메뉴 건너뛰기




Volumn 7, Issue 37, 2016, Pages 59115-59128

Single-strand DNA library preparation improves sequencing of formalin-fixed and paraffin-embedded (FFPE) cancer DNA

Author keywords

Cancer; Formalin fixed paraffin embedded (FFPE) tissue; High throughput sequencing; Library preparation; Whole exome sequencing

Indexed keywords

DNA; DOUBLE STRANDED DNA; FORMALIN FIXED AND PARAFFIN EMBEDDED CANCER DNA; SINGLE STRANDED DNA; UNCLASSIFIED DRUG; FORMALDEHYDE; PARAFFIN;

EID: 84991334146     PISSN: None     EISSN: 19492553     Source Type: Journal    
DOI: 10.18632/oncotarget.10827     Document Type: Article
Times cited : (25)

References (43)
  • 6
    • 84864351002 scopus 로고    scopus 로고
    • Exome Enrichment and SOLiD Sequencing of Formalin Fixed Paraffin Embedded (FFPE) Prostate Cancer Tissue
    • Menon R, Deng M, Boehm D, Braun M, Fend F, Boehm D, Biskup S, Perner S. Exome Enrichment and SOLiD Sequencing of Formalin Fixed Paraffin Embedded (FFPE) Prostate Cancer Tissue. Int J Mol Sci. 2012; 13:8933-8942
    • (2012) Int J Mol Sci , vol.13 , pp. 8933-8942
    • Menon, R.1    Deng, M.2    Boehm, D.3    Braun, M.4    Fend, F.5    Boehm, D.6    Biskup, S.7    Perner, S.8
  • 11
    • 84875500588 scopus 로고    scopus 로고
    • Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA
    • Gansauge M-T, Meyer M. Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nat Protoc. 2013; 8:737-748
    • (2013) Nat Protoc , vol.8 , pp. 737-748
    • Gansauge, M.-T.1    Meyer, M.2
  • 13
    • 77956285690 scopus 로고    scopus 로고
    • Illumina Sequencing Library Preparation for Highly Multiplexed Target Capture and Sequencing
    • Meyer M, Kircher M. Illumina Sequencing Library Preparation for Highly Multiplexed Target Capture and Sequencing. Cold Spring Harb Protoc. 2010; 2010:pdb. prot5448
    • (2010) Cold Spring Harb Protoc , vol.2010
    • Meyer, M.1    Kircher, M.2
  • 14
    • 84875700725 scopus 로고    scopus 로고
    • Predicting the molecular complexity of sequencing libraries
    • Daley T, Smith AD. Predicting the molecular complexity of sequencing libraries. Nat Methods. 2013; 10:325-327
    • (2013) Nat Methods , vol.10 , pp. 325-327
    • Daley, T.1    Smith, A.D.2
  • 16
    • 0016694032 scopus 로고
    • Formaldehyde as a probe of DNA structure. I. Reaction with exocyclic amino groups of DNA bases
    • McGhee JD, Von Hippel PH. Formaldehyde as a probe of DNA structure. I. Reaction with exocyclic amino groups of DNA bases. Biochemistry. 1975; 14:1281-1296
    • (1975) Biochemistry , vol.14 , pp. 1281-1296
    • McGhee, J.D.1    Von Hippel, P.H.2
  • 17
    • 84872784631 scopus 로고
    • Formaldehyde preferentially interstrand cross-links duplex DNA through deoxyadenosine residues at the sequence 5'-d (AT)
    • Huang H, Solomon MS, Hopkins PB. Formaldehyde preferentially interstrand cross-links duplex DNA through deoxyadenosine residues at the sequence 5'-d (AT). J Am Chem Soc. 1992; 114:9240-9241
    • (1992) J Am Chem Soc , vol.114 , pp. 9240-9241
    • Huang, H.1    Solomon, M.S.2    Hopkins, P.B.3
  • 20
    • 84882261506 scopus 로고    scopus 로고
    • Comparison of clinical targeted nextgeneration sequence data from formalin-fixed and freshfrozen tissue specimens
    • Spencer DH, Sehn JK, Abel HJ, Watson MA, Pfeifer JD, Duncavage EJ. Comparison of clinical targeted nextgeneration sequence data from formalin-fixed and freshfrozen tissue specimens. J Mol Diagn. 2013; 15:623-633
    • (2013) J Mol Diagn , vol.15 , pp. 623-633
    • Spencer, D.H.1    Sehn, J.K.2    Abel, H.J.3    Watson, M.A.4    Pfeifer, J.D.5    Duncavage, E.J.6
  • 21
    • 0000668611 scopus 로고
    • DNA interstrand cross-linking by formaldehyde: nucleotide sequence preference and covalent structure of the predominant cross-link formed in synthetic oligonucleotides
    • Huang H, Hopkins PB. DNA interstrand cross-linking by formaldehyde: nucleotide sequence preference and covalent structure of the predominant cross-link formed in synthetic oligonucleotides. J Am Chem Soc. 1993; 115:9402-9408
    • (1993) J Am Chem Soc , vol.115 , pp. 9402-9408
    • Huang, H.1    Hopkins, P.B.2
  • 22
    • 85060263973 scopus 로고    scopus 로고
    • Genotoxicity of formaldehyde: molecular basis of DNA damage and mutation
    • Kawanishi M, Matsuda T, Yagi T. Genotoxicity of formaldehyde: molecular basis of DNA damage and mutation. Front Environ Sci. 2014; 2:36
    • (2014) Front Environ Sci , vol.2 , pp. 36
    • Kawanishi, M.1    Matsuda, T.2    Yagi, T.3
  • 25
    • 13944278588 scopus 로고
    • ENZYMATIC DEAMINATION OF CYTOSINE NUCLEOSIDES
    • Wang TP, Sable HZ, Lampen JO. ENZYMATIC DEAMINATION OF CYTOSINE NUCLEOSIDES. J Biol Chem. 1950; 184:17-28
    • (1950) J Biol Chem , vol.184 , pp. 17-28
    • Wang, T.P.1    Sable, H.Z.2    Lampen, J.O.3
  • 28
    • 0021102439 scopus 로고
    • Enzymic detection of uracil in a cloned and sequenced deoxyribonucleic acid segment
    • Weiss RB, Mineura K, Henderson EE, Duker NJ, DeRiel JK. Enzymic detection of uracil in a cloned and sequenced deoxyribonucleic acid segment. Biochemistry. 1983; 22:4501-4507
    • (1983) Biochemistry , vol.22 , pp. 4501-4507
    • Weiss, R.B.1    Mineura, K.2    Henderson, E.E.3    Duker, N.J.4    DeRiel, J.K.5
  • 34
    • 84857244374 scopus 로고    scopus 로고
    • Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform
    • Kircher M, Sawyer S, Meyer M. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res. 2011:gkr771
    • (2011) Nucleic Acids Res
    • Kircher, M.1    Sawyer, S.2    Meyer, M.3
  • 35
    • 84857271408 scopus 로고    scopus 로고
    • Length and GC-biases during sequencing library amplification: a comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries
    • Dabney J, Meyer M. Length and GC-biases during sequencing library amplification: a comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries. Biotechniques. 2012; 52:87-94
    • (2012) Biotechniques , vol.52 , pp. 87-94
    • Dabney, J.1    Meyer, M.2
  • 37
    • 84886402148 scopus 로고    scopus 로고
    • freeIbis: an efficient basecaller with calibrated quality scores for Illumina sequencers
    • Renaud G, Kircher M, Stenzel U, Kelso J. freeIbis: an efficient basecaller with calibrated quality scores for Illumina sequencers. Bioinformatics. 2013; 29:1208-1209
    • (2013) Bioinformatics , vol.29 , pp. 1208-1209
    • Renaud, G.1    Kircher, M.2    Stenzel, U.3    Kelso, J.4
  • 38
    • 84922394220 scopus 로고    scopus 로고
    • leeHom: adaptor trimming and merging for Illumina sequencing reads
    • Renaud G, Stenzel U, Kelso J. leeHom: adaptor trimming and merging for Illumina sequencing reads. Nucleic Acids Res. 2014; 42:e141-e141
    • (2014) Nucleic Acids Res , vol.42 , pp. e141-e141
    • Renaud, G.1    Stenzel, U.2    Kelso, J.3
  • 39
    • 84929008489 scopus 로고    scopus 로고
    • deML: robust demultiplexing of Illumina sequences using a likelihood-based approach
    • Renaud G, Stenzel U, Maricic T, Wiebe V, Kelso J. deML: robust demultiplexing of Illumina sequences using a likelihood-based approach. Bioinformatics. 2015; 31:770-772
    • (2015) Bioinformatics , vol.31 , pp. 770-772
    • Renaud, G.1    Stenzel, U.2    Maricic, T.3    Wiebe, V.4    Kelso, J.5
  • 40
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: a flexible suite of utilities for comparing genomic features
    • Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010; 26:841-842
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 42
    • 77956534324 scopus 로고    scopus 로고
    • ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
    • Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010; 38:e164-e164
    • (2010) Nucleic Acids Res , vol.38 , pp. e164-e164
    • Wang, K.1    Li, M.2    Hakonarson, H.3
  • 43
    • 84973418649 scopus 로고    scopus 로고
    • R Foundation for Statistical Computing. Vienna, Austria. 2005
    • Team RDC. R: A language and environment for statistical computing. ISBN 3-900051-07-0. R Foundation for Statistical Computing. Vienna, Austria, 2013. url: http://www.R-project.org). 2005
    • (2013) R: A language and environment for statistical computing


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.