Technology for automated, rapid, and quantitative PCR or reverse transcription-PCR clinical testing

Clinical Chemistry

Volumn 51, Issue 5, 2005, Pages 882-890

  Raja, Siva ^a   Ching, Jesus ^b   Xi, Liqiang ^a,c   Hughes, Steven J ^a   Chang, Ronald ^b   Wong, Wendy ^b   McMillan, William ^b   Gooding, William E ^a   McCarty Jr , Kenneth S ^a   Chestney, Melissa ^a   Luketich, James D ^a   Godfrey, Tony E ^a,c  

^a UNIVERSITY OF PITTSBURGH CANCER INSTITUTE   (United States)

^b Cepeid   (United States)

^c MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

ARTICLE; AUTOMATION; BREAST CANCER; CONTROLLED STUDY; FLUORESCENCE; GEL ELECTROPHORESIS; HUMAN; HUMAN TISSUE; INSTRUMENT; INTRAOPERATIVE PERIOD; LUNG ADENOCARCINOMA; LUNG CANCER; LUNG METASTASIS; LUNG PARENCHYMA; LYMPH NODE; MELANOMA; NUCLEIC ACID ANALYSIS; PATIENT CARE; POLYMERASE CHAIN REACTION; REPRODUCIBILITY; REVERSE TRANSCRIPTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ISOLATION; TECHNOLOGY;

ADENOCARCINOMA; AUTOANALYSIS; BREAST NEOPLASMS; FEMALE; FLUORESCENCE; FROZEN SECTIONS; HUMANS; LUNG NEOPLASMS; LYMPHATIC METASTASIS; MELANOMA; POLYMERASE CHAIN REACTION; PREDICTIVE VALUE OF TESTS; REPRODUCIBILITY OF RESULTS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA;

EID: 20244370885     PISSN: 00099147     EISSN: None     Source Type: Journal    
DOI: 10.1373/clinchem.2004.046474     Document Type: Article

References (31)

1. Ginzinger DG, Godfrey TE, Nigro J, Moore DH, Suzuki S, Pallavicini MG, et al. Measurement of DNA copy number at microsatellite loci using quantitative PCR analysis. Cancer Res 2000;60:5405-9.
2. Godfrey TE, Raja S, Finkelstein SD, Gooding WE, Kelly LA, Luketich JD. Prognostic value of quantitative reverse transcription-polymerase chain reaction in lymph node-negative esophageal cancer patients. Clin Cancer Res 2001;7:4041-8.
3. Suzuki S, Moore DH, Ginzinger DG, GodfreyTE, Barclay J, Powell B, et al. An approach to analysis of large-scale correlations between genome changes and clinical endpoints in ovarian cancer. Cancer Res 2000;60:5382-5.
4. Tassone F, Hagerman RJ, Taylor AK, Gane LW, Godfrey TE, Hagerman PJ. Elevated levels of FMR1 mRNA in carrier males: a new mechanism of involvement in the fragile-X syndrome. Am J Hum Genet 2000;66:6-15.
5. Wittwer CT, Fillmore GC, Garling DJ. Minimizing the time required for DNA amplification by efficient heat transfer to small samples. Anal Biochem 1990;186:328-31.
6. Wittwer CT, Garling DJ. Rapid cycle DNA amplification: time and temperature optimization. Biotechniques 1991;10:76-83.
7. Raja S, Luketich JD, Kelly LA, Gooding WE, Finkelstein SD, Godfrey TE. Rapid, quantitative reverse transcriptase-polymerase chain reaction: application to intraoperative molecular detection of occult metastases in esophageal cancer. J Thorac Cardiovasc Surg 2002;123:475-83.
8. Bergeron MG, Ke D, Menard C, Picard FJ, Gagnon M, Bernier M, et al. Rapid detection of group B streptococci in pregnant women at delivery. N Engl J Med 2000;343:175-9.
9. Ke D, Menard C, Picard FJ, Boissinot M, Ouellette M, Roy PH, et al. Development of conventional and real-time PCR assays for the rapid detection of group B streptococci. Clin Chem 2000;46:324-31.
10. Raja S, Luketich JD, Ruff DW, Kelly LA, Godfrey TE. A method for increased sensitivity of one-step, quantitative RT-PCR. Biotechniques 2000;29:702-5.
11. Raja S, El Hefnawy T, Kelly LA, Chestney ML, Luketich JD, Godfrey TE. Temperature-controlled primer limit for multiplexing of rapid, quantitative reverse transcription-PCR assays: application to intraoperative cancer diagnostics. Clin Chem 2002;48:1329-37.
12. Godfrey TE, Kely LA. Development of quantitative RT-PCR assays for measuring gene expression. In: Phouthone K, Grant SG, eds. Molecular toxicology protocols. Totowa, NJ: Humana Press, 2004: 415-45.
13. Godfrey TE, Kim S-H, Chavira M, Ruff DW, Warren RS, Gray JW, et al. Quantitative mRNA expression analysis from formalin-fixed, paraffin-embedded tissues using 5′ nuclease quantitative RT-PCR. J Mol Diagn 2000;2:84-91.
14. Perkin-Elmer Applied Biosystems. Relative quantitation of gene expression. User bulletin #2. Foster City, CA: Perkin-Elmer Applied Biosystems, 1997.
15. Xi L, Luketich JD, Raja S, Gooding WE, Litle VR, Coello MC, et al. Molecular staging of lymph nodes from patients with esophageal adenocarcinoma. Clin Cancer Res 2005;11:1099-109.
16. Ferris RL, XI L, Raja S, Hunt JL, Wang J, Gooding WE, et al. Molecular staging of cervical lymph nodes in squamous cell carcinoma of the head and neck. Cancer Res 2005;65:in press.
17. Palmieri G, Ascierto PA, Cossu A, Mozzillo N, Motti ML, Satriano SM, et al. Detection of occult melanoma cells in paraffin-embedded histologically negative sentinel lymph nodes using a reverse transcriptase polymerase chain reaction assay. J Clin Oncol 2001;19:1437-43.
18. Wrightson WR, Wong SL, Edwards MJ, Chao C, Conrad AJ, Albrecht J, et al. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis of nonsentinel nodes following completion lymphadenectomy for melanoma. J Surg Res 2001;98:47-51.
19. Takeuchi H, Kuo C, Morton DL, Wang HJ, Hoon DS. Expression of differentiation melanoma-associated antigen genes is associated with favorable disease outcome in advanced-stage melanomas. Cancer Res 2003;63:441-8.
20. Kuo CT, Hoon DS, Takeuchi H, Turner R, Wang HJ, Morton DL, et al. Prediction of disease outcome in melanoma patients by molecular analysis of paraffin-embedded sentinel lymph nodes. J Clin Oncol 2003;21:3566-72.
21. Davids V, Kidson SH, Hanekom GS. Accurate molecular detection of melanoma nodal metastases: an assessment of multimarker assay specificity, sensitivity, and detection rate. Mol Pathol 2003;56:43-51.
22. Keilholz U, Willhauck M, Rimoldi D, Brasseur F, Dummer W, Rass K, et al. Reliability of reverse transcription-polymerase chain reaction (RT-PCR)-based assays for the detection of circulating tumour cells: a quality-assurance initiative of the EORTC Melanoma Cooperative Group. Eur J Cancer 1998;34:750-3.
23. van Dongen JJ, Macintyre EA, Gabert JA, Delabesse E, Rossi V, Saglio G, et al. Standardized RT-PCR analysis of fusion gene transcripts from chromosome aberrations in acute leukemia for detection of minimal residual disease. Report of the BIOMED-1 Concerted Action: investigation of minimal residual disease in acute leukemia. Leukemia 1999;13:1901-28.
24. Bolufer P, Lo CF, Grimwade D, Barragan E, Diverio D, Cassinat B, et al. Variability in the levels of PML-RAR α fusion transcripts detected by the laboratories participating in an external quality control program using several reverse transcription polymerase chain reaction protocols. Haematologica 2001;86:570-6.
25. Reinhold U, Berkin C, Bosserhoff AK, Deutschmann A, Garbe C, Glaser R, et al. Interlaboratory evaluation of a new reverse transcriptase polymerase chain reaction-based enzyme-linked immunosorbent assay for the detection of circulating melanoma cells: a multicenter study of the Dermatologic Cooperative Oncology Group. J Clin Oncol 2001;19:1723-7.
26. Raggi CC, Pinzani P, Paradiso A, Pazzagli M, Orlando C. External quality assurance program for PCR amplification of genomic DNA: an Italian experience. Clin Chem 2003;49:782-91.
27. Gibbs JF, Huang PP, Zhang PJ, Kraybill WG, Cheney R, Accuracy of pathologic techniques for the diagnosis of metastatic melanoma in sentinel lymph nodes. Ann Surg Oncol 1999;6:699-704.
28. Tanis PJ, Boom RP, Koops HS, Faneyte IF, Peterse JL, Nieweg OE, et al. Frozen section investigation of the sentinel node in malignant melanoma and breast cancer. Ann Surg Oncol 2001;8: 222-6.
29. Stojadinovic A, Allen PJ, Clary BM, Busam KJ, Coit DG. Value of frozen-section analysis of sentinel lymph nodes for primary cutaneous malignant melanoma. Ann Surg 2002;235:92-8.
30. Cochran AJ, Huang RR, Guo J, Wen DR. Current practice and future directions in pathology and laboratory evaluation of the sentinel node. Ann Surg Oncol 2001;8:13S-7S.
31. Ke D, Picard FJ, Martineau F, Menard C, Roy PH, Ouellette M, et al. Development of a PCR assay for rapid detection of enterococci. J Clin Microbiol 1999;37:3497-503.