A high-throughput real-time PCR tissue-of-origin test to distinguish blood from lymphoblastoid cell line DNA for (epi)genomic studies.
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
18 03 2022
18 03 2022
Historique:
received:
07
12
2021
accepted:
09
03
2022
entrez:
19
3
2022
pubmed:
20
3
2022
medline:
6
5
2022
Statut:
epublish
Résumé
Lymphoblastoid cell lines (LCLs) derive from blood infected in vitro by Epstein-Barr virus and were used in several genetic, transcriptomic and epigenomic studies. Although few changes were shown between LCL and blood genotypes (SNPs) validating their use in genetics, more were highlighted for other genomic features and/or in their transcriptome and epigenome. This could render them less appropriate for these studies, notably when blood DNA could still be available. Here we developed a simple, high-throughput and cost-effective real-time PCR approach allowing to distinguish blood from LCL DNA samples based on the presence of EBV relative load and rearranged T-cell receptors γ and β. Our approach was able to achieve 98.5% sensitivity and 100% specificity on DNA of known origin (458 blood and 316 LCL DNA). It was further applied to 1957 DNA samples from the CEPH Aging cohort comprising DNA of uncertain origin, identifying 784 blood and 1016 LCL DNA. A subset of these DNA was further analyzed with an epigenetic clock indicating that DNA extracted from blood should be preferred to LCL for DNA methylation-based age prediction analysis. Our approach could thereby be a powerful tool to ascertain the origin of DNA in old collections prior to (epi)genomic studies.
Identifiants
pubmed: 35304543
doi: 10.1038/s41598-022-08663-6
pii: 10.1038/s41598-022-08663-6
pmc: PMC8933453
doi:
Substances chimiques
DNA
9007-49-2
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
4684Informations de copyright
© 2022. The Author(s).
Références
Lancet. 1973 Jul 14;2(7820):93-4
pubmed: 4123640
Epigenetics. 2011 Apr;6(4):508-15
pubmed: 21304276
Eur J Hum Genet. 2012 Sep;20(9):953-5
pubmed: 22378283
Plant Mol Biol. 2015 Jul;88(4-5):471-85
pubmed: 26072424
Nature. 2012 Jun 06;486(7401):141-6
pubmed: 22678297
Hum Mol Genet. 2016 Nov 1;25(21):4819-4834
pubmed: 28173075
Biostatistics. 2000 Jun;1(2):123-40
pubmed: 12933515
Blood. 1994 Jun 1;83(11):3271-8
pubmed: 8193362
Science. 2019 Oct 18;366(6463):
pubmed: 31624180
PLoS Genet. 2012;8(4):e1002639
pubmed: 22532805
Diagn Microbiol Infect Dis. 2007 Jan;57(1):47-51
pubmed: 17141448
Biopreserv Biobank. 2021 Oct;19(5):438-443
pubmed: 34468209
Nat Rev Genet. 2018 Jun;19(6):371-384
pubmed: 29643443
Int J Mol Sci. 2021 Apr 26;22(9):
pubmed: 33926115
Curr Opin Immunol. 2009 Apr;21(2):133-9
pubmed: 19362456
PLoS One. 2017 Jul 10;12(7):e0180841
pubmed: 28700679
Neuromuscul Disord. 2017 Mar;27(3):221-238
pubmed: 28161093
Rev Med Virol. 2008 Sep-Oct;18(5):305-19
pubmed: 18494041
Cancers (Basel). 2020 Sep 09;12(9):
pubmed: 32916819
J Transl Med. 2019 May 22;17(1):172
pubmed: 31118074
Hum Mol Genet. 2011 Apr 15;20(8):1643-52
pubmed: 21289059
Cancer Res. 2004 May 15;64(10):3361-4
pubmed: 15150084
Methods Mol Biol. 2015;1315:83-101
pubmed: 26103893
BMC Infect Dis. 2020 Mar 12;20(1):210
pubmed: 32164538
Mol Cell. 2013 Jan 24;49(2):359-367
pubmed: 23177740
PLoS One. 2017 Jun 27;12(6):e0179446
pubmed: 28654678
BMC Genomics. 2012 Sep 14;13:477
pubmed: 22974163
Adv Virus Res. 2014;88:279-313
pubmed: 24373315
Arch Intern Med. 2004 Nov 22;164(21):2335-42
pubmed: 15557412
Sci Rep. 2017 Mar 08;7:43833
pubmed: 28272413
Leukemia. 2003 Dec;17(12):2257-317
pubmed: 14671650
Epidemiology. 2002 May;13(3):246-54
pubmed: 11964924
Arch Pathol Lab Med. 2015 Jun;139(6):812-8
pubmed: 26030251
Leukemia. 2008 Mar;22(3):511-20
pubmed: 18094716
Hum Mutat. 2012 Jul;33(7):1075-86
pubmed: 22374857
Sci Rep. 2020 Sep 24;10(1):15652
pubmed: 32973211
Genomics. 2013 Oct;102(4):270-7
pubmed: 23743231
Biopreserv Biobank. 2018 Feb;16(1):3-6
pubmed: 29393664
Genomics. 1990 Mar;6(3):575-7
pubmed: 2184120
Scand J Immunol. 2016 Apr;83(4):255-66
pubmed: 26808160
Nat Genet. 1994 Jan;6(1):29-32
pubmed: 8136829
Pharmacogenomics. 2015;16(3):273-85
pubmed: 25712190
Science. 2020 Mar 20;367(6484):
pubmed: 32193295
Nature. 2005 Oct 27;437(7063):1299-320
pubmed: 16255080
Sci Rep. 2019 Jun 20;9(1):8862
pubmed: 31222117
Virchows Arch. 2021 Aug;479(2):233-246
pubmed: 34255145
Genomics. 2010 Feb;95(2):73-83
pubmed: 20005943
Nat Rev Cancer. 2004 Oct;4(10):757-68
pubmed: 15510157
Genom Data. 2016 May 12;9:18-21
pubmed: 27330997
Front Microbiol. 2016 Oct 25;7:1602
pubmed: 27826287
J Neurosci Res. 2009 Jul;87(9):1953-9
pubmed: 19224581
Pharmacogenomics. 2010 Mar;11(3):449-57
pubmed: 20235797
PLoS One. 2009 Sep 04;4(9):e6915
pubmed: 19730697
Hum Genomics. 2017 May 12;11(1):8
pubmed: 28499412
Nat Commun. 2021 May 25;12(1):3116
pubmed: 34035253
Mol Immunol. 2007 Jul;44(13):3380-8
pubmed: 17391765
Immun Ageing. 2010 Mar 16;7:4
pubmed: 20233447
Aging Cell. 2015 Dec;14(6):924-32
pubmed: 25913071
Adv Genomics Genet. 2017;7:1-9
pubmed: 28736497
Immunol Cell Biol. 2018 Feb;96(2):204-211
pubmed: 29363169
Science. 2002 Dec 20;298(5602):2381-5
pubmed: 12493913
J Hum Genet. 2009 Oct;54(10):612-3
pubmed: 19745834
PLoS Genet. 2014 Aug 14;10(8):e1004549
pubmed: 25121757
J Clin Microbiol. 2003 Nov;41(11):5245-9
pubmed: 14605174
C R Acad Sci III. 2001 Feb;324(2):129-35
pubmed: 11280044
Sci Rep. 2015 Jan 22;5:7960
pubmed: 25609584
Am J Clin Pathol. 2000 Jun;113(6):838-50
pubmed: 10874885
Methods Mol Biol. 2009;507:325-37
pubmed: 18987824
C R Acad Sci III. 1998 Jun;321(6):443-6
pubmed: 9769857
J Immunol Methods. 2000 Apr 3;237(1-2):187-97
pubmed: 10725462
J Immunol. 2003 Jul 15;171(2):524-7
pubmed: 12847212
Aging (Albany NY). 2018 Jul 26;10(7):1758-1775
pubmed: 30048243
Genet Med. 2018 Jul;20(7):697-707
pubmed: 29095815
Aging (Albany NY). 2015 Dec;7(12):1159-70
pubmed: 26678252
Clin Microbiol Rev. 2011 Jan;24(1):193-209
pubmed: 21233512
In Vitro Cell Dev Biol Anim. 2018 Aug;54(7):523-527
pubmed: 29948745
Curr Biol. 2010 Nov 23;20(22):R970-1
pubmed: 21093786
Genome Biol. 2013;14(10):R115
pubmed: 24138928
Curr Top Microbiol Immunol. 2001;258:13-33
pubmed: 11443858
Exp Gerontol. 2007 Jun;42(6):563-70
pubmed: 17337145
BMC Genomics. 2017 Sep 12;18(1):723
pubmed: 28899340