Optimization of quantitative real-time RT-PCR parameters for the study of lymphoid malignancies

Leukemia

Volumn 17, Issue 4, 2003, Pages 789-795

  Lossos, I S ^a   Czerwinski, D K ^a   Wechser, M A ^b   Levy, R ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b APPLIED BIOSYSTEMS   (United States)

Author keywords

Endogenous controls; Lymphoma; Real time quantitative RT PCR

Indexed keywords

BETA 2 MICROGLOBULIN; BETA ACTIN; BETA GLUCURONIDASE; COMPLEMENTARY DNA; CYCLIC AMP DEPENDENT PROTEIN KINASE; CYCLOPHILIN; GENE PRODUCT; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE; MESSENGER RNA; NUCLEIC ACID; RIBOSOME PROTEIN; RNA; RNA 18S; TATA BINDING PROTEIN; TRANSFERRIN RECEPTOR;

ANALYZER; ARTICLE; B CELL LYMPHOMA; B LYMPHOCYTE ACTIVATION; CHEMICAL PARAMETERS; CONTROLLED STUDY; FLUOROMETRY; GENE EXPRESSION REGULATION; GENETIC VARIABILITY; HUMAN; HUMAN CELL; HUMAN TISSUE; LEUKEMIA CELL LINE; LYMPHATIC SYSTEM DISEASE; LYMPHOID CELL; LYMPHOMA CELL LINE; NONHODGKIN LYMPHOMA; PRIORITY JOURNAL; PROGNOSIS; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SPECTROPHOTOMETRY; T CELL LYMPHOMA; T LYMPHOCYTE ACTIVATION; TATA BOX;

EID: 0037397619     PISSN: 08876924     EISSN: None     Source Type: Journal    
DOI: 10.1038/sj.leu.2402880     Document Type: Article

References (23)

1. Heid CA, Stevens J, Livak KJ, Williams PM. Real time quantitative PCR. Genome Res 1996; 6: 986-994.
2. Lossos IS, Jones KD, Warnke R, Natkunam Y, Kaizer H, Zehnder JL et al. The expression of a single gene, BCL-6, strongly predicts survival in patients with diffuse large B-cell lymphoma. Blood 2001; 98: 945-951.
3. Bruggemann M, Droese J, Bolz I, Luth P, Pott C, von Neuhoff N et al. Improved assessment of minimal residual disease in B cell malignancies using fluorogenic consensus probes for real-time quantitative PCR. Leukemia 2000; 14: 1419-1425.
4. Medeiros LJ, Hai S, Thomazy VA, Estalilla OC, Romaguera J, Luthra R. Real-time RT-PCR assay for quantifying cyclin D1 mRNA in B-cell NON-Hodgkin's lymphomas. Mod Pathol 2002; 15: 556-564.
5. Maes B, Vanhentenrijk V, Wlodarska I, Cools J, Peeters B, Marynen P et al. The NPM-ALK and the ATIC-ALK fusion genes can be detected in non-neoplastic cells. Am J Pathol 2001; 158: 2185-2193.
6. Snider JV, Wechser MA, Lossos IS. Human disease characterization: real-time quantitative PCR analysis of gene expression. Drug Discov Today 2001; 6: 1062-1067.
7. Suzuki T, Higgins PJ, Crawford DR. Control selection for RNA quantitation. Biotechniques 2000; 29: 332-337.
8. Bustin SA. Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J Mol Endocrinol 2000; 25: 169-193.
9. Baseggio L, Bienvenu J, Charlot C, Picollet J, Felman P, Coiffier B et al. Higher LPS-stimulated TNF-αmRNA levels in peripheral blood mononuclear cells from non-Hodgkin's lymphoma patients. Exp Hematol 2001; 29: 330-338.
10. Bijwaard KE, Aguilera NS, Monczak Y, Trudel M, Taubenberger JK, Lichy JH. Quantitative real-time reverse transcription-PCR assay for cyclin D1 expression: utility in the diagnosis of mantle cell lymphoma. Clin Chem 2001; 47: 195-201.
11. Husson H, Carideo EG, Neuberg D, Schultze J, Munoz O, Marks PW et al. Gene expression profiling of follicular lymphoma and normal germinal center B cells using cDNA arrays. Blood 2002; 99: 282-289.
12. Harris NL, Jaffe ES, Stein H, Banks PM, Chan JK, Cleary ML et al. A revised European-American classification of lymphoid neoplasms: a proposal from the International Lymphoma Study Group [see comments]. Blood 1994; 84: 1361-1392.
13. Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 2000; 403: 503-511.
14. Rosenwald A, Wright G, Chan WC, Connors JM, Campo E, Fisher RI et al. The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma. N Engl J Med 2002; 346: 1937-1947.
15. Shipp MA, Ross KN, Tamayo P, Weng AP, Kutok JL, Aguiar RC et al. Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning. Nat Med 2002; 8: 68-74.
16. Feroze-Merzoug F, Berquin IM, Dey J, Chen YQ. Peptidylprolyl isomerase A (PPIA) as a preferred internal control over GAPDH and β-actin in quantitative RNA analyses. Biotechniques 2002; 32: 776-778,780,782.
17. Finnegan MC, Goepel JR, Hancock BW, Goyns MH. Investigation of the expression of housekeeping genes in non-Hodgkin's lymphoma. Leukemia Lymphoma 1993; 10: 387-393.
18. Lossos IS, Alizadeh AA, Diehn M, Warnke R, Thorstenson Y, Oefner PJ et al. Transformation of follicular lymphoma to diffuse large-cell lymphoma: alternative patterns with increased or decreased expression of c-myc and its regulated genes. Proc Natl Acad Sci USA 2002; 99: 8886-8891.
19. Aviles A, Zepeda G, Diaz-Maqueo JC, Rodriguez L, Guzman R, Garcia EL et al. β2 microglobulin level as an indicator of prognosis in diffuse large cell lymphoma. Leukemia Lymphoma 1992; 7: 135-138.
20. Ripple MO, Wilding G. Alteration of glyceraldehyde-3-phosphate dehydrogenase activity and messenger RNA content by androgen in human prostate carcinoma cells. Cancer Res 1995; 55: 4234-4236.
21. Mansur NR, Meyer-Siegler K, Wurzer JC, Sirover MA. Cell cycle regulation of the glyceraldehyde-3-phosphate dehydrogenase/uracil DNA glycosylase gene in normal human cells. Nucleic Acids Res 1993; 21: 993-998.
22. Noguchi I, Arai H, Iizuka R. A study on postmortem stability of vasopressin messenger RNA in rat brain compared with those in total RNA and ribosomal RNA. J Neural Transm Gen Sect 1991; 83: 171-178.
23. Santiago TC, Purvis IJ, Bettany AJ, Brown AJ. The relationship between mRNA stability and length in Saccharomyces cerevisiae. Nucleic Acids Res 1986; 14: 8347-8360.