema:Person
182 sg:person.0622103172.05 schema:affiliation Ne93bd55de0134151bab1530138c0fe87
183 schema:familyName Nam
184 schema:givenName Hye-Young
185 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0622103172.05
186 rdf:type schema:Person
187 sg:person.0761452454.04 schema:affiliation https://www.grid.ac/institutes/grid.15444.30
188 schema:familyName Oh
189 schema:givenName Ji Hee
190 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0761452454.04
191 rdf:type schema:Person
192 sg:person.0772303416.18 schema:affiliation https://www.grid.ac/institutes/grid.415482.e
193 schema:familyName Moon
194 schema:givenName Sanghoon
195 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0772303416.18
196 rdf:type schema:Person
197 sg:pub.10.1007/s10059-009-0018-y schema:sameAs https://app.dimensions.ai/details/publication/pub.1047224152
198 https://doi.org/10.1007/s10059-009-0018-y
199 rdf:type schema:CreativeWork
200 sg:pub.10.1038/labinvest.3700593 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019231500
201 https://doi.org/10.1038/labinvest.3700593
202 rdf:type schema:CreativeWork
203 sg:pub.10.1038/nature02168 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033654326
204 https://doi.org/10.1038/nature02168
205 rdf:type schema:CreativeWork
206 sg:pub.10.1038/nature05329 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052925490
207 https://doi.org/10.1038/nature05329
208 rdf:type schema:CreativeWork
209 sg:pub.10.1038/nature08979 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003788883
210 https://doi.org/10.1038/nature08979
211 rdf:type schema:CreativeWork
212 sg:pub.10.1038/ng.238 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047420273
213 https://doi.org/10.1038/ng.238
214 rdf:type schema:CreativeWork
215 sg:pub.10.1038/ng.357 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025919373
216 https://doi.org/10.1038/ng.357
217 rdf:type schema:CreativeWork
218 sg:pub.10.1038/sj.ejhg.5201164 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017348559
219 https://doi.org/10.1038/sj.ejhg.5201164
220 rdf:type schema:CreativeWork
221 sg:pub.10.1186/1471-2156-10-15 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039230383
222 https://doi.org/10.1186/1471-2156-10-15
223 rdf:type schema:CreativeWork
224 sg:pub.10.1186/1471-2164-10-106 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001678851
225 https://doi.org/10.1186/1471-2164-10-106
226 rdf:type schema:CreativeWork
227 https://app.dimensions.ai/details/publication/pub.1074555905 schema:CreativeWork
228 https://doi.org/10.1016/j.bbagen.2003.10.014 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007688444
229 rdf:type schema:CreativeWork
230 https://doi.org/10.1016/j.cancergencyto.2006.10.010 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049954226
231 rdf:type schema:CreativeWork
232 https://doi.org/10.1073/pnas.94.17.8988 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025475250
233 rdf:type schema:CreativeWork
234 https://doi.org/10.1086/519795 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019061180
235 rdf:type schema:CreativeWork
236 https://doi.org/10.1093/bioinformatics/bth034 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002445505
237 rdf:type schema:CreativeWork
238 https://doi.org/10.1093/bioinformatics/bti741 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040127778
239 rdf:type schema:CreativeWork
240 https://doi.org/10.1093/gbe/evr014 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045727474
241 rdf:type schema:CreativeWork
242 https://doi.org/10.1093/hmg/ddl436 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050878215
243 rdf:type schema:CreativeWork
244 https://doi.org/10.1111/j.1365-2184.2010.00687.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1021846538
245 rdf:type schema:CreativeWork
246 https://doi.org/10.1111/j.1365-2184.2010.00717.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1011451994
247 rdf:type schema:CreativeWork
248 https://doi.org/10.1158/0008-5472.can-04-0079 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005835469
249 rdf:type schema:CreativeWork
250 https://doi.org/10.1371/journal.pgen.1000287 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049217674
251 rdf:type schema:CreativeWork
252 https://doi.org/10.1371/journal.pone.0006915 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051679823
253 rdf:type schema:CreativeWork
254 https://www.grid.ac/institutes/grid.15444.30 schema:alternateName Yonsei University
255 schema:name Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, Republic of Korea
256 Yonsei University Research Institute of Science for Ageing, Yonsei University, Seoul, Republic of Korea
257 rdf:type schema:Organization
258 https://www.grid.ac/institutes/grid.256753.0 schema:alternateName Hallym University
259 schema:name Department of Biomedical Science, Hallym University, Gangwon-do, Republic of Korea
260 Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, Republic of Korea
261 rdf:type schema:Organization
262 https://www.grid.ac/institutes/grid.31501.36 schema:alternateName Seoul National University
263 schema:name Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, Republic of Korea
264 Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
265 rdf:type schema:Organization
266 https://www.grid.ac/institutes/grid.415482.e schema:alternateName Korea National Institute of Health
267 schema:name Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, Republic of Korea
268 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...