메뉴 건너뛰기




Volumn 9, Issue 8, 2014, Pages

Comparison of pre-analytical FFPE sample preparation methods and their impact on massively parallel sequencing in routine diagnostics

Author keywords

[No Author keywords available]

Indexed keywords

DNA; EPIDERMAL GROWTH FACTOR RECEPTOR; FLUORESCENT DYE; FORMALDEHYDE; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; HFE PROTEIN; PARAFFIN;

EID: 84905668712     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0104566     Document Type: Article
Times cited : (44)

References (31)
  • 1
    • 77955277111 scopus 로고    scopus 로고
    • Effects of KRAS, BRAF, NRAS, and PIK3CA mutations on the efficacy of cetuximab plus chemotherapy in chemotherapy-refractory metastatic colorectal cancer: A retrospective consortium analysis
    • De Roock W, Claes B, Bernasconi D, De Schutter J, Biesmans B, et al. (2010) Effects of KRAS, BRAF, NRAS, and PIK3CA mutations on the efficacy of cetuximab plus chemotherapy in chemotherapy-refractory metastatic colorectal cancer: a retrospective consortium analysis. Lancet Oncol 11: 753-762.
    • (2010) Lancet Oncol , vol.11 , pp. 753-762
    • De Roock, W.1    Claes, B.2    Bernasconi, D.3    De Schutter, J.4    Biesmans, B.5
  • 2
    • 84882261506 scopus 로고    scopus 로고
    • Comparison of Clinical Targeted Next-Generation Sequence Data from Formalin-Fixed and Fresh-Frozen Tissue Specimens
    • Spencer DH, Sehn JK, Abel HJ, Watson MA, Pfeifer JD, et al. (2013) Comparison of Clinical Targeted Next-Generation Sequence Data from Formalin-Fixed and Fresh-Frozen Tissue Specimens. J Mol Diagn 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
  • 3
    • 84875077830 scopus 로고    scopus 로고
    • Comparison of Targeted Next-Generation Sequencing (NGS) and Real-Time PCR in the Detection of EGFR, KRAS, and BRAF Mutations on Formalin-Fixed, Paraffin-Embedded Tumor Material of Non-Small Cell Lung Carcinoma - Superiority of NGS
    • Tuononen K, Mäki-Nevala S, Sarhadi VK, Wirtanen A, Rönty M, et al. (2013) Comparison of Targeted Next-Generation Sequencing (NGS) and Real-Time PCR in the Detection of EGFR, KRAS, and BRAF Mutations on Formalin-Fixed, Paraffin-Embedded Tumor Material of Non-Small Cell Lung Carcinoma - Superiority of NGS. Genes Chromosom Cancer 52: 503-511.
    • (2013) Genes Chromosom Cancer , vol.52 , pp. 503-511
    • Tuononen, K.1    Mäki-Nevala, S.2    Sarhadi, V.K.3    Wirtanen, A.4    Rönty, M.5
  • 4
    • 84874519595 scopus 로고    scopus 로고
    • Targeted, High-Depth, Next-Generation Sequencing of Cancer Genes in Formalin-Fixed, Paraffin-Embedded and Fine-Needle Aspiration Tumor Specimens
    • Hadd AG, Houghton J, Choudhary A, Sah S, Chen L, et al. (2013) Targeted, High-Depth, Next-Generation Sequencing of Cancer Genes in Formalin-Fixed, Paraffin-Embedded and Fine-Needle Aspiration Tumor Specimens. J Mol Diagn 15: 234-247.
    • (2013) J Mol Diagn , vol.15 , pp. 234-247
    • Hadd, A.G.1    Houghton, J.2    Choudhary, A.3    Sah, S.4    Chen, L.5
  • 5
    • 84865783136 scopus 로고    scopus 로고
    • Tackling Formalin-Fixed, Paraffin-Embedded Tumor Tissue with Next-Generation Sequencing
    • Corless CL, Spellman PT (2012) Tackling Formalin-Fixed, Paraffin-Embedded Tumor Tissue with Next-Generation Sequencing. Cancer Discov 2: 23-24.
    • (2012) Cancer Discov , vol.2 , pp. 23-24
    • Corless, C.L.1    Spellman, P.T.2
  • 6
    • 84887491073 scopus 로고    scopus 로고
    • Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing
    • Frampton GM, Fichtenholtz A, Otto GA, Wang K, Downing SR, et al. (2013) Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing. Nat Biotech 31: 1023-1031.
    • (2013) Nat Biotech , vol.31 , pp. 1023-1031
    • Frampton, G.M.1    Fichtenholtz, A.2    Otto, G.A.3    Wang, K.4    Downing, S.R.5
  • 7
    • 77951631386 scopus 로고    scopus 로고
    • The Isolation of Nucleic Acids from Fixed, Paraffin-Embedded Tissues-Which Methods Are Useful When?
    • Gilbert MTP, Haselkorn T, Bunce M, Sanchez JJ, Lucas SB, et al. (2007) The Isolation of Nucleic Acids from Fixed, Paraffin-Embedded Tissues-Which Methods Are Useful When? PLoS ONE 2: e537.
    • (2007) PLoS ONE , vol.2
    • Gilbert, M.T.P.1    Haselkorn, T.2    Bunce, M.3    Sanchez, J.J.4    Lucas, S.B.5
  • 8
    • 77957744517 scopus 로고    scopus 로고
    • Comparative analysis of four methods to extract DNA from paraffin-embedded tissues: Effect on downstream molecular applications
    • Huijsmans C, Damen J, van der Linden J, Savelkoul P, Hermans M (2010) Comparative analysis of four methods to extract DNA from paraffin-embedded tissues: effect on downstream molecular applications. BMC Res Notes 3: 239.
    • (2010) BMC Res Notes , vol.3 , pp. 239
    • Huijsmans, C.1    Damen, J.2    Van Der Linden, J.3    Savelkoul, P.4    Hermans, M.5
  • 9
    • 84893748187 scopus 로고    scopus 로고
    • Evaluation of five DNA extraction methods for detection of H. Pylori in formalin-fixed paraffin-embedded (FFPE) liver tissue from patients with hepatocellular carcinoma
    • Rabelo-Gonçalves E, Roesler B, Guardia AC, Milan A, Hara N, et al. (2014) Evaluation of five DNA extraction methods for detection of H. pylori in formalin-fixed paraffin-embedded (FFPE) liver tissue from patients with hepatocellular carcinoma. Pathol Res Pract 210: 142-146.
    • (2014) Pathol Res Pract , vol.210 , pp. 142-146
    • Rabelo-Gonçalves, E.1    Roesler, B.2    Guardia, A.C.3    Milan, A.4    Hara, N.5
  • 10
    • 84860529611 scopus 로고    scopus 로고
    • Evaluation of Maxwell 16 for automated DNA extraction from whole blood and formalin-fixed paraffin embedded (FFPE) tissue
    • Khokhar Shama K, Mitui M, Leos Nora K, Rogers Beverly B, Park Jason Y (2012) Evaluation of Maxwell 16 for automated DNA extraction from whole blood and formalin-fixed paraffin embedded (FFPE) tissue. Clin Chem Lab Med. pp.267.
    • (2012) Clin Chem Lab Med , pp. 267
    • Khokhar Shama, K.1    Mitui, M.2    Leos Nora, K.3    Rogers Beverly, B.4    Park Jason, Y.5
  • 11
    • 84878774401 scopus 로고    scopus 로고
    • DNA Qualification Workflow for Next Generation Sequencing of Histopathological Samples
    • Simbolo M, Gottardi M, Corbo V, Fassan M, Mafficini A, et al. (2013) DNA Qualification Workflow for Next Generation Sequencing of Histopathological Samples. PLoS ONE 8: e62692.
    • (2013) PLoS ONE , vol.8
    • Simbolo, M.1    Gottardi, M.2    Corbo, V.3    Fassan, M.4    Mafficini, A.5
  • 12
    • 77956910135 scopus 로고    scopus 로고
    • Multicentre validation study of nucleic acids extraction from FFPE tissues
    • Bonin S, Hlubek F, Benhattar J, Denkert C, Dietel M, et al. (2010) Multicentre validation study of nucleic acids extraction from FFPE tissues. Virchows Arch 457: 309-317.
    • (2010) Virchows Arch , vol.457 , pp. 309-317
    • Bonin, S.1    Hlubek, F.2    Benhattar, J.3    Denkert, C.4    Dietel, M.5
  • 13
    • 84883178389 scopus 로고    scopus 로고
    • Functional DNA quantification guides accurate next-generation sequencing mutation detection in formalin-fixed, paraffin-embedded tumor biopsies
    • Sah S, Chen L, Houghton J, Kemppainen J, Marko A, et al. (2013) Functional DNA quantification guides accurate next-generation sequencing mutation detection in formalin-fixed, paraffin-embedded tumor biopsies. Genome Med 5: 77.
    • (2013) Genome Med , vol.5 , pp. 77
    • Sah, S.1    Chen, L.2    Houghton, J.3    Kemppainen, J.4    Marko, A.5
  • 14
    • 80155187105 scopus 로고    scopus 로고
    • Nucleic acid quantity and quality from paraffin blocks: Defining optimal fixation, processing and DNA/RNA extraction techniques
    • Turashvili G, Yang W, McKinney S, Kalloger S, Gale N, et al. (2012) Nucleic acid quantity and quality from paraffin blocks: Defining optimal fixation, processing and DNA/RNA extraction techniques. Exp Mol Pathol 92: 33-43.
    • (2012) Exp Mol Pathol , vol.92 , pp. 33-43
    • Turashvili, G.1    Yang, W.2    McKinney, S.3    Kalloger, S.4    Gale, N.5
  • 15
    • 84874073176 scopus 로고    scopus 로고
    • Fragmentation of DNA affects the accuracy of the DNA quantitation by the commonly used methods
    • Sedlackova T, Repiska G, Celec P, Szemes T, Minarik G (2013) Fragmentation of DNA affects the accuracy of the DNA quantitation by the commonly used methods. Biol Proced Online 15: 5.
    • (2013) Biol Proced Online , vol.15 , pp. 5
    • Sedlackova, T.1    Repiska, G.2    Celec, P.3    Szemes, T.4    Minarik, G.5
  • 16
    • 84892377126 scopus 로고    scopus 로고
    • Comparison of high resolution melting analysis, pyrosequencing, next generation sequencing and immunohistochemistry to conventional Sanger sequencing for the detection of p.V600E and non-p.V600E BRAF mutations
    • Ihle MA, Fassunke J, Konig K, Grunewald I, Schlaak M, et al. (2014) Comparison of high resolution melting analysis, pyrosequencing, next generation sequencing and immunohistochemistry to conventional Sanger sequencing for the detection of p.V600E and non-p.V600E BRAF mutations. BMC Cancer 14: 13.
    • (2014) BMC Cancer , vol.14 , pp. 13
    • Ihle, M.A.1    Fassunke, J.2    Konig, K.3    Grunewald, I.4    Schlaak, M.5
  • 18
    • 84905641197 scopus 로고    scopus 로고
    • Qiagen Biorobot EZ1/Geno-M6/M48/M96 Recommendations MRC-Holland
    • MRC-Holland Available: Accessed 2014 March 07
    • MRC-Holland (2010) Qiagen Biorobot EZ1/Geno-M6/M48/M96 Recommendations MRC-Holland. Recommendation Qiagen Biorobot version 02. Available: http://www.mlpa.com/WebForms/WebFormDBData.aspx?Tag=- xxS62fvE1n5ZTUWvPoGB6xXS6zchqCoRQmInQtyM7lw. Accessed 2014 March 07.
    • (2010) Recommendation Qiagen Biorobot Version 02
  • 19
    • 70449674353 scopus 로고    scopus 로고
    • Limited copy number-high resolution melting (LCN-HRM) enables the detection and identification by sequencing of low level mutations in cancer biopsies
    • Do H, Dobrovic A (2009) Limited copy number-high resolution melting (LCN-HRM) enables the detection and identification by sequencing of low level mutations in cancer biopsies. Mol Cancer 8: 82.
    • (2009) Mol Cancer , vol.8 , pp. 82
    • Do, H.1    Dobrovic, A.2
  • 20
    • 0035194394 scopus 로고    scopus 로고
    • Comparison of the DNA extraction methods for polymerase chain reaction amplification from formalin-fixed and paraffin-embedded tissues
    • DOI 10.1097/00019606-200112000-00009
    • Sato Y, Sugie R, Tsuchiya B, Kameya T, Natori M, et al. (2001) Comparison of the DNA extraction methods for polymerase chain reaction amplification from formalin-fixed and paraffin-embedded tissues. Diagn Mol Pathol 10: 265-271. (Pubitemid 33130034)
    • (2001) Diagnostic Molecular Pathology , vol.10 , Issue.4 , pp. 265-271
    • Sato, Y.1    Sugie, R.2    Tsuchiya, B.3    Kameya, T.4    Natori, M.5    Mukai, K.6
  • 21
    • 0035710433 scopus 로고    scopus 로고
    • Real-time PCR analysis of DNA and RNA extracted from formalin-fixed and paraffin-embedded biopsies
    • DOI 10.1006/meth.2001.1263
    • Lehmann U, Kreipe H (2001) Real-time PCR analysis of DNA and RNA extracted from formalin-fixed and paraffin-embedded biopsies. Methods 25: 409-418. (Pubitemid 34164013)
    • (2001) Methods , vol.25 , Issue.4 , pp. 409-418
    • Lehmann, U.1    Kreipe, H.2
  • 22
    • 84876946468 scopus 로고    scopus 로고
    • Multiplex picoliter-droplet digital PCR for quantitative assessment of DNA integrity in clinical samples
    • Didelot A, Kotsopoulos SK, Lupo A, Pekin D, Li X, et al. (2013) Multiplex picoliter-droplet digital PCR for quantitative assessment of DNA integrity in clinical samples. Clin Chem 59: 815-823.
    • (2013) Clin Chem , vol.59 , pp. 815-823
    • Didelot, A.1    Kotsopoulos, S.K.2    Lupo, A.3    Pekin, D.4    Li, X.5
  • 23
    • 0037129827 scopus 로고    scopus 로고
    • Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes
    • Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, et al. (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3: Research0034.
    • (2002) Genome Biol , vol.3
    • Vandesompele, J.1    De Preter, K.2    Pattyn, F.3    Poppe, B.4    Van Roy, N.5
  • 26
    • 84905650165 scopus 로고    scopus 로고
    • Available: Accessed 2014 March 07
    • Illumina (2014) MiSeq Desktop Sequencer Specifications. Available: http://www.illumina.com/systems/miseq/performance-specifications.ilmn. Accessed 2014 March 07.
    • (2014) MiSeq Desktop Sequencer Specifications
  • 27
    • 0036898005 scopus 로고    scopus 로고
    • Effect of fixatives and tissue processing on the content and integrity of nucleic acids
    • Srinivasan M, Sedmak D, Jewell S (2002) Effect of fixatives and tissue processing on the content and integrity of nucleic acids. Am J Pathol 161: 1961-1971. (Pubitemid 35434840)
    • (2002) American Journal of Pathology , vol.161 , Issue.6 , pp. 1961-1971
    • Srinivasan, M.1    Sedmak, D.2    Jewell, S.3
  • 28
    • 0032755991 scopus 로고    scopus 로고
    • A high frequency of sequence alterations is due to formalin fixation of archival specimens
    • Williams C, Ponten F, Moberg C, Soderkvist P, Uhlen M, et al. (1999) A high frequency of sequence alterations is due to formalin fixation of archival specimens. Am J Pathol 155: 1467-1471.
    • (1999) Am J Pathol , vol.155 , pp. 1467-1471
    • Williams, C.1    Ponten, F.2    Moberg, C.3    Soderkvist, P.4    Uhlen, M.5
  • 29
    • 14644418434 scopus 로고    scopus 로고
    • Low copy number DNA template can render polymerase chain reaction error prone in a sequence-dependent manner
    • Akbari M, Hansen MD, Halgunset J, Skorpen F, Krokan HE (2005) Low copy number DNA template can render polymerase chain reaction error prone in a sequence-dependent manner. J Mol Diagn 7: 36-39. (Pubitemid 40310163)
    • (2005) Journal of Molecular Diagnostics , vol.7 , Issue.1 , pp. 36-39
    • Akbari, M.1    Hansen, M.D.2    Halgunset, J.3    Skorpen, F.4    Krokan, H.E.5
  • 30
    • 84883316129 scopus 로고    scopus 로고
    • Reducing sequence artifacts in amplicon-based massively parallel sequencing of formalin-fixed paraffin-embedded DNA by enzymatic depletion of uracil-containing templates
    • Do H, Wong SQ, Li J, Dobrovic A (2013) Reducing sequence artifacts in amplicon-based massively parallel sequencing of formalin-fixed paraffin-embedded DNA by enzymatic depletion of uracil-containing templates. Clin Chem 59: 1376-1383.
    • (2013) Clin Chem , vol.59 , pp. 1376-1383
    • Do, H.1    Wong, S.Q.2    Li, J.3    Dobrovic, A.4
  • 31
    • 80053173227 scopus 로고    scopus 로고
    • Targeted high throughput sequencing in clinical cancer settings: Formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity
    • Kerick M, Isau M, Timmermann B, Sultmann H, Herwig R, et al. (2011) Targeted high throughput sequencing in clinical cancer settings: formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity. BMC Med Genomics 4: 68.
    • (2011) BMC Med Genomics , vol.4 , pp. 68
    • Kerick, M.1    Isau, M.2    Timmermann, B.3    Sultmann, H.4    Herwig, R.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.