CUTseq is a versatile method for preparing multiplexed DNA sequencing libraries from low-input samples.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
18 10 2019
18 10 2019
Historique:
received:
04
11
2018
accepted:
17
09
2019
entrez:
20
10
2019
pubmed:
20
10
2019
medline:
25
1
2020
Statut:
epublish
Résumé
Current multiplexing strategies for massively parallel sequencing of genomic DNA mainly rely on library indexing in the final steps of library preparation. This procedure is costly and time-consuming, because a library must be generated separately for each sample. Furthermore, library preparation is challenging in the case of fixed samples, such as DNA extracted from formalin-fixed paraffin-embedded (FFPE) tissues. Here we describe CUTseq, a method that uses restriction enzymes and in vitro transcription to barcode and amplify genomic DNA prior to library construction. We thoroughly assess the sensitivity and reproducibility of CUTseq in both cell lines and FFPE samples, and demonstrate an application of CUTseq for multi-region DNA copy number profiling within single FFPE tumor sections, to assess intratumor genetic heterogeneity at high spatial resolution. In conclusion, CUTseq is a versatile and cost-effective method for library preparation for reduced representation genome sequencing, which can find numerous applications in research and diagnostics.
Identifiants
pubmed: 31628304
doi: 10.1038/s41467-019-12570-2
pii: 10.1038/s41467-019-12570-2
pmc: PMC6802095
doi:
Substances chimiques
DNA
9007-49-2
DNA Restriction Enzymes
EC 3.1.21.-
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
4732Références
Nature. 2012 Dec 13;492(7428):186
pubmed: 23235867
Cell. 2017 Feb 9;168(4):613-628
pubmed: 28187284
Bioinformatics. 2017 Oct 1;33(19):3088-3090
pubmed: 28575171
Nature. 2016 May 02;534(7605):47-54
pubmed: 27135926
Nat Biotechnol. 2018 Sep;36(8):765-771
pubmed: 30010673
Nat Rev Genet. 2016 May 17;17(6):333-51
pubmed: 27184599
Nat Rev Genet. 2011 Jun 17;12(7):499-510
pubmed: 21681211
Bioinformatics. 2019 Jul 15;35(14):2489-2491
pubmed: 30520945
Bioinformatics. 2016 Oct 1;32(19):3047-8
pubmed: 27312411
J Clin Invest. 2018 Apr 2;128(4):1355-1370
pubmed: 29480816
Cancer Cell. 2017 Aug 14;32(2):169-184.e7
pubmed: 28810143
Nature. 2013 Oct 17;502(7471):333-339
pubmed: 24132290
Science. 2017 Apr 14;356(6334):189-194
pubmed: 28408603
Nat Methods. 2011 Nov 20;9(1):72-4
pubmed: 22101854
J Nucl Med. 2016 Oct;57(10):1523-1528
pubmed: 27151988
Science. 2012 Dec 21;338(6114):1622-6
pubmed: 23258894
Trends Genet. 1997 Dec;13(12):497-8
pubmed: 9433140
Nat Genet. 2016 Oct;48(10):1119-30
pubmed: 27526321
Mol Cell. 2015 May 21;58(4):586-97
pubmed: 26000844
Bioinformatics. 2009 Jun 1;25(11):1422-3
pubmed: 19304878
Nat Methods. 2012 Jun 28;9(7):676-82
pubmed: 22743772
Genome Res. 2014 Dec;24(12):2022-32
pubmed: 25236618
Biostatistics. 2004 Oct;5(4):557-72
pubmed: 15475419
Nucleic Acids Res. 2017 Jan 4;45(D1):D777-D783
pubmed: 27899578
PLoS One. 2008;3(10):e3376
pubmed: 18852878
Cancer Cell. 2006 Dec;10(6):515-27
pubmed: 17157791
Proc Natl Acad Sci U S A. 2002 Apr 16;99(8):5261-6
pubmed: 11959976
Genome Res. 2017 Mar;27(3):491-499
pubmed: 28100584
Nat Methods. 2017 May;14(5):491-493
pubmed: 28319112
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Lab Invest. 2008 May;88(5):491-503
pubmed: 18332872
Nature. 2018 Aug;560(7717):E8-E9
pubmed: 30089922
Genomics. 1992 Jul;13(3):718-25
pubmed: 1639399
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Nucleic Acids Res. 2016 Jun 20;44(11):e108
pubmed: 27060149