Interlaboratory comparability study of cancer gene expression analysis using oligonucleotide microarrays

Clinical Cancer Research

Volumn 11, Issue 2 I, 2005, Pages 565-572

  Dobbin, Kevin K ^a   Beer, David G ^b   Meyerson, Matthew ^d,e   Yeatman, Timothy J ^f   Gerald, William L ^g   Jacobson, James W ^a   Conley, Barbara ^a   Buetow, Kenneth H ^a   Heiskanen, Mervi ^a   Simon, Richard M ^a   Minna, John D ^h   Girard, Luc ^h   Misek, David E ^b   Taylor, Jeremy M G ^c   Hanash, Samir ^b   Naoki, Katsuhiko ^d,e   Hayes, D Neil ^d,e   Ladd Acosta, Christine ⁱ   Enkemann, Steven A ^f   Viale, Agnes ^g   Giordano, Thomas J ^b   more..

^a NATIONAL CANCER INSTITUTE   (United States)

^b UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^c UNIVERSITY OF MICHIGAN   (United States)

^d DANA FARBER CANCER INSTITUTE   (United States)

^e HARVARD MEDICAL SCHOOL   (United States)

^f H LEE MOFFITT CANCER CENTER AND RESEARCH INSTITUTE   (United States)

^g MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^h UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

ⁱ WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

ARTICLE; CANCER DIAGNOSIS; CANCER TISSUE; CELL LINE; CLUSTER ANALYSIS; COMPARATIVE STUDY; CORRELATION ANALYSIS; DNA MICROARRAY; FROZEN SECTION; GENE EXPRESSION; GENOME; HUMAN; LABORATORY TEST; LUNG ADENOCARCINOMA; PERFORMANCE; PRIORITY JOURNAL; REPRODUCIBILITY; RNA EXTRACTION; RNA PURIFICATION;

ADENOCARCINOMA; COMPUTATIONAL BIOLOGY; FEASIBILITY STUDIES; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; LABORATORIES; NEOPLASMS; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 19944429996     PISSN: 10780432     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (18)

1. Golub TR, Slonim DK, Tamayo P, et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 1999;286:531-7.
2. Bittner M, Meltzer P, Chen Y, et al. Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature 2000;406:536-40.
3. Alizadeh AA, Eisen MB, Davis RE, et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 2000;403:503-11.
4. Bhattacharjee A, Richards WG, Staunton J, et al. Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proc Natl Acad Sci U S A 2001;98:13790-5.
5. Garber ME, Troyanskaya OG, Schluens K, et al. Diversity of gene expression in adenocarcinoma of the lung. Proc Natl Acad Sci U S A 2001;98:13784-9.
6. Beer DG, Kardia SL, Huang CC, et al. Gene-expression profiles predict survival of patients with lung adenocarcinoma. Nat Med 2002;8:816-24.
7. Rosenwald A, Wright G, Chan WC, et al. The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma. N Engl J Med 2002 Jun 20;346:1937-47.
8. van't Veer LJ, Dai H, van de Vijver MJ, et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002;415:530-6.
9. Gordon GJ, Jensen RV, Hsiao LL, et al. Using gene expression ratios to predict outcome among patients with mesothelioma. J Natl Cancer Inst 2003;95:598-605.
10. McShane LM, Aamodt R, Cordon-Cardo C, et al. Reproducibility of p53 immunohistochemistry in bladder tumors. Clin Cancer Res 2000;6:1854-64.
11. Sweep CG, Geurts-Moespot J. EORTC external quality assurance program for ER and PgR measurements: trial 1998/1999. Int J Biol Markers 2000;15:62-9.
12. Piper MDW, Daran-Lapujade P, Bro C, et al. Reproducibility of oligonucleotide microarray transcriptome analyses: an interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J Biol Chem 2002;277:37001-8.
13. Wright G, Tan B, Rosenwald A, Hurg EH, Wiestner A, Staudt LM. A gene expression-based method to diagnose clinically distinct subgroups of diffuse large B cell lymphoma. Proc Natl Acad Sci U S A 2003;100:10585-7.
14. Lin L, Hedaya AS, Sinha B, Yang M. Statistical methods in assessing agreement: models, issues, and tools. J Am Stat Assoc 2002;97:257-70.
15. Rousson V, Gasser T, Seifert B. Assessing intrarater, interrater, and test-retest reliability of continuous measurements. Stat Med 2002;21:3431-46.
16. Pellis L, Franssen-van Hal NLW, Burema J, Keijer J. The intraclass correlation coefficient applied for evaluation of data correction, labeling methods, and rectal biopsy sampling in DNA microarray experiments. Physiol Genomics 2003;16:99-106.
17. Tan PK, Downey TJ, Spitznagel EL Jr, et al. Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res 2003;31:5676-84.
18. Bloom G, Yang IV, Boulware D, et al. Multi-platform, multi-site, microarray-based human tumor classification. Am J Pathol 2004;164:9-16.