Quality-controlled measurement methods for quantification of variations in transcript abundance in whole blood samples from healthy volunteers

Clinical Chemistry

Volumn 53, Issue 6, 2007, Pages 1030-1037

  Peters, Elizabeth Herness ^a   Rojas Caro, Sandra ^b   Brigell, Mitchell G ^b   Zahorchak, Robert J ^a   Des Etages, Shelley Ann ^b   Ruppel, Patricia L ^c   Knight, Charles R ^d   Austermiller, Bradley ^d   Graham, Myrna C ^a   Wowk, Steve ^e   Banks, Sean ^e   Madabusi, Lakshmi V ^e   Turk, Patrick ^f   Wilder, Donna ^f   Kempfer, Carole ^f   Osborn, Terry W ^a   Willey, James C ^d  

^a Gene Express Inc   (United States)

^b PFIZER INC   (United States)

^c Innovative Analytics   (United States)

^d MEDICAL COLLEGE OF OHIO   (United States)

^e ASURAGEN INC   (United States)

^f RADIANT RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER;

ADULT; ARTICLE; BIOASSAY; BIOLOGICAL MONITORING; BLOOD SAMPLING; CHEMICAL PARAMETERS; DISEASE MARKER; FEMALE; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; HUMAN; HUMAN EXPERIMENT; MALE; NORMAL HUMAN; QUALITY CONTROL; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SAMPLE SIZE; STATISTICAL PARAMETERS; TRANSCRIPT ABUNDANCE; VALIDATION PROCESS; VOLUNTEER;

BIOLOGICAL MARKERS; DATA INTERPRETATION, STATISTICAL; GENE EXPRESSION PROFILING; HUMANS; MOLECULAR DIAGNOSTIC TECHNIQUES; QUALITY CONTROL; REFERENCE VALUES; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; VARIATION (GENETICS);

EID: 34249864812     PISSN: 00099147     EISSN: None     Source Type: Journal    
DOI: 10.1373/clinchem.2006.078154     Document Type: Article

References (20)

1. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, et al. International Human Genome Sequencing Consortium: initial sequencing and analysis of the human genome. Nature 2001;409:860-921.
2. McPherson JD, Marra M, Hillier L, Waterston RH, Chinwalla A, Wallis J, et al. International Human Genome Mapping Consortium: a physical map of the human genome. Nature 2001;409:934-41.
3. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, et al. The sequence of the human genome. Science 2001;291:1304-51.
4. Whitney AR, Diehn M, Popper SJ, Alizadeh AA, Boldrick JC, Relman DA, et al. Individuality and variation in gene expression patterns in human blood. Proc Natl Acad Sci U S A 2003;100:1896-901.
5. Cobb JP, Mindrinos MN, Miller-Grezieno C, Calvano SE, Beker HV, Xiao W, et al. Application of genome-wide expression analysis to human health and disease. Proc Natl Acad Sci U S A 2005;102:4801-6.
6. McLoughlin K, Turteltaub K, Bankaitis-Davis D, Gerren R, Siconolfi L, Storm K, et al. Limited dynamic range of immune response gene expression observed in healthy blood donors using RT-PCR. Mol Med 2006;12:185-95.
7. Palmer C, Diehn M, Alizadeh AA, Brown PO. Cell-type specific gene expression profiles of leukocytes in human peripheral blood. BMC Genomics 2006;7:115.
8. US Department of Health and Human Services, Food and Drug Administration, Center for Drug Evaluation and Research, Center for Biologics Evaluation and Rasearch, Center for Devices and Radiological Health. Guidance for Industry: pharmacogenomic data submissions. http://www.fda.gov/OHRMS/DOCKETS/98fr/2003d- 0497-gdl0002.pdf (accessed March 2005).
9. US Department of Health and Human Services, Food and Drug Administration, Center for Devices and Radiological Health. Guidance for industry and FDA staff class II special controls guidance document: drug metabolizing enzyme genotyping system. http://www.fda.gov/cdrh/olvd/guidance/1551.html#7 (accessed March 2005).
10. Ehrmeyer, SS. US Department of Health and Human Services. Method validation: the regulations. http://www.westgard.com/guest11.htm (accessed 1992).
11. US Department of Health and Human Services, Food and Drug Administration, Center for Devices and Radiological Health. Guidance for industry and FDA staff class II special controls guidance document: Instrumentation for clinical multiplex test systems. http://www.fda.gov/cdrh/olvd/guidance/1546.html (accessed March 2005).
12. Canales RD, Luo Y, Willey JC, Austermiller B, Barbacloru CC, Boysen C, et al. Evaluation of DNA microarray results with quantitative gene expression platforms. Nat Biotechnol 2006;9: 1115-22.
13. Willey JC, Crawford EL, Knight CR, Wamer KA, Motten CA, Hemess EA, et al. Standardized RT-PCR and the standardized expression measurement center, Methods Mol Biol 2004;258:13-41.
14. Rots MG, Willey JC, Jansen G, Van Zantwijk CH, Noordhuis P, DeMuth JP, et al. mRNA expression levels of methotrexate resistance-related proteins in childhood leukemia as determined by a standardized competitiva template-based RT-PCR method. Leukemia 2000;14:2166-75.
15. Crawford EL, Khuder SA, Durham SJ, Frempton, M, Utell, MA, Thilly WG, et al. Normal bronchial epithelial cell expression of glutathione transferase P1, glutathione transferese M3, and glutathione peroxidese is low in subjects with bronchogenic carcinoma. Cancer Res 2000;60:1609-18.
16. Warner KA, Crawford EL, Zaher A, Coombs RJ, Elsamaloty H, Roshong-Denk SL, et al. The c-myc x E2F-1/p21 interactive gene expression index augments cytomorphologic diagnosis of lung cancer in fine-needle aspirate specimens. J Mol Diagn 2003;5: 176-83.
17. Vondracek M, Weaver DA, Sareng Z, Hedberg JJ, Willey JC, Wamgard L, et al. Transcript profiling of enzymes involved in detoxification of xenobiotics and reactive oxygen in human normal and simian virus 40 T antigen-immortalized oral keratinocytes. Int J Cancer 2002;99:776-82.
18. Mitre AP, Almal AA, George B, Fry DW, Lenehen PF, Pagliarulo V, et al. The use of genetic programming in the analysis of quantitative gene expression profiles for identification of nodal status in bladder cancer. BMC Cancer 2006;6:159.
19. Kevorkian L, Young DA, Darrah C, Donell ST, Shepstone L, Porter S, et al. Expression profiling of metalloproteinases and their inhibitors in cartilage. Arthritis Rheum 2004;50:131-41.
20. Ali A, Langdon J, Stem P, Partridge M. The pattem of expression of the 5T4 oncofoetal antigen on normal, dysplastic and malignant oral mucosa. Oral Oncol 2001;37:57-64.