A direct comparison of interphase FISH versus low-coverage single cell sequencing to detect aneuploidy reveals respective strengths and weaknesses.
Aneuploidy
Animals
Cerebral Cortex
/ cytology
Fibroblasts
/ ultrastructure
Hepatocytes
/ ultrastructure
Humans
In Situ Hybridization, Fluorescence
/ methods
Interphase
Karyotyping
/ methods
Mice
Neurons
/ ultrastructure
Polyploidy
Reproducibility of Results
Sensitivity and Specificity
Single-Cell Analysis
Whole Genome Sequencing
/ methods
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
19 07 2019
19 07 2019
Historique:
received:
20
12
2018
accepted:
21
06
2019
entrez:
21
7
2019
pubmed:
22
7
2019
medline:
3
11
2020
Statut:
epublish
Résumé
Aneuploidy has been reported to occur at remarkably high levels in normal somatic tissues using Fluorescence In Situ Hybridization (FISH). Recently, these reports were contradicted by single-cell low-coverage whole genome sequencing (scL-WGS) analyses, which showed aneuploidy frequencies at least an order of magnitude lower. To explain these seemingly contradictory findings, we used both techniques to analyze artificially generated mock aneuploid cells and cells with natural random aneuploidy. Our data indicate that while FISH tended to over-report aneuploidies, a modified 2-probe approach can accurately detect low levels of aneuploidy. Further, scL-WGS tends to underestimate aneuploidy levels, especially in a polyploid background.
Identifiants
pubmed: 31324840
doi: 10.1038/s41598-019-46606-w
pii: 10.1038/s41598-019-46606-w
pmc: PMC6642082
doi:
Types de publication
Comparative Study
Evaluation Study
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
10508Subventions
Organisme : NIA NIH HHS
ID : P01 AG017242
Pays : United States
Organisme : NCI NIH HHS
ID : P30 CA013330
Pays : United States
Références
J Histochem Cytochem. 2005 Mar;53(3):385-90
pubmed: 15750026
Cell Rep. 2014 Sep 11;8(5):1280-9
pubmed: 25159146
J Comp Neurol. 2010 Oct 1;518(19):3981-4000
pubmed: 20737596
Genome Biol. 2016 May 31;17(1):116
pubmed: 27246599
Exp Cell Res. 1975 Nov;96(1):1-6
pubmed: 1193162
PLoS Biol. 2008 Dec 2;6(12):2853-68
pubmed: 19053174
J Clin Invest. 2012 Sep;122(9):3307-15
pubmed: 22863619
Neurobiol Aging. 2017 Aug;56:50-66
pubmed: 28494436
Hum Mol Genet. 2012 Dec 15;21(24):5246-53
pubmed: 22962300
Am J Hum Genet. 1976 Sep;28(5):465-73
pubmed: 984042
Methods Mol Biol. 2014;1136:291-305
pubmed: 24633803
Gastroenterology. 2012 Jan;142(1):25-8
pubmed: 22057114
Proc Natl Acad Sci U S A. 1963 Aug;50:390-5
pubmed: 14060661
Expert Rev Mol Diagn. 2004 Sep;4(5):663-76
pubmed: 15347260
J Gerontol. 1982 Jan;37(1):33-7
pubmed: 7053395
In Vitro. 1973 Mar-Apr;8(5):353-61
pubmed: 4695793
J Neurosci. 2005 Mar 2;25(9):2176-80
pubmed: 15745943
Sci Rep. 2016 Oct 12;6:35218
pubmed: 27731420
Science. 2013 Nov 1;342(6158):632-7
pubmed: 24179226
Mol Cytogenet. 2010 Jan 11;3:1
pubmed: 20180947
Nat Methods. 2015 Nov;12(11):1058-60
pubmed: 26344043
Bioessays. 2015 May;37(5):570-7
pubmed: 25739518
PLoS One. 2011;6(10):e26080
pubmed: 22022514
Nucleic Acids Res. 2011 Jan;39(Database issue):D19-21
pubmed: 21062823
Biomark Res. 2014 Feb 05;2(1):3
pubmed: 24499728
Commun Integr Biol. 2010 Mar;3(2):201-3
pubmed: 20585523
Nature. 2010 Oct 7;467(7316):707-10
pubmed: 20861837
Proc Natl Acad Sci U S A. 2001 Nov 6;98(23):13361-6
pubmed: 11698687
Proc Natl Acad Sci U S A. 1988 Dec;85(23):9086-90
pubmed: 3194411
J Cell Sci. 2003 Jul 15;116(Pt 14):2833-8
pubmed: 12808017
Proc Natl Acad Sci U S A. 1995 Sep 26;92(20):9363-7
pubmed: 7568133
Proc Natl Acad Sci U S A. 2014 Sep 16;111(37):13409-14
pubmed: 25197050
Hum Mol Genet. 2016 Feb 15;25(4):755-65
pubmed: 26681803