메뉴 건너뛰기




Volumn 19, Issue 1, 2008, Pages 10-18

Reproducible and reliable microarray results through quality control: good laboratory proficiency and appropriate data analysis practices are essential

Author keywords

[No Author keywords available]

Indexed keywords

BIOMARKERS; DATA REDUCTION; DISEASES; GENE EXPRESSION; QUALITY CONTROL; TOXICITY;

EID: 39149111585     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.copbio.2007.11.003     Document Type: Review
Times cited : (115)

References (49)
  • 1
    • 33748481775 scopus 로고    scopus 로고
    • Impact of microarray data quality on genomic data submissions to the FDA
    • Description of the FDA's Voluntary Genomic Data Submission (VGDS) program.
    • Frueh F.W. Impact of microarray data quality on genomic data submissions to the FDA. Nat Biotechnol 24 (2006) 1105-1107. Description of the FDA's Voluntary Genomic Data Submission (VGDS) program.
    • (2006) Nat Biotechnol , vol.24 , pp. 1105-1107
    • Frueh, F.W.1
  • 2
    • 39149097438 scopus 로고    scopus 로고
    • Tong W, Fang H, Shi L, Perkins R, Goodsaid FM, Frueh FW: An integrated bioinformatics infrastructure essential for advancing pharmacogenomics and personalized medicine in the context of the FDA's Critical Path Initiative. Drug Discov Today 2007, in press.
    • Tong W, Fang H, Shi L, Perkins R, Goodsaid FM, Frueh FW: An integrated bioinformatics infrastructure essential for advancing pharmacogenomics and personalized medicine in the context of the FDA's Critical Path Initiative. Drug Discov Today 2007, in press.
  • 3
    • 18944407169 scopus 로고    scopus 로고
    • FDA pharmacogenomics guidance sends clear message to industry
    • Ratner M. FDA pharmacogenomics guidance sends clear message to industry. Nat Rev Drug Discov 4 (2005) 359
    • (2005) Nat Rev Drug Discov , vol.4 , pp. 359
    • Ratner, M.1
  • 4
    • 0141905890 scopus 로고    scopus 로고
    • Evaluation of gene expression measurements from commercial microarray platforms
    • A highly cited negative study on microarray crossplatform comparability.
    • Tan P.K., Downey T.J., Spitznagel Jr. E.L., Xu P., Fu D., Dimitrov D.S., Lempicki R.A., Raaka B.M., and Cam M.C. Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res 31 (2003) 5676-5684. A highly cited negative study on microarray crossplatform comparability.
    • (2003) Nucleic Acids Res , vol.31 , pp. 5676-5684
    • Tan, P.K.1    Downey, T.J.2    Spitznagel Jr., E.L.3    Xu, P.4    Fu, D.5    Dimitrov, D.S.6    Lempicki, R.A.7    Raaka, B.M.8    Cam, M.C.9
  • 5
    • 7444234286 scopus 로고    scopus 로고
    • Getting the noise out of gene arrays
    • ••], this article painted an excessively negative view on the reliability of microarrays in detecting differentially expressed genes.
    • ••], this article painted an excessively negative view on the reliability of microarrays in detecting differentially expressed genes.
    • (2004) Science , vol.306 , pp. 630-631
    • Marshall, E.1
  • 6
    • 13444249852 scopus 로고    scopus 로고
    • Prediction of cancer outcome with microarrays: a multiple random validation strategy
    • This paper is about questioning the reliability of microarrays in predicting patient outcomes.
    • Michiels S., Koscielny S., and Hill C. Prediction of cancer outcome with microarrays: a multiple random validation strategy. Lancet 365 (2005) 488-492. This paper is about questioning the reliability of microarrays in predicting patient outcomes.
    • (2005) Lancet , vol.365 , pp. 488-492
    • Michiels, S.1    Koscielny, S.2    Hill, C.3
  • 7
    • 13444304216 scopus 로고    scopus 로고
    • Microarrays and molecular research: noise discovery?
    • Ioannidis J.P. Microarrays and molecular research: noise discovery?. Lancet 365 (2005) 454-455
    • (2005) Lancet , vol.365 , pp. 454-455
    • Ioannidis, J.P.1
  • 8
    • 18944394950 scopus 로고    scopus 로고
    • An array of problems
    • Frantz S. An array of problems. Nat Rev Drug Discov 4 (2005) 362-363
    • (2005) Nat Rev Drug Discov , vol.4 , pp. 362-363
    • Frantz, S.1
  • 9
    • 33645825183 scopus 로고    scopus 로고
    • Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer
    • This paper is about questioning the reliability of microarrays in predicting patient outcomes.
    • Ein-Dor L., Zuk O., and Domany E. Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer. Proc Natl Acad Sci U S A 103 (2006) 5923-5928. This paper is about questioning the reliability of microarrays in predicting patient outcomes.
    • (2006) Proc Natl Acad Sci U S A , vol.103 , pp. 5923-5928
    • Ein-Dor, L.1    Zuk, O.2    Domany, E.3
  • 10
    • 29244448340 scopus 로고    scopus 로고
    • Microarray data analysis: from disarray to consolidation and consensus
    • Allison D.B., Cui X., Page G.P., and Sabripour M. Microarray data analysis: from disarray to consolidation and consensus. Nat Rev Genet 7 (2006) 55-65
    • (2006) Nat Rev Genet , vol.7 , pp. 55-65
    • Allison, D.B.1    Cui, X.2    Page, G.P.3    Sabripour, M.4
  • 13
    • 9144256854 scopus 로고    scopus 로고
    • Performance evaluation of commercial short-oligonucleotide microarrays and the impact of noise in making cross-platform correlations
    • Shippy R., Sendera T.J., Lockner R., Palaniappan C., Kaysser-Kranich T., Watts G., and Alsobrook J. Performance evaluation of commercial short-oligonucleotide microarrays and the impact of noise in making cross-platform correlations. BMC Genomics 5 (2004) 61
    • (2004) BMC Genomics , vol.5 , pp. 61
    • Shippy, R.1    Sendera, T.J.2    Lockner, R.3    Palaniappan, C.4    Kaysser-Kranich, T.5    Watts, G.6    Alsobrook, J.7
  • 15
    • 1542290446 scopus 로고    scopus 로고
    • Expression profiling - best practices for data generation and interpretation in clinical trials
    • Hoffman E.P., et al. Expression profiling - best practices for data generation and interpretation in clinical trials. Nat Rev Genet 5 (2004) 229-237
    • (2004) Nat Rev Genet , vol.5 , pp. 229-237
    • Hoffman, E.P.1
  • 16
    • 33847240050 scopus 로고    scopus 로고
    • Improvement in the reproducibility and accuracy of DNA microarray quantification by optimizing hybridization conditions
    • Han T., Melvin C.D., Shi L., Branham W.S., Moland C.L., Pine P.S., Thompson K.L., and Fuscoe J.C. Improvement in the reproducibility and accuracy of DNA microarray quantification by optimizing hybridization conditions. BMC Bioinformat 7 Suppl 2 (2006) S17
    • (2006) BMC Bioinformat , vol.7 , Issue.SUPPL. 2
    • Han, T.1    Melvin, C.D.2    Shi, L.3    Branham, W.S.4    Moland, C.L.5    Pine, P.S.6    Thompson, K.L.7    Fuscoe, J.C.8
  • 17
    • 33748295678 scopus 로고    scopus 로고
    • Microarrays: quality control
    • Eisenstein M. Microarrays: quality control. Nature 442 (2006) 1067-1070
    • (2006) Nature , vol.442 , pp. 1067-1070
    • Eisenstein, M.1
  • 18
    • 33748491517 scopus 로고    scopus 로고
    • The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements
    • The main manuscript about the MicroArray Quality Control (MAQC) project, the most ambitious study so far on microarray quality control and data analysis issues.
    • Shi L., Reid L.H., Jones W.D., Shippy R., Warrington J.A., Baker S.C., Collins J., Longueville Fd., Kawasaki E.S., Lee K.Y., et al. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 24 (2006) 1151-1161. The main manuscript about the MicroArray Quality Control (MAQC) project, the most ambitious study so far on microarray quality control and data analysis issues.
    • (2006) Nat Biotechnol , vol.24 , pp. 1151-1161
    • Shi, L.1    Reid, L.H.2    Jones, W.D.3    Shippy, R.4    Warrington, J.A.5    Baker, S.C.6    Collins, J.7    Longueville, Fd.8    Kawasaki, E.S.9    Lee, K.Y.10
  • 19
    • 33748495591 scopus 로고    scopus 로고
    • Rat toxicogenomic study reveals analytical consistency across microarray platforms
    • This paper is about validation of MAQC results with a toxicogenomic data set.
    • Guo L., Lobenhofer E.K., Wang C., Shippy R., Harris S.C., Zhang L., Mei N., Chen T., Herman D., Goodsaid F.M., et al. Rat toxicogenomic study reveals analytical consistency across microarray platforms. Nat Biotechnol 24 (2006) 1162-1169. This paper is about validation of MAQC results with a toxicogenomic data set.
    • (2006) Nat Biotechnol , vol.24 , pp. 1162-1169
    • Guo, L.1    Lobenhofer, E.K.2    Wang, C.3    Shippy, R.4    Harris, S.C.5    Zhang, L.6    Mei, N.7    Chen, T.8    Herman, D.9    Goodsaid, F.M.10
  • 20
    • 33748503420 scopus 로고    scopus 로고
    • Evaluation of DNA microarray results with quantitative gene expression platforms
    • The most comprehensive study comparing microarrays with other gene expression technologies.
    • Canales R.D., Luo Y., Willey J.C., Austermiller B., Barbacioru C.C., Boysen C., Hunkapiller K., Jensen R.V., Knight C., Lee K.Y., et al. Evaluation of DNA microarray results with quantitative gene expression platforms. Nat Biotechnol 24 (2006) 1115-1122. The most comprehensive study comparing microarrays with other gene expression technologies.
    • (2006) Nat Biotechnol , vol.24 , pp. 1115-1122
    • Canales, R.D.1    Luo, Y.2    Willey, J.C.3    Austermiller, B.4    Barbacioru, C.C.5    Boysen, C.6    Hunkapiller, K.7    Jensen, R.V.8    Knight, C.9    Lee, K.Y.10
  • 30
    • 8444246272 scopus 로고    scopus 로고
    • QA/QC: challenges and pitfalls facing the microarray community and regulatory agencies
    • This paper is the illustration of many pitfalls in microarray gene expression analysis.
    • Shi L., Tong W., Goodsaid F., Frueh F.W., Fang H., Han T., Fuscoe J.C., and Casciano D.A. QA/QC: challenges and pitfalls facing the microarray community and regulatory agencies. Expert Rev Mol Diagn 4 (2004) 761-777. This paper is the illustration of many pitfalls in microarray gene expression analysis.
    • (2004) Expert Rev Mol Diagn , vol.4 , pp. 761-777
    • Shi, L.1    Tong, W.2    Goodsaid, F.3    Frueh, F.W.4    Fang, H.5    Han, T.6    Fuscoe, J.C.7    Casciano, D.A.8
  • 31
    • 33748490332 scopus 로고    scopus 로고
    • The value of a proficiency testing program to monitor performance in microarray laboratories
    • Reid L.H. The value of a proficiency testing program to monitor performance in microarray laboratories. Pharmaceut Discov 5 (2005) 20-25
    • (2005) Pharmaceut Discov , vol.5 , pp. 20-25
    • Reid, L.H.1
  • 33
    • 0035942271 scopus 로고    scopus 로고
    • Significance analysis of microarrays applied to the ionizing radiation response
    • Tusher V.G., Tibshirani R., and Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 98 (2001) 5116-5121
    • (2001) Proc Natl Acad Sci U S A , vol.98 , pp. 5116-5121
    • Tusher, V.G.1    Tibshirani, R.2    Chu, G.3
  • 34
    • 33845704885 scopus 로고    scopus 로고
    • Reproducibility Probability Score-incorporating measurement variability across laboratories for gene selection
    • Lin G., He X., Ji H., Shi L., Davis R.W., and Zhong S. Reproducibility Probability Score-incorporating measurement variability across laboratories for gene selection. Nat Biotechnol 24 (2006) 1476-1477
    • (2006) Nat Biotechnol , vol.24 , pp. 1476-1477
    • Lin, G.1    He, X.2    Ji, H.3    Shi, L.4    Davis, R.W.5    Zhong, S.6
  • 35
    • 33750827097 scopus 로고    scopus 로고
    • Arrays of hope
    • Strauss E. Arrays of hope. Cell 127 (2006) 657-659
    • (2006) Cell , vol.127 , pp. 657-659
    • Strauss, E.1
  • 36
    • 33748912421 scopus 로고    scopus 로고
    • Genomics. Microarray data reproduced, but some concerns remain
    • Couzin J. Genomics. Microarray data reproduced, but some concerns remain. Science 313 (2006) 1559
    • (2006) Science , vol.313 , pp. 1559
    • Couzin, J.1
  • 37
    • 33748995356 scopus 로고    scopus 로고
    • Microarray quality in the spotlight again
    • Kiermer V. Microarray quality in the spotlight again. Nat Methods 3 (2006) 772
    • (2006) Nat Methods , vol.3 , pp. 772
    • Kiermer, V.1
  • 38
    • 34347335532 scopus 로고    scopus 로고
    • Do microarrays measure up?
    • Sage L. Do microarrays measure up?. Anal Chem 78 (2006) 7358-7360
    • (2006) Anal Chem , vol.78 , pp. 7358-7360
    • Sage, L.1
  • 40
    • 33846156876 scopus 로고    scopus 로고
    • Reply to statistical methods and microarray data
    • This paper is about explanations of the common misconceptions of statisticians in microarray data analysis.
    • Shi L., Jones W.D., Jensen R.V., Wolfinger R.D., Kawasaki E.S., Herman D., Guo L., Goodsaid F.M., and Tong W. Reply to statistical methods and microarray data. Nat Biotechnol 25 (2007) 26-27. This paper is about explanations of the common misconceptions of statisticians in microarray data analysis.
    • (2007) Nat Biotechnol , vol.25 , pp. 26-27
    • Shi, L.1    Jones, W.D.2    Jensen, R.V.3    Wolfinger, R.D.4    Kawasaki, E.S.5    Herman, D.6    Guo, L.7    Goodsaid, F.M.8    Tong, W.9
  • 41
    • 39149109519 scopus 로고    scopus 로고
    • Shi L, Jones W, Jensen RV, Harris SC, Perkins R, Goodsaid FM, Guo L, Croner LJ, Boysen C, Fang H et al.: The reproducibility of lists of differentially expressed genes in microarray studies. Nat Precedings 2007. http://precedings.nature.com/documents/306/version/2.
    • Shi L, Jones W, Jensen RV, Harris SC, Perkins R, Goodsaid FM, Guo L, Croner LJ, Boysen C, Fang H et al.: The reproducibility of lists of differentially expressed genes in microarray studies. Nat Precedings 2007. http://precedings.nature.com/documents/306/version/2. This paper reports that the apparent lack of reproducibility of microarray results is largely because of the misuse or overuse of statistics in determining differentially expressed genes, instead of the microarray technology itself.
  • 42
    • 39149143579 scopus 로고    scopus 로고
    • Shi L: New hot paper comment. ESI Special Topics 2007. http://www.esi-topics.com/nhp/2007/march-07-LemingShi.html.
    • Shi L: New hot paper comment. ESI Special Topics 2007. http://www.esi-topics.com/nhp/2007/march-07-LemingShi.html.
  • 43
    • 34248532878 scopus 로고    scopus 로고
    • Selection of differentially expressed genes in microarray data analysis
    • Chen J.J., Wang S.J., Tsai C.A., and Lin C.J. Selection of differentially expressed genes in microarray data analysis. Pharmacogenomics J 7 (2007) 212-220
    • (2007) Pharmacogenomics J , vol.7 , pp. 212-220
    • Chen, J.J.1    Wang, S.J.2    Tsai, C.A.3    Lin, C.J.4
  • 44
    • 38349088960 scopus 로고    scopus 로고
    • Reproducibility of microarray data: a further analysis of microarray quality control (MAQC) data
    • This paper is an example of the misuse of statistics in microarray data analysis and the lack of understanding of the essential importance of data reproducibility in science.
    • Chen J., Hsueh H.M., Delongchamp R., Lin C.J., and Tsai C.A. Reproducibility of microarray data: a further analysis of microarray quality control (MAQC) data. BMC Bioinformat 8 (2007) 412. This paper is an example of the misuse of statistics in microarray data analysis and the lack of understanding of the essential importance of data reproducibility in science.
    • (2007) BMC Bioinformat , vol.8 , pp. 412
    • Chen, J.1    Hsueh, H.M.2    Delongchamp, R.3    Lin, C.J.4    Tsai, C.A.5
  • 45
    • 33748710231 scopus 로고    scopus 로고
    • Development and evaluation of therapeutically relevant predictive classifiers using gene expression profiling
    • This paper is about good advices on the development and validation of microarray-based predictive models.
    • Simon R. Development and evaluation of therapeutically relevant predictive classifiers using gene expression profiling. J Natl Cancer Inst 98 (2006) 1169-1171. This paper is about good advices on the development and validation of microarray-based predictive models.
    • (2006) J Natl Cancer Inst , vol.98 , pp. 1169-1171
    • Simon, R.1
  • 46
    • 34347342575 scopus 로고    scopus 로고
    • QA/QC issues to aid regulatory acceptance of microarray gene expression data
    • Fuscoe J.C., Tong W., and Shi L. QA/QC issues to aid regulatory acceptance of microarray gene expression data. Environ Mol Mutagen 48 (2007) 349-353
    • (2007) Environ Mol Mutagen , vol.48 , pp. 349-353
    • Fuscoe, J.C.1    Tong, W.2    Shi, L.3
  • 47
    • 39149093894 scopus 로고    scopus 로고
    • Shi L, Goodsaid FM, Frueh FW, Tong W: Microarray technology: unresolved issues and future challenges from a regulatory perspective. In Standardization in Fluorometry: State-of-the-Art and Future Challenges, Edited by Resch-Genger U. Springer; 2008, in press.
    • Shi L, Goodsaid FM, Frueh FW, Tong W: Microarray technology: unresolved issues and future challenges from a regulatory perspective. In Standardization in Fluorometry: State-of-the-Art and Future Challenges, Edited by Resch-Genger U. Springer; 2008, in press.
  • 48
    • 34548761943 scopus 로고    scopus 로고
    • Selection and validation of normalization methods for c-DNA microarrays using within-array replications
    • Fan J., and Niu Y. Selection and validation of normalization methods for c-DNA microarrays using within-array replications. Bioinformatics 23 (2007) 2391-2398
    • (2007) Bioinformatics , vol.23 , pp. 2391-2398
    • Fan, J.1    Niu, Y.2
  • 49
    • 37848998510 scopus 로고    scopus 로고
    • Extended analysis of benchmark datasets for Agilent two-color microarrays
    • Kerr K.F. Extended analysis of benchmark datasets for Agilent two-color microarrays. BMC Bioinformat 8 (2007) 371
    • (2007) BMC Bioinformat , vol.8 , pp. 371
    • Kerr, K.F.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.