메뉴 건너뛰기




Volumn 9, Issue 11, 2008, Pages 1753-1763

Use of diagnostic accuracy as a metric for evaluating laboratory proficiency with microarray assays using mixed-tissue RNA reference samples

Author keywords

microarrays; performance; proficiency testing; quality control; standards

Indexed keywords

RNA;

EID: 61349095462     PISSN: 14622416     EISSN: 17448042     Source Type: Journal    
DOI: 10.2217/14622416.9.11.1753     Document Type: Article
Times cited : (11)

References (31)
  • 1
    • 34347330024 scopus 로고    scopus 로고
    • Implementing the U.S. FDA guidance on pharmacogenomic data submissions
    • DOI 10.1002/em.20294
    • Goodsaid F, Frueh FW: Implementing the US FDA guidance on pharmacogenomic data submissions. Environ. Mol. Mutagen. 48, 354-358 (2007). (Pubitemid 47011763)
    • (2007) Environmental and Molecular Mutagenesis , vol.48 , Issue.5 , pp. 354-358
    • Goodsaid, F.1    Frueh, F.W.2
  • 2
    • 33748494248 scopus 로고    scopus 로고
    • A framework for the use of genomics at the EPA
    • Dix DJ, Gallagher K, Benson WH, et al. A framework for the use of genomics at the EPA. Nat. Biotechnol. 24, 1108-1111 (2006).
    • (2006) Nat. Biotechnol. , vol.24 , pp. 1108-1111
    • Dix, D.J.1    Gallagher, K.2    Benson, W.H.3
  • 3
    • 33748491517 scopus 로고    scopus 로고
    • The MicroArray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements
    • MAQC Consortium
    • MAQC Consortium: The MicroArray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements. Nat. Biotechnol. 24, 1151-1161 (2006).
    • (2006) Nat. Biotechnol. , vol.24 , pp. 1151-1161
  • 5
    • 33847221847 scopus 로고    scopus 로고
    • Elimination of laboratory ozone leads to a dramatic improvement in the reproducibility of microarray gene expression measurements
    • DOI 10.1186/1472-6750-7-8
    • Branham WS, Melvin CD, Han T, et al. Elimination of laboratory ozone leads to a dramatic improvement in the reproducibility of microarray gene expression measurements. BMC Biotechnol. 12, 8 (2007). (Pubitemid 46306405)
    • (2007) BMC Biotechnology , vol.7 , pp. 8
    • Branham, W.S.1    Melvin, C.D.2    Han, T.3    Desai, V.G.4    Moland, C.L.5    Scully, A.T.6    Fuscoe, J.C.7
  • 7
    • 27144548491 scopus 로고    scopus 로고
    • External RNA Controls Consortium: The External RNA Controls Consortium: A progress report
    • External RNA Controls Consortium: The External RNA Controls Consortium: a progress report. Nat. Methods 2, 731-734 (2005).
    • (2005) Nat. Methods , vol.2 , pp. 731-734
  • 8
    • 27844529344 scopus 로고    scopus 로고
    • External RNA Controls Consortium: Proposed methods for testing and selecting the ERCC external RNA controls
    • External RNA Controls Consortium: Proposed methods for testing and selecting the ERCC external RNA controls. BMC Genomics 6, 150 (2005).
    • (2005) BMC Genomics , vol.6 , pp. 150
  • 9
    • 0033636288 scopus 로고    scopus 로고
    • Implementation of reference systems in laboratory medicine
    • Mueller MM: Implementation of reference systems in laboratory medicine. Clin. Chem. 46, 1907-1909 (2000).
    • (2000) Clin. Chem. , vol.46 , pp. 1907-1909
    • Mueller, M.M.1
  • 10
    • 31144477774 scopus 로고    scopus 로고
    • Use of a mixed tissue RNA design for performance assessments on multiple microarray formats
    • Thompson KL, Rosenzweig BA, Pine PS, et al. Use of a mixed tissue RNA design for performance assessments on multiple microarray formats. Nucleic Acids Res. 33, E187 (2005).
    • (2005) Nucleic Acids Res. , vol.33
    • Thompson, K.L.1    Rosenzweig, B.A.2    Pine, P.S.3
  • 13
    • 0020083498 scopus 로고
    • The meaning and use of the area under a receiver operating characteristic (ROC) curve
    • Hanley JA, McNeil BJ: The meaning and use of the area under a receiver operating characteristic (ROC) curve. Radiology 143, 29-36 (1982). (Pubitemid 12142173)
    • (1982) Radiology , vol.143 , Issue.1 , pp. 29-36
    • Hanley, J.A.1    McNeil, B.J.2
  • 14
    • 0023890867 scopus 로고
    • Measuring the accuracy of diagnostic systems
    • Swets JA: Measuring the accuracy of diagnostic systems. Science 240, 1285-1293 (1988).
    • (1988) Science , vol.240 , pp. 1285-1293
    • Swets, J.A.1
  • 16
    • 22144461265 scopus 로고    scopus 로고
    • Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset
    • Choe SE, Boutros M, Michelson AM, Church GM, Halfon MS: Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset. Genome Biol. 6, R16 (2005).
    • (2005) Genome Biol. , vol.6
    • Choe, S.E.1    Boutros, M.2    Michelson, A.M.3    Church, G.M.4    Halfon, M.S.5
  • 17
    • 1342330572 scopus 로고    scopus 로고
    • A benchmark for Affymetrix GeneChip expression measures
    • DOI 10.1093/bioinformatics/btg410
    • Cope LM, Irizarry RA, Jaffee HA, Wu Z, Speed TP: A benchmark for Affymetrix GeneChip expression measures. Bioinformatics 20, 323-331 (2004). (Pubitemid 38262763)
    • (2004) Bioinformatics , vol.20 , Issue.3 , pp. 323-331
    • Cope, L.M.1    Irizarry, R.A.2    Jaffee, H.A.3    Wu, Z.4    Speed, T.P.5
  • 20
    • 0142121516 scopus 로고    scopus 로고
    • Exploration, normalization, and summaries of high density oligonucleotide array probe level data
    • Irizarry RA, Hobbs B, Collin F, et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4, 249-264 (2003).
    • (2003) Biostatistics , vol.4 , pp. 249-264
    • Irizarry, R.A.1    Hobbs, B.2    Collin, F.3
  • 21
    • 1542290446 scopus 로고    scopus 로고
    • Expression profiling-best practices for data generation and interpretation in clinical trials
    • Tumor Analysis Best Practices Working Group
    • Tumor Analysis Best Practices Working Group: Expression profiling -best practices for data generation and interpretation in clinical trials. Nat. Rev. Genetics 5, 229-237 (2004).
    • (2004) Nat. Rev. Genetics , vol.5 , pp. 229-237
  • 23
    • 54349106642 scopus 로고    scopus 로고
    • Assessment of repeated microarray experiments using mixed tissue RNA reference samples
    • Mongan MA, Higgins MA, Pine PS, Afshari CA, Hamadeh HK: Assessment of repeated microarray experiments using mixed tissue RNA reference samples. Biotechniques 45, 283-292 (2008).
    • (2008) Biotechniques , vol.45 , pp. 283-292
    • Mongan, M.A.1    Higgins, M.A.2    Pine, P.S.3    Afshari, C.A.4    Hamadeh, H.K.5
  • 24
    • 34347337394 scopus 로고    scopus 로고
    • Review of the literature examining the correlation among DNA microarray technologies
    • Yauk CL, Berndt ML: Review of the literature examining the correlation among DNA microarray technologies. Environ. Mol. Mutagen. 48, 380-394 (2007).
    • (2007) Environ. Mol. Mutagen. , vol.48 , pp. 380-394
    • Yauk, C.L.1    Berndt, M.L.2
  • 25
    • 27144486151 scopus 로고    scopus 로고
    • Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms
    • DOI 10.1093/nar/gki890
    • Barnes M, Freudenberg J, Thompson S, Aronow B, Pavlidis P: Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms. Nucleic Acids Res. 33, 5914-5923 (2005). (Pubitemid 41742611)
    • (2005) Nucleic Acids Research , vol.33 , Issue.18 , pp. 5914-5923
    • Barnes, M.1    Freudenberg, J.2    Thompson, S.3    Aronow, B.4    Pavlidis, P.5
  • 26
    • 61349198183 scopus 로고    scopus 로고
    • Comparison of the diagnostic performance of human whole genome microarrays using mixed-tissue RNA reference samples
    • doi 10.1016/j.toxlet.2008.08.018 Epub Ahead of Print)
    • Thompson KL, Pine PS: Comparison of the diagnostic performance of human whole genome microarrays using mixed-tissue RNA reference samples. Toxicol. Lett. doi 10.1016/j. toxlet.2008.08.018 (2008) (Epub ahead of print)
    • (2008) Toxicol. Lett.
    • Thompson, K.L.1    Pine, P.S.2
  • 27
    • 34447321058 scopus 로고    scopus 로고
    • Modeling nonlinearity in dilution design microarray data
    • DOI 10.1093/bioinformatics/btm002
    • Zheng X, Huang HC, Li W, Liu P, Li QZ, Liu Y: Modeling nonlinearity in dilution design microarray data. Bioinformatics 23, 1339-1347 (2007). (Pubitemid 47050515)
    • (2007) Bioinformatics , vol.23 , Issue.11 , pp. 1339-1347
    • Zheng, X.1    Huang, H.-C.2    Li, W.3    Liu, P.4    Li, Q.-Z.5    Liu, Y.6
  • 28
    • 33747888862 scopus 로고    scopus 로고
    • Standards in Gene Expression Microarray Experiments
    • DOI 10.1016/S0076-6879(06)11005-8, PII S0076687906110058, DNA Microarrays, Part B: Databases and Statistics
    • Salit M: Standards in gene expression microarray experiments. Methods Enzymol. 411, 63-78 (2006). (Pubitemid 44291421)
    • (2006) Methods in Enzymology , vol.411 , pp. 63-78
    • Salit, M.1
  • 29
    • 77957325445 scopus 로고    scopus 로고
    • ArrayExpress at the European Bioinformatics Institute
    • ArrayExpress at the European Bioinformatics Institute http://www.ebi.ac.uk/microarray-as/ae/
  • 30
    • 77957306897 scopus 로고    scopus 로고
    • Critical Path Opportunities List. US Food and Drug Administration, Accessed March
    • Critical Path Opportunities List. US Food and Drug Administration, Accessed March 2006. www.fda.gov/oc/initiatives/criticalpath/reports/opp-list. pdf
    • (2006)
  • 31
    • 77955630483 scopus 로고    scopus 로고
    • US System of Oversight of Genetic Testing: A Response to the Charge of the Secretary of Health and Human Services
    • Report of the Secretarys Advisory Committee on Genetics, Health, and Society. US System of Oversight of Genetic Testing: A Response to the Charge of the Secretary of Health and Human Services (2008) www4.od.nih.gov/oba/sacghs/ reports/SACGHS-oversight-report.pdf
    • (2008) Report of the Secretarys Advisory Committee on Genetics, Health, and Society


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.