Quantitative detection of low-copy-number mRNAs differing at single nucleotide positions

BioTechniques

Volumn 34, Issue 1, 2003, Pages 172-177

  Stenman, Jakob ^a   Lintula, S ^a   Rissanen, O ^a   Finne, P ^a   Hedstrom J ^a   Palotie, A ^a,b   Orpana, A ^a  

^a HELSINKI UNIVERSITY CENTRAL HOSPITAL   (Finland)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENES; PROTEINS;

NUCLEOTIDES;

RNA;

COMPLEMENTARY RNA; MESSENGER RNA; SQUAMOUS CELL CARCINOMA ANTIGEN;

ACCURACY; ARTICLE; CALIBRATION; CONTROLLED STUDY; HUMAN; HUMAN CELL; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS; SAMPLING; SINGLE NUCLEOTIDE POLYMORPHISM; SQUAMOUS CELL CARCINOMA; STOCHASTIC MODEL;

EID: 0037227021     PISSN: 07366205     EISSN: None     Source Type: Journal    
DOI: 10.2144/03341dd05     Document Type: Article

References (21)

1. Compton, J. 1991. Nucleic acid sequencebased amplification. Nature 350:91-92.
2. Guatelli, J.C., K.M. Whitfield, D.Y. Kwoh, K.J. Barringer, D.D. Richman, and T.R. Gingeras. 1990. Isothermal, in vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication. Proc. Natl. Acad. Sci. USA 87:7797.
3. Haase, A.T., E.F. Retzel, and K.A. Staskus. 1990. Amplification and detection of lentiviral DNA inside cells. Proc. Natl. Acad. Sci. USA 87:4971-4975.
4. Ihalainen, J., H. Siitari, S. Laine, A.C. Syvanen, and A. Palotie. 1994. Towards automatic detection of point mutations: use of scintillating microplates in solid-phase minisequencing. BioTechniques 16:938-943.
5. Karrer, E.E., J.E. Lincoln, S. Hogenhout, A.B. Bennett, R.M. Bostock, B. Martineau, W.J. Lucas, D.G. Gilchrist, and D. Alexander. 1995. In situ isolation of mRNA from individual plant cells: creation of cell-specific cDNA libraries. Proc. Natl. Acad. Sci. USA 92:3814-3818.
6. Karttunen, L., L. Lonnqvist, M. Godfrey, L. Peltonen, and A.C. Syvanen. 1996. An accurate method for comparing transcript levels of two alleles or highly homologous genes: application to fibrillin transcripts in Marfan patients fibroblasts. Genome Res. 6:392-403.
7. Lizardi, P.M., X. Huang, Z. Zhu, P. BrayWard, D.C. Thomas, and D.C. Ward. 1998. Mutation detection and single-molecule counting using isothermal rolling-circle amplification. Nat. Genet. 19:225-232.
8. Mullis, K., E Faloona, S. Scharf, R. Saiki, G. Horn, and H. Erlich. 1986. Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harb. Symp. Quant. Biol. 51:263-273.
9. Nedelman, J., P. Heagerty, and C. Lawrence. 1992. Quantitative PCR with internal controls. Comput. Appl. Biosci. 8:65-70.
10. Nuovo, G.J., G.A. Gorgone, P. MacConnell, M. Margiotta, and P.D. Gorevic. 1992. In situ localization of PCR-amplified human and viral cDNAs. PCR Methods Appl. 2:117-123.
11. Peccoud, J. and C. Jacob. 1996. Theoretical uncertainty of measurements using quantitative polymerase chain reaction. Biophys. J. 71:101-108.
12. Raeymaekers, L. 2000. Basic principles of quantitative PCR. Mol. Biotechnol. 15:115-122.
13. Saiki, R.K., T.L. Bugawan, G.T. Horn, K.B. Mullis, and H.A. Erlich. 1986. Analysis of enzymatically amplified P-globin and HLA-DQ a DNA with allele-specific oligonucleotide probes. Nature 324:163-166.
14. Schutze, K. and G. Lahr. 1998. Identification of expressed genes by laser-mediated manipulation of single cells. Nat. Biotechnol. 16:737-742.
15. Stenman, J., P. Finne, A. Stahls, R. Grenman, U.H. Stenman, A. Palotie, and A. Orpana. 1999. Accurate determination of relative messenger RNA levels by RT-PCR. Nat. Biotechnol. 17:720-722.
16. Stenman, J., J. Hedstrom, R. Grenman, I. Leivo, P. Finne, A. Palotie, and A. Orpana. 2001. Relative levels of SCCA2 and SCCA1 mRNA in primary tumors predicts recurrent disease in squamous cell cancer of the head and neck. Int. J. Cancer 95:39-43.
17. Stenman, J. and A. Orpana. 2001. Accuracy in amplification. Nat. Biotechnol. 19:1011-1012.
18. Sykes, P.J., S.H. Neoh, M.J. Brisco, E. Hughes, J. Condon, and A.A. Morley. 1992. Quantitation of targets for PCR by use of limiting dilution. BioTechniques 13:444-449.
19. Syvanen, A.C., K. Aalto-Setala, L. Harju, K. Kontula, and H. Soderlund. 1990. A primer-guided nucleotide incorporation assay in the genotyping of apolipoprotein E. Genomics 8:684-692.
20. Tyagi, S. and F.R. Kramer. 1996. Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. 14:303-308.
21. Zhou Y., M. Calciano, S. Hamann, J.H. Leamon, T. Strugnell, M.W. Christian, and P.M. Lizardi. 2001. In situ detection of messenger RNA using digoxigenin-labeled oligonucleotides and rolling circle amplification. Exp. Mol. Pathol. 70:281-288.