What information should be required to support clinical "omics" publications?

Clinical Chemistry

Volumn 57, Issue 5, 2011, Pages 688-690

  Baggerly, Keith A ^a   Coombes, Kevin R ^a  

^a UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CLINICAL CHEMISTRY; INFORMATION; INFORMATION PROCESSING; NOTE; PUBLICATION;

ANTINEOPLASTIC AGENTS; BIOMEDICAL RESEARCH; CLINICAL TRIALS AS TOPIC; GENE EXPRESSION PROFILING; GENOMICS; HUMANS; INDIVIDUALIZED MEDICINE; NEOPLASMS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PERIODICALS AS TOPIC; REPRODUCIBILITY OF RESULTS; RESEARCH DESIGN;

EID: 79956088412     PISSN: 00099147     EISSN: 15308561     Source Type: Journal    
DOI: 10.1373/clinchem.2010.158618     Document Type: Note

References (20)

1. Potti A, Dressman HK, Bild A, Riedel RF, Chan G, Sayer R, et al. Genomic signatures to guide the use of chemotherapeutics. Nat Med 2006;12:1294-300. Retracted January 7, 2011.
2. Hsu DS, Balakumaran BS, Acharya CR, Vlahovic V, Walters KS, Garman K, et al. Pharmacogenomic strategies provide a rational approach to the treatment of cisplatin-resistant patients with advanced cancer. J Clin Oncol 2007;25:4350-7. Retracted November 16, 2010.
3. Bonnefoi H, Potti A, Delorenzi M, Mauriac L, Campone M, Tubiana-Hulin M, et al. Validation of gene signatures that predict the response of breast cancer to neoadjuvant chemotherapy: a substudy of the EORTC 10994/BIG 00-01 clinical trial. Lancet Oncol 2007;8:1071-8. Retracted January 29, 2011.
4. Coombes KR, Wang J, Baggerly KA. Microarrays: retracing steps. Nat Med 2007;13:1276-7.
5. Baggerly KA, Coombes KR. Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology. Ann Appl Stat 2009;3:1309-34.
6. Baggerly K. Disclose all data in publications. Nature 2010;467:401.
7. The Cancer Letter. Lisa McShane testimony audio [MP3 file]. NCI official Lisa McShane's testimony before IOM, December 20, 2010. http://www.cancerletter. com/downloads/20110128-1 (Accessed March 2011).
8. The Cancer Letter. Robert Becker testimony audio [MP3 file]. FDA official Robert Becker's testimony before IOM, December 20, 2010. http://www. cancerletter.com/downloads/20110128 (Accessed March 2011).
9. National Cancer Institute. Documents referenced in the Cancer Letter: 2011 volume 37. http://www.cancerletter.com/categories/documents (Accessed March 2011).
10. See "Internal NCI documents (zip files 1, 2 and 3) related to the Duke genomics controversy (The Cancer Letter, Jan. 7, 2011)."
11. Baggerly KA, Coombes KR. Annotation and time-line to accompany NCI documents. The Cancer Letter, January 14, 2011. http://bioinformatics. mdanderson.org/Supplements/ReproRsch-All/Modified/ (Accessed March 2011).
12. Potti A, Mukherjee S, Petersen R, Dressman HK, Bild A, Koontz J, et al. A genomic strategy to refine prognosis in early-stage non-small-cell lung cancer. N Engl J Med 2006;355:570-80. (Pubitemid 44200650)
13. McShane LM, Altman DG, Sauerbrei W, Taube SE, Gion M, Clark GM, on behalf of the Statistics Subcommittee of NCI-EORTC Working Group on Cancer Diagnostics. Reporting recommendations for tumor marker prognostic studies (REMARK). J Natl Cancer Inst 2005;97:1180-4.
14. Ransohoff DF. Bias as a threat to the validity of cancer molecular-marker driven research. Nat Rev Cancer 2005;5:142-9. (Pubitemid 40215862)
15. FDA. Draft guidance for industry, clinical laboratories, and FDA staff-in vitro diagnostic multivariate index assays. http://www.fda.gov/MedicalDevices/ DeviceRegulationandGuidance/GuidanceDocuments/ucm079148.htm (Accessed March 2011).
16. Goldberg P. FDA auditors spend two weeks at Duke; Nevins loses position in reorganization. The Cancer Letter 2011;37:1-5.
17. Leisch F. Dynamic generation of statistical reports using literate data analysis. In: Hardle W, Ronz B, eds. Compstat 2002 - proceedings in computational statistics. Heidelberg: Physika Verlag; 2002. p 575-80.
18. Mesirov JP. Accessible reproducible research. Science 2010;327:415-6.
19. Goecks J, Nekrutenko A, Taylor J, Galaxy Team. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 2010;11:R86.
20. Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, et al. Minimum information about a microarray experiment (MIAME) - toward standards for microarray data. Nat Genet 2001;29:365-71. (Pubitemid 34326681)