메뉴 건너뛰기




Volumn 7, Issue 3, 2015, Pages 1313-1332

Not all next generation sequencing diagnostics are created equal: Understanding the nuances of solid tumor assay design for somatic mutation detection

Author keywords

Cancer panels; Copy number; Germline; Molecular inversion probes; Next generation sequencing; Somatic; Target enrichment

Indexed keywords

BIOINFORMATICS; COPY NUMBER VARIATION; DNA PROBE; FLUORESCENCE IN SITU HYBRIDIZATION; GERMLINE MUTATION; HUMAN; KARYOTYPING; MICROARRAY ANALYSIS; NEXT GENERATION SEQUENCING; POLYMERASE CHAIN REACTION; REVIEW; SOLID TUMOR; SOMATIC MUTATION;

EID: 84937412447     PISSN: None     EISSN: 20726694     Source Type: Journal    
DOI: 10.3390/cancers7030837     Document Type: Review
Times cited : (48)

References (84)
  • 2
    • 84871924245 scopus 로고    scopus 로고
    • Immunohistochemistry in the era of personalised medicine
    • [CrossRef] [PubMed]
    • McCourt, C. M.; Boyle, D.; James, J.; Salto-Tellez, M. Immunohistochemistry in the era of personalised medicine. J. Clin. Pathol. 2013, 66, 58-61. [CrossRef] [PubMed].
    • (2013) J. Clin. Pathol , vol.66 , pp. 58-61
    • McCourt, C.M.1    Boyle, D.2    James, J.3    Salto-Tellez, M.4
  • 3
    • 0034327895 scopus 로고    scopus 로고
    • Assessment of methods for tissue-based detection of the her-2/neu alteration in human breast cancer: A direct comparison of fluorescence in situ hybridization and immunohistochemistry
    • [PubMed]
    • Pauletti, G.; Dandekar, S.; Rong, H.; Ramos, L.; Peng, H.; Seshadri, R.; Slamon, D. J. Assessment of methods for tissue-based detection of the her-2/neu alteration in human breast cancer: A direct comparison of fluorescence in situ hybridization and immunohistochemistry. J. Clin. Oncol. 2000, 18, 3651-3664. [PubMed].
    • (2000) J. Clin. Oncol , vol.18 , pp. 3651-3664
    • Pauletti, G.1    Dandekar, S.2    Rong, H.3    Ramos, L.4    Peng, H.5    Seshadri, R.6    Slamon, D.J.7
  • 4
    • 0035863284 scopus 로고    scopus 로고
    • Her-2/neu analysis in archival tissue samples of human breast cancer: Comparison of immunohistochemistry and fluorescence in situ hybridization
    • [PubMed]
    • Lebeau, A.; Deimling, D.; Kaltz, C.; Sendelhofert, A.; Iff, A.; Luthardt, B.; Untch, M.; Lohrs, U. Her-2/neu analysis in archival tissue samples of human breast cancer: Comparison of immunohistochemistry and fluorescence in situ hybridization. J. Clin. Oncol. 2001, 19, 354-363. [PubMed].
    • (2001) J. Clin. Oncol , vol.19 , pp. 354-363
    • Lebeau, A.1    Deimling, D.2    Kaltz, C.3    Sendelhofert, A.4    Iff, A.5    Luthardt, B.6    Untch, M.7    Lohrs, U.8
  • 5
    • 77951725120 scopus 로고    scopus 로고
    • A commercial real-time pcr kit provides greater sensitivity than direct sequencing to detect kras mutations: A morphology-based approach in colorectal carcinoma
    • [CrossRef] [PubMed]
    • Angulo, B.; Garcia-Garcia, E.; Martinez, R.; Suarez-Gauthier, A.; Conde, E.; Hidalgo, M.; Lopez-Rios, F. A commercial real-time pcr kit provides greater sensitivity than direct sequencing to detect kras mutations: A morphology-based approach in colorectal carcinoma. J. Mol. Diagn. 2010, 12, 292-299. [CrossRef] [PubMed].
    • (2010) J. Mol. Diagn , vol.12 , pp. 292-299
    • Angulo, B.1    Garcia-Garcia, E.2    Martinez, R.3    Suarez-Gauthier, A.4    Conde, E.5    Hidalgo, M.6    Lopez-Rios, F.7
  • 7
    • 84872257074 scopus 로고    scopus 로고
    • Comparison of testing methods for the detection of braf v600e mutations in malignant melanoma: Pre-approval validation study of the companion diagnostic test for vemurafenib
    • [CrossRef] [PubMed]
    • Lopez-Rios, F.; Angulo, B.; Gomez, B.; Mair, D.; Martinez, R.; Conde, E.; Shieh, F.; Vaks, J.; Langland, R.; Lawrence, H. J.; et al. Comparison of testing methods for the detection of braf v600e mutations in malignant melanoma: Pre-approval validation study of the companion diagnostic test for vemurafenib. PLoS ONE 2013, 8, e53733. [CrossRef] [PubMed].
    • (2013) PLoS ONE , vol.8
    • Lopez-Rios, F.1    Angulo, B.2    Gomez, B.3    Mair, D.4    Martinez, R.5    Conde, E.6    Shieh, F.7    Vaks, J.8    Langland, R.9    Lawrence, H.J.10
  • 9
    • 84907090849 scopus 로고    scopus 로고
    • (accessed on 15 May 2015)
    • Cobas 4800 braf v600 mutation test. Available online: http://molecular. roche. com/assays/Pages/cobas4800BRAFV600MutationTest. aspx (accessed on 15 May 2015).
    • Cobas 4800 braf v600 mutation test
  • 10
    • 84937391927 scopus 로고    scopus 로고
    • (accessed on 15 May 2015)
    • Cobas egfr mutation test. Available online: http://molecular. roche. com/assays/Pages/cobasEGFRMutationTest. aspx (accessed on 15 May 2015).
    • Cobas egfr mutation test
  • 11
    • 34447295638 scopus 로고    scopus 로고
    • Chromogenic and fluorescent in situ hybridization in breast cancer
    • [CrossRef] [PubMed]
    • Lambros, M. B.; Natrajan, R.; Reis-Filho, J. S. Chromogenic and fluorescent in situ hybridization in breast cancer. Hum. Pathol. 2007, 38, 1105-1122. [CrossRef] [PubMed].
    • (2007) Hum. Pathol , vol.38 , pp. 1105-1122
    • Lambros, M.B.1    Natrajan, R.2    Reis-Filho, J.S.3
  • 12
    • 77749295019 scopus 로고    scopus 로고
    • Out of the darkness and into the light: Bright field in situ hybridisation for delineation of erbb2 (her2) status in breast carcinoma
    • [CrossRef] [PubMed]
    • Gruver, A. M.; Peerwani, Z.; Tubbs, R. R. Out of the darkness and into the light: Bright field in situ hybridisation for delineation of erbb2 (her2) status in breast carcinoma. J. Clin. Pathol. 2010, 63, 210-219. [CrossRef] [PubMed].
    • (2010) J. Clin. Pathol , vol.63 , pp. 210-219
    • Gruver, A.M.1    Peerwani, Z.2    Tubbs, R.R.3
  • 20
    • 84890409823 scopus 로고    scopus 로고
    • Validation and implementation of targeted capture and sequencing for the detection of actionable mutation, copy number variation, and gene rearrangement in clinical cancer specimens
    • [CrossRef] [PubMed]
    • Pritchard, C. C.; Salipante, S. J.; Koehler, K.; Smith, C.; Scroggins, S.; Wood, B.; Wu, D.; Lee, M. K.; Dintzis, S.; Adey, A.; et al. Validation and implementation of targeted capture and sequencing for the detection of actionable mutation, copy number variation, and gene rearrangement in clinical cancer specimens. J. Mol. Diagn. 2014, 16, 56-67. [CrossRef] [PubMed].
    • (2014) J. Mol. Diagn , vol.16 , pp. 56-67
    • Pritchard, C.C.1    Salipante, S.J.2    Koehler, K.3    Smith, C.4    Scroggins, S.5    Wood, B.6    Wu, D.7    Lee, M.K.8    Dintzis, S.9    Adey, A.10
  • 23
    • 84942521554 scopus 로고    scopus 로고
    • Broad, hybrid capture-based next-generation sequencing identifies actionable genomic alterations in lung adenocarcinomas otherwise negative for such alterations by other genomic testing approaches
    • [CrossRef] [PubMed]
    • Drilon, A.; Wang, L.; Arcila, M. E.; Balasubramanian, S.; Greenbowe, J. R.; Ross, J. S.; Stephens, P.; Lipson, D.; Miller, V. A.; Kris, M. G.; et al. Broad, hybrid capture-based next-generation sequencing identifies actionable genomic alterations in lung adenocarcinomas otherwise negative for such alterations by other genomic testing approaches. Clin. Cancer Res. 2015. [CrossRef] [PubMed].
    • (2015) Clin. Cancer Res
    • Drilon, A.1    Wang, L.2    Arcila, M.E.3    Balasubramanian, S.4    Greenbowe, J.R.5    Ross, J.S.6    Stephens, P.7    Lipson, D.8    Miller, V.A.9    Kris, M.G.10
  • 24
    • 0036626516 scopus 로고    scopus 로고
    • Allele-specific pcr amplification due to sequence identity between a pcr primer and an amplicon: Is direct sequencing so reliable?
    • [CrossRef] [PubMed]
    • Ikegawa, S.; Mabuchi, A.; Ogawa, M.; Ikeda, T. Allele-specific pcr amplification due to sequence identity between a pcr primer and an amplicon: Is direct sequencing so reliable? Hum. Genet. 2002, 110, 606-608. [CrossRef] [PubMed].
    • (2002) Hum. Genet , vol.110 , pp. 606-608
    • Ikegawa, S.1    Mabuchi, A.2    Ogawa, M.3    Ikeda, T.4
  • 25
    • 0032242849 scopus 로고    scopus 로고
    • Allele drop-out can occur in alleles differing by a single nucleotide and is not alleviated by preamplification or minor template increments
    • [CrossRef] [PubMed]
    • Hahn, S.; Garvin, A. M.; Di Naro, E.; Holzgreve, W. Allele drop-out can occur in alleles differing by a single nucleotide and is not alleviated by preamplification or minor template increments. Genet. Test 1998, 2, 351-355. [CrossRef] [PubMed].
    • (1998) Genet. Test , vol.2 , pp. 351-355
    • Hahn, S.1    Garvin, A.M.2    Di Naro, E.3    Holzgreve, W.4
  • 26
    • 0031667780 scopus 로고    scopus 로고
    • Pcr bias toward the wild-type k-ras and p53 sequences: Implications for pcr detection of mutations and cancer diagnosis
    • [PubMed]
    • Barnard, R.; Futo, V.; Pecheniuk, N.; Slattery, M.; Walsh, T. Pcr bias toward the wild-type k-ras and p53 sequences: Implications for pcr detection of mutations and cancer diagnosis. BioTechniques 1998, 25, 684-691. [PubMed].
    • (1998) BioTechniques , vol.25 , pp. 684-691
    • Barnard, R.1    Futo, V.2    Pecheniuk, N.3    Slattery, M.4    Walsh, T.5
  • 27
    • 84901328103 scopus 로고    scopus 로고
    • The validation and clinical implementation of brcaplus: A comprehensive high-risk breast cancer diagnostic assay
    • [CrossRef] [PubMed]
    • Chong, H. K.; Wang, T.; Lu, H. M.; Seidler, S.; Lu, H.; Keiles, S.; Chao, E. C.; Stuenkel, A. J.; Li, X.; Elliott, A. M. The validation and clinical implementation of brcaplus: A comprehensive high-risk breast cancer diagnostic assay. PLoS ONE 2014, 9, e97408. [CrossRef] [PubMed].
    • (2014) PLoS ONE , vol.9
    • Chong, H.K.1    Wang, T.2    Lu, H.M.3    Seidler, S.4    Lu, H.5    Keiles, S.6    Chao, E.C.7    Stuenkel, A.J.8    Li, X.9    Elliott, A.M.10
  • 28
    • 63949083912 scopus 로고    scopus 로고
    • Amplification-free illumina sequencing-library preparation facilitates improved mapping and assembly of (g+c)-biased genomes
    • [CrossRef] [PubMed]
    • Kozarewa, I.; Ning, Z.; Quail, M. A.; Sanders, M. J.; Berriman, M.; Turner, D. J. Amplification-free illumina sequencing-library preparation facilitates improved mapping and assembly of (g+c)-biased genomes. Nat. Methods 2009, 6, 291-295. [CrossRef] [PubMed].
    • (2009) Nat. Methods , vol.6 , pp. 291-295
    • Kozarewa, I.1    Ning, Z.2    Quail, M.A.3    Sanders, M.J.4    Berriman, M.5    Turner, D.J.6
  • 30
    • 79960410567 scopus 로고    scopus 로고
    • Seal: A distributed short read mapping and duplicate removal tool
    • [CrossRef] [PubMed]
    • Pireddu, L.; Leo, S.; Zanetti, G. Seal: A distributed short read mapping and duplicate removal tool. Bioinformatics 2011, 27, 2159-2160. [CrossRef] [PubMed].
    • (2011) Bioinformatics , vol.27 , pp. 2159-2160
    • Pireddu, L.1    Leo, S.2    Zanetti, G.3
  • 31
    • 84937432096 scopus 로고    scopus 로고
    • (accessed on 15 May 2015)
    • Picard. Available online: http://broadinstitute. github. io/picard/(accessed on 15 May 2015).
    • Picard
  • 33
    • 0344629203 scopus 로고    scopus 로고
    • Bias and artifacts in multitemplate polymerase chain reactions (pcr)
    • [CrossRef]
    • Kanagawa, T. Bias and artifacts in multitemplate polymerase chain reactions (pcr). J. Biosci. Bioeng. 2003, 96, 317-323. [CrossRef].
    • (2003) J. Biosci. Bioeng , vol.96 , pp. 317-323
    • Kanagawa, T.1
  • 34
    • 33344469813 scopus 로고    scopus 로고
    • Conversions of formaldehyde-modified 2'-deoxyadenosine 5'-monophosphate in conditions modeling formalin-fixed tissue dehydration
    • [CrossRef] [PubMed]
    • Rait, V. K.; Zhang, Q.; Fabris, D.; Mason, J. T.; O'Leary, T. J. Conversions of formaldehyde-modified 2'-deoxyadenosine 5'-monophosphate in conditions modeling formalin-fixed tissue dehydration. J. Histochem. Cytochem. 2006, 54, 301-310. [CrossRef] [PubMed].
    • (2006) J. Histochem. Cytochem , vol.54 , pp. 301-310
    • Rait, V.K.1    Zhang, Q.2    Fabris, D.3    Mason, J.T.4    O'Leary, T.J.5
  • 35
    • 19444379602 scopus 로고    scopus 로고
    • Molecular barcodes detect redundancy and contamination in hairpin-bisulfite pcr
    • [CrossRef] [PubMed]
    • Miner, B. E.; Stoger, R. J.; Burden, A. F.; Laird, C. D.; Hansen, R. S. Molecular barcodes detect redundancy and contamination in hairpin-bisulfite pcr. Nucleic Acids Res. 2004, 32, e135. [CrossRef] [PubMed].
    • (2004) Nucleic Acids Res , vol.32
    • Miner, B.E.1    Stoger, R.J.2    Burden, A.F.3    Laird, C.D.4    Hansen, R.S.5
  • 36
    • 79960226263 scopus 로고    scopus 로고
    • A method for counting pcr template molecules with application to next-generation sequencing
    • [CrossRef] [PubMed]
    • Casbon, J. A.; Osborne, R. J.; Brenner, S.; Lichtenstein, C. P. A method for counting pcr template molecules with application to next-generation sequencing. Nucleic Acids Res. 2011, 39, e81. [CrossRef] [PubMed].
    • (2011) Nucleic Acids Res , vol.39
    • Casbon, J.A.1    Osborne, R.J.2    Brenner, S.3    Lichtenstein, C.P.4
  • 37
    • 84877108149 scopus 로고    scopus 로고
    • Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation
    • [CrossRef] [PubMed]
    • Hiatt, J. B.; Pritchard, C. C.; Salipante, S. J.; O'Roak, B. J.; Shendure, J. Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation. Genome Res. 2013, 23, 843-854. [CrossRef] [PubMed].
    • (2013) Genome Res , vol.23 , pp. 843-854
    • Hiatt, J.B.1    Pritchard, C.C.2    Salipante, S.J.3    O'Roak, B.J.4    Shendure, J.5
  • 40
    • 35748959649 scopus 로고    scopus 로고
    • Microarray-based genomic selection for high-throughput resequencing
    • [CrossRef] [PubMed]
    • Okou, D. T.; Steinberg, K. M.; Middle, C.; Cutler, D. J.; Albert, T. J.; Zwick, M. E. Microarray-based genomic selection for high-throughput resequencing. Nat. Methods 2007, 4, 907-909. [CrossRef] [PubMed].
    • (2007) Nat. Methods , vol.4 , pp. 907-909
    • Okou, D.T.1    Steinberg, K.M.2    Middle, C.3    Cutler, D.J.4    Albert, T.J.5    Zwick, M.E.6
  • 42
    • 84890244872 scopus 로고    scopus 로고
    • Computational methods for detecting copy number variations in cancer genome using next generation sequencing: Principles and challenges
    • [PubMed]
    • Liu, B.; Morrison, C. D.; Johnson, C. S.; Trump, D. L.; Qin, M.; Conroy, J. C.; Wang, J.; Liu, S. Computational methods for detecting copy number variations in cancer genome using next generation sequencing: Principles and challenges. Oncotarget 2013, 4, 1868-1881. [PubMed].
    • (2013) Oncotarget , vol.4 , pp. 1868-1881
    • Liu, B.1    Morrison, C.D.2    Johnson, C.S.3    Trump, D.L.4    Qin, M.5    Conroy, J.C.6    Wang, J.7    Liu, S.8
  • 43
    • 84886811866 scopus 로고    scopus 로고
    • Computational tools for copy number variation (cnv) detection using next-generation sequencing data: Features and perspectives
    • [CrossRef] [PubMed]
    • Zhao, M.; Wang, Q.; Wang, Q.; Jia, P.; Zhao, Z. Computational tools for copy number variation (cnv) detection using next-generation sequencing data: Features and perspectives. BMC Bioinformatics 2013, 14, S1. [CrossRef] [PubMed].
    • (2013) BMC Bioinformatics , vol.14
    • Zhao, M.1    Wang, Q.2    Wang, Q.3    Jia, P.4    Zhao, Z.5
  • 44
    • 84899932270 scopus 로고    scopus 로고
    • Development and validation of a next-generation sequencing-based protocol for 24-chromosome aneuploidy screening of embryos
    • [CrossRef] [PubMed]
    • Fiorentino, F.; Biricik, A.; Bono, S.; Spizzichino, L.; Cotroneo, E.; Cottone, G.; Kokocinski, F.; Michel, C. E. Development and validation of a next-generation sequencing-based protocol for 24-chromosome aneuploidy screening of embryos. Fertil. Steril. 2014, 101, 1375-1382. [CrossRef] [PubMed].
    • (2014) Fertil. Steril , vol.101 , pp. 1375-1382
    • Fiorentino, F.1    Biricik, A.2    Bono, S.3    Spizzichino, L.4    Cotroneo, E.5    Cottone, G.6    Kokocinski, F.7    Michel, C.E.8
  • 45
    • 84928973006 scopus 로고    scopus 로고
    • Application of next-generation sequencing technology for comprehensive aneuploidy screening of blastocysts in clinical preimplantation genetic screening cycles
    • [CrossRef] [PubMed]
    • Fiorentino, F.; Bono, S.; Biricik, A.; Nuccitelli, A.; Cotroneo, E.; Cottone, G.; Kokocinski, F.; Michel, C. E.; Minasi, M. G.; Greco, E. Application of next-generation sequencing technology for comprehensive aneuploidy screening of blastocysts in clinical preimplantation genetic screening cycles. Hum. Reprod. 2014, 29, 2802-2813. [CrossRef] [PubMed].
    • (2014) Hum. Reprod , vol.29 , pp. 2802-2813
    • Fiorentino, F.1    Bono, S.2    Biricik, A.3    Nuccitelli, A.4    Cotroneo, E.5    Cottone, G.6    Kokocinski, F.7    Michel, C.E.8    Minasi, M.G.9    Greco, E.10
  • 46
    • 17344371740 scopus 로고    scopus 로고
    • High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays
    • [CrossRef] [PubMed]
    • Pinkel, D.; Segraves, R.; Sudar, D.; Clark, S.; Poole, I.; Kowbel, D.; Collins, C.; Kuo, W. L.; Chen, C.; Zhai, Y.; et al. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat. Genet. 1998, 20, 207-211. [CrossRef] [PubMed].
    • (1998) Nat. Genet , vol.20 , pp. 207-211
    • Pinkel, D.1    Segraves, R.2    Sudar, D.3    Clark, S.4    Poole, I.5    Kowbel, D.6    Collins, C.7    Kuo, W.L.8    Chen, C.9    Zhai, Y.10
  • 48
    • 0029828526 scopus 로고    scopus 로고
    • Correlation of DNA ploidy and histologic diagnosis from prostate core-needle biopsies: Is DNA ploidy more sensitive than histology for the diagnosis of carcinoma in small specimens?
    • [CrossRef]
    • Lo, J.; Kerns, B. J.; Amling, C. L.; Robertson, C. N.; Layfield, L. J. Correlation of DNA ploidy and histologic diagnosis from prostate core-needle biopsies: Is DNA ploidy more sensitive than histology for the diagnosis of carcinoma in small specimens? J. Surg. Oncol. 1996, 63, 41-45. [CrossRef].
    • (1996) J. Surg. Oncol , vol.63 , pp. 41-45
    • Lo, J.1    Kerns, B.J.2    Amling, C.L.3    Robertson, C.N.4    Layfield, L.J.5
  • 49
    • 0006636076 scopus 로고    scopus 로고
    • Aneuploidy and rapid cell proliferation in recurrent prostate cancers with androgen receptor gene amplification
    • [CrossRef] [PubMed]
    • Koivisto, P. Aneuploidy and rapid cell proliferation in recurrent prostate cancers with androgen receptor gene amplification. Prostate Cancer Prostat. Dis. 1997, 1, 21-25. [CrossRef] [PubMed].
    • (1997) Prostate Cancer Prostat. Dis , vol.1 , pp. 21-25
    • Koivisto, P.1
  • 50
  • 51
    • 68249110633 scopus 로고    scopus 로고
    • Poor prognostic significance of unamplified chromosome 17 polysomy in invasive breast carcinoma
    • [CrossRef] [PubMed]
    • Krishnamurti, U.; Hammers, J. L.; Atem, F. D.; Storto, P. D.; Silverman, J. F. Poor prognostic significance of unamplified chromosome 17 polysomy in invasive breast carcinoma. Mod. Pathol. 2009, 22, 1044-1048. [CrossRef] [PubMed].
    • (2009) Mod. Pathol , vol.22 , pp. 1044-1048
    • Krishnamurti, U.1    Hammers, J.L.2    Atem, F.D.3    Storto, P.D.4    Silverman, J.F.5
  • 52
    • 0037272682 scopus 로고    scopus 로고
    • Chromosome 17 aneusomy is associated with poor prognostic factors in invasive breast carcinoma
    • [CrossRef] [PubMed]
    • Watters, A. D.; Going, J. J.; Cooke, T. G.; Bartlett, J. M. Chromosome 17 aneusomy is associated with poor prognostic factors in invasive breast carcinoma. Breast Cancer Res. Treat. 2003, 77, 109-114. [CrossRef] [PubMed].
    • (2003) Breast Cancer Res. Treat , vol.77 , pp. 109-114
    • Watters, A.D.1    Going, J.J.2    Cooke, T.G.3    Bartlett, J.M.4
  • 53
    • 65549158870 scopus 로고    scopus 로고
    • The rewards and challenges of array-based karyotyping for clinical oncology applications
    • [CrossRef] [PubMed]
    • Hagenkord, J. M.; Chang, C. C. The rewards and challenges of array-based karyotyping for clinical oncology applications. Leukemia 2009, 23, 829-833. [CrossRef] [PubMed].
    • (2009) Leukemia , vol.23 , pp. 829-833
    • Hagenkord, J.M.1    Chang, C.C.2
  • 54
    • 52249091511 scopus 로고    scopus 로고
    • Whole-genome scanning by array comparative genomic hybridization as a clinical tool for risk assessment in chronic lymphocytic leukemia
    • [CrossRef] [PubMed]
    • Gunn, S. R.; Mohammed, M. S.; Gorre, M. E.; Cotter, P. D.; Kim, J.; Bahler, D. W.; Preobrazhensky, S. N.; Higgins, R. A.; Bolla, A. R.; Ismail, S. H.; et al. Whole-genome scanning by array comparative genomic hybridization as a clinical tool for risk assessment in chronic lymphocytic leukemia. J. Mol. Diagn. 2008, 10, 442-451. [CrossRef] [PubMed].
    • (2008) J. Mol. Diagn , vol.10 , pp. 442-451
    • Gunn, S.R.1    Mohammed, M.S.2    Gorre, M.E.3    Cotter, P.D.4    Kim, J.5    Bahler, D.W.6    Preobrazhensky, S.N.7    Higgins, R.A.8    Bolla, A.R.9    Ismail, S.H.10
  • 55
    • 41749121507 scopus 로고    scopus 로고
    • Optimization of the affymetrix genechip mapping 10k 2. 0 assay for routine clinical use on formalin-fixed paraffin-embedded tissues
    • [CrossRef] [PubMed]
    • Lyons-Weiler, M.; Hagenkord, J.; Sciulli, C.; Dhir, R.; Monzon, F. A. Optimization of the affymetrix genechip mapping 10k 2. 0 assay for routine clinical use on formalin-fixed paraffin-embedded tissues. Diagn. Mol. Pathol. 2008, 17, 3-13. [CrossRef] [PubMed].
    • (2008) Diagn. Mol. Pathol , vol.17 , pp. 3-13
    • Lyons-Weiler, M.1    Hagenkord, J.2    Sciulli, C.3    Dhir, R.4    Monzon, F.A.5
  • 56
    • 84884997982 scopus 로고    scopus 로고
    • Emerging landscape of oncogenic signatures across human cancers
    • [CrossRef] [PubMed]
    • Ciriello, G.; Miller, M. L.; Aksoy, B. A.; Senbabaoglu, Y.; Schultz, N.; Sander, C. Emerging landscape of oncogenic signatures across human cancers. Nat. Genet. 2013, 45, 1127-1133. [CrossRef] [PubMed].
    • (2013) Nat. Genet , vol.45 , pp. 1127-1133
    • Ciriello, G.1    Miller, M.L.2    Aksoy, B.A.3    Senbabaoglu, Y.4    Schultz, N.5    Sander, C.6
  • 57
    • 41449105551 scopus 로고    scopus 로고
    • Her2 status and benefit from adjuvant trastuzumab in breast cancer
    • [CrossRef] [PubMed]
    • Paik, S.; Kim, C.; Wolmark, N. Her2 status and benefit from adjuvant trastuzumab in breast cancer. N. Engl. J. Med. 2008, 358, 1409-1411. [CrossRef] [PubMed].
    • (2008) N. Engl. J. Med , vol.358 , pp. 1409-1411
    • Paik, S.1    Kim, C.2    Wolmark, N.3
  • 58
    • 84890254448 scopus 로고    scopus 로고
    • Recommendations for human epidermal growth factor receptor 2 testing in breast cancer: American society of clinical oncology/college of american pathologists clinical practice guideline update
    • [CrossRef] [PubMed]
    • Wolff, A. C.; Hammond, M. E.; Hicks, D. G.; Dowsett, M.; McShane, L. M.; Allison, K. H.; Allred, D. C.; Bartlett, J. M.; Bilous, M.; Fitzgibbons, P.; et al. Recommendations for human epidermal growth factor receptor 2 testing in breast cancer: American society of clinical oncology/college of american pathologists clinical practice guideline update. J. Clin. Oncol. 2013, 31, 3997-4013. [CrossRef] [PubMed].
    • (2013) J. Clin. Oncol , vol.31 , pp. 3997-4013
    • Wolff, A.C.1    Hammond, M.E.2    Hicks, D.G.3    Dowsett, M.4    McShane, L.M.5    Allison, K.H.6    Allred, D.C.7    Bartlett, J.M.8    Bilous, M.9    Fitzgibbons, P.10
  • 60
    • 77955496491 scopus 로고    scopus 로고
    • Clinical array-based karyotyping of breast cancer with equivocal her2 status resolves gene copy number and reveals chromosome 17 complexity
    • [CrossRef] [PubMed]
    • Gunn, S.; Yeh, I. T.; Lytvak, I.; Tirtorahardjo, B.; Dzidic, N.; Zadeh, S.; Kim, J.; McCaskill, C.; Lim, L.; Gorre, M.; et al. Clinical array-based karyotyping of breast cancer with equivocal her2 status resolves gene copy number and reveals chromosome 17 complexity. BMC Cancer 2010, 10. [CrossRef] [PubMed].
    • (2010) BMC Cancer
    • Gunn, S.1    Yeh, I.T.2    Lytvak, I.3    Tirtorahardjo, B.4    Dzidic, N.5    Zadeh, S.6    Kim, J.7    McCaskill, C.8    Lim, L.9    Gorre, M.10
  • 61
    • 84891058756 scopus 로고    scopus 로고
    • Current challenges for her2 testing in diagnostic pathology: State of the art and controversial issues
    • [CrossRef] [PubMed]
    • Sapino, A.; Goia, M.; Recupero, D.; Marchio, C. Current challenges for her2 testing in diagnostic pathology: State of the art and controversial issues. Front. Oncol. 2013, 3, 129. [CrossRef] [PubMed].
    • (2013) Front. Oncol , vol.3
    • Sapino, A.1    Goia, M.2    Recupero, D.3    Marchio, C.4
  • 62
    • 84924038823 scopus 로고    scopus 로고
    • High-density snp arrays improve detection of her2 amplification and polyploidy in breast tumors
    • [CrossRef] [PubMed]
    • Hansen, T. V.; Vikesaa, J.; Buhl, S. S.; Rossing, H. H.; Timmermans-Wielenga, V.; Nielsen, F. C. High-density snp arrays improve detection of her2 amplification and polyploidy in breast tumors. BMC Cancer 2015, 15. [CrossRef] [PubMed].
    • (2015) BMC Cancer
    • Hansen, T.V.1    Vikesaa, J.2    Buhl, S.S.3    Rossing, H.H.4    Timmermans-Wielenga, V.5    Nielsen, F.C.6
  • 63
    • 77649144588 scopus 로고    scopus 로고
    • The vanguard has arrived in the clinical laboratory: Array-based karyotyping for prognostic markers in chronic lymphocytic leukemia
    • [CrossRef] [PubMed]
    • Gunn, S. R. The vanguard has arrived in the clinical laboratory: Array-based karyotyping for prognostic markers in chronic lymphocytic leukemia. J. Mol. Diagn. 2010, 12, 144-146. [CrossRef] [PubMed].
    • (2010) J. Mol. Diagn , vol.12 , pp. 144-146
    • Gunn, S.R.1
  • 65
    • 84885368416 scopus 로고    scopus 로고
    • Detecting somatic point mutations in cancer genome sequencing data: A comparison of mutation callers
    • [CrossRef] [PubMed]
    • Wang, Q.; Jia, P.; Li, F.; Chen, H.; Ji, H.; Hucks, D.; Dahlman, K. B.; Pao, W.; Zhao, Z. Detecting somatic point mutations in cancer genome sequencing data: A comparison of mutation callers. Genome Med. 2013, 5. [CrossRef] [PubMed].
    • (2013) Genome Med
    • Wang, Q.1    Jia, P.2    Li, F.3    Chen, H.4    Ji, H.5    Hucks, D.6    Dahlman, K.B.7    Pao, W.8    Zhao, Z.9
  • 66
    • 84884521244 scopus 로고    scopus 로고
    • Accurately identifying low-allelic fraction variants in single samples with next-generation sequencing: Applications in tumor subclone resolution
    • [CrossRef] [PubMed]
    • Stead, L. F.; Sutton, K. M.; Taylor, G. R.; Quirke, P.; Rabbitts, P. Accurately identifying low-allelic fraction variants in single samples with next-generation sequencing: Applications in tumor subclone resolution. Hum. Mutat. 2013, 34, 1432-1438. [CrossRef] [PubMed].
    • (2013) Hum. Mutat , vol.34 , pp. 1432-1438
    • Stead, L.F.1    Sutton, K.M.2    Taylor, G.R.3    Quirke, P.4    Rabbitts, P.5
  • 71
    • 41149124135 scopus 로고    scopus 로고
    • Mechanisms of inherited cancer susceptibility
    • [CrossRef] [PubMed]
    • Hodgson, S. Mechanisms of inherited cancer susceptibility. J. Zhejiang Uni. Sci. B 2008, 9, 1-4. [CrossRef] [PubMed].
    • (2008) J. Zhejiang Uni. Sci. B , vol.9 , pp. 1-4
    • Hodgson, S.1
  • 72
    • 84905815773 scopus 로고    scopus 로고
    • Clinical tumor sequencing: An incidental casualty of the american college of medical genetics and genomics recommendations for reporting of incidental findings
    • [CrossRef] [PubMed]
    • Parsons, D. W.; Roy, A.; Plon, S. E.; Roychowdhury, S.; Chinnaiyan, A. M. Clinical tumor sequencing: An incidental casualty of the american college of medical genetics and genomics recommendations for reporting of incidental findings. J. Clin. Oncol. 2014, 32, 2203-2205. [CrossRef] [PubMed].
    • (2014) J. Clin. Oncol , vol.32 , pp. 2203-2205
    • Parsons, D.W.1    Roy, A.2    Plon, S.E.3    Roychowdhury, S.4    Chinnaiyan, A.M.5
  • 74
    • 17344362697 scopus 로고    scopus 로고
    • Atm mutations and phenotypes in ataxia-telangiectasia families in the british isles: Expression of mutant atm and the risk of leukemia, lymphoma, and breast cancer
    • [CrossRef] [PubMed]
    • Stankovic, T.; Kidd, A. M.; Sutcliffe, A.; McGuire, G. M.; Robinson, P.; Weber, P.; Bedenham, T.; Bradwell, A. R.; Easton, D. F.; Lennox, G. G.; et al. Atm mutations and phenotypes in ataxia-telangiectasia families in the british isles: Expression of mutant atm and the risk of leukemia, lymphoma, and breast cancer. Am. J. Hum. Genet. 1998, 62, 334-345. [CrossRef] [PubMed].
    • (1998) Am. J. Hum. Genet , vol.62 , pp. 334-345
    • Stankovic, T.1    Kidd, A.M.2    Sutcliffe, A.3    McGuire, G.M.4    Robinson, P.5    Weber, P.6    Bedenham, T.7    Bradwell, A.R.8    Easton, D.F.9    Lennox, G.G.10
  • 75
    • 33750904243 scopus 로고    scopus 로고
    • Population-based estimates of breast cancer risks associated with atm gene variants c. 7271t>g and c. 1066-6t>g (ivs10-6t>g) from the breast cancer family registry
    • [CrossRef] [PubMed]
    • Bernstein, J. L.; Teraoka, S.; Southey, M. C.; Jenkins, M. A.; Andrulis, I. L.; Knight, J. A.; John, E. M.; Lapinski, R.; Wolitzer, A. L.; Whittemore, A. S.; et al. Population-based estimates of breast cancer risks associated with atm gene variants c. 7271t>g and c. 1066-6t>g (ivs10-6t>g) from the breast cancer family registry. Hum. Mutat. 2006, 27, 1122-1128. [CrossRef] [PubMed].
    • (2006) Hum. Mutat , vol.27 , pp. 1122-1128
    • Bernstein, J.L.1    Teraoka, S.2    Southey, M.C.3    Jenkins, M.A.4    Andrulis, I.L.5    Knight, J.A.6    John, E.M.7    Lapinski, R.8    Wolitzer, A.L.9    Whittemore, A.S.10
  • 77
    • 0035449355 scopus 로고    scopus 로고
    • Cell cycle checkpoint signaling through the atm and atr kinases
    • [CrossRef] [PubMed]
    • Abraham, R. T. Cell cycle checkpoint signaling through the atm and atr kinases. Genes Dev. 2001, 15, 2177-2196. [CrossRef] [PubMed].
    • (2001) Genes Dev , vol.15 , pp. 2177-2196
    • Abraham, R.T.1
  • 78
    • 52449114574 scopus 로고    scopus 로고
    • Ataxia-telangiectasia: From a rare disorder to a paradigm for cell signalling and cancer
    • [CrossRef] [PubMed]
    • Lavin, M. F. Ataxia-telangiectasia: From a rare disorder to a paradigm for cell signalling and cancer. Nat. Rev. Mol. Cell Biol. 2008, 9, 759-769. [CrossRef] [PubMed].
    • (2008) Nat. Rev. Mol. Cell Biol , vol.9 , pp. 759-769
    • Lavin, M.F.1
  • 79
    • 33746407124 scopus 로고    scopus 로고
    • The ATM-dependent DNA damage signaling pathway
    • [CrossRef] [PubMed]
    • Kitagawa, R.; Kastan, M. B. The ATM-dependent DNA damage signaling pathway. Cold Spring Harb. Symp. Quant. Biol. 2005, 70, 99-109. [CrossRef] [PubMed].
    • (2005) Cold Spring Harb. Symp. Quant. Biol , vol.70 , pp. 99-109
    • Kitagawa, R.1    Kastan, M.B.2
  • 81
    • 84928060317 scopus 로고    scopus 로고
    • Parp inhibitors: A new era of targeted therapy
    • [CrossRef] [PubMed]
    • Tangutoori, S.; Baldwin, P.; Sridhar, S. Parp inhibitors: A new era of targeted therapy. Maturitas 2015, 81, 5-9. [CrossRef] [PubMed].
    • (2015) Maturitas , vol.81 , pp. 5-9
    • Tangutoori, S.1    Baldwin, P.2    Sridhar, S.3
  • 82
    • 84867158363 scopus 로고    scopus 로고
    • Molecular inversion probes: A novel microarray technology and its application in cancer research
    • [CrossRef] [PubMed]
    • Wang, Y.; Cottman, M.; Schiffman, J. D. Molecular inversion probes: A novel microarray technology and its application in cancer research. Cancer Genet. 2012, 205, 34-55. [CrossRef] [PubMed].
    • (2012) Cancer Genet , vol.205 , pp. 34-55
    • Wang, Y.1    Cottman, M.2    Schiffman, J.D.3
  • 83
    • 84937492053 scopus 로고    scopus 로고
    • (accessed on 15 May 2015)
    • Piha-Paul, S. Phase II study of BMN 673. Available online: https://clinicaltrials. gov/ct2/show/NCT02286687 (accessed on 15 May 2015).
    • Phase II study of BMN 673
    • Piha-Paul, S.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.