Quantitative detection of single nucleotide polymorphisms for a pooled sample by a bioluminometric assay coupled with modified primer extension reactions (BAMPER)

Nucleic Acids Research

Volumn 29, Issue 19, 2020, Pages

  Zhou, Guo Hua ^a   Kamahori, Masao ^a   Okano, Kazunori ^a   Chuan, Gao ^a   Harada, Kunio ^a   Kambara, Hideki ^a  

^a HITACHI LTD   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; PYROPHOSPHATE; LUCIFERASE; LUCIFERIN; PRIMER DNA;

3' FLANKING REGION; ACCURACY; ARTICLE; ASSAY; BIODEGRADATION; BIOLUMINOMETRIC ASSAY COUPLED MODIFIED PRIMER EXTENSION REACTION; CHEMICAL REACTION; CONTAMINATION; CONTROLLED STUDY; DNA DETERMINATION; GENE FREQUENCY; GENE MUTATION; GENETIC ASSOCIATION; HUMAN; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; WILD TYPE; BASE MISPAIRING; CHEMISTRY; EVALUATION; LUMINESCENCE; METHODOLOGY; NUCLEOTIDE SEQUENCE; SENSITIVITY AND SPECIFICITY;

BASE PAIR MISMATCH; DIPHOSPHATES; DNA MUTATIONAL ANALYSIS; DNA PRIMERS; FIREFLY LUCIFERIN; GENE FREQUENCY; HUMANS; LUCIFERASES; LUMINESCENT MEASUREMENTS; POLYMORPHISM, SINGLE NUCLEOTIDE; SENSITIVITY AND SPECIFICITY;

MLCS; MLOWN;

EID: 0035487816     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/29.19.e93     Document Type: Article

References (34)

1. Wang, D.G., Fan, J.B., Siao, C.J., Berno, A., Young, P., Sapolsky, R., Ghandour, G., Perkins, N., Winchester, E., Spencer, J. et al. (1998) Largescale identification, mapping and genotyping of single-nucleotide polymorphisms in the human genome. Science, 280, 1077-1082.
2. See, D., Kanazin, V., Talbert, H. and Blake, T. (2000) Electrophoretic detection of single-nucleotide polymorphisms. Biotechniques, 28, 710-714, 716.
3. Schmalzing, D., Belenky, A., Novotny, M.A., Koutny, L., Salas-Solano, O., El-Difrawy, S., Adourian, A., Matsudaira, P. and Ehrlich, D. (2000) Microchip electrophoresis: a method for high-speed SNP detection. Nucleic Acids Res., 28, e43.
4. Newton, C.R., Graham, A., Heptinstall, L.E., Powell, S.J., Summers, C., Kalsheker, N., Smith, J.C. andMarkham, A.F. (1989) Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acids Res., 17, 2503-2516.
5. Lyamichev, V., Mast, A.L., Hall, J.G., Prudent, J.R., Kaiser, M.W., Takova, T., Kwiatkowski, R.W., Sander, T.J., de Arruda, M., Arco, D.A., Neri, B.P. and Brow, M.A. (1999) Polymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes. Nat. Biotechnol., 17, 292-296.
6. Hall, J.G., Eis, P.S., Law, S.M., Reynaldo, L.P., Prudent, J.R., Marshall, D.J., Allawi, H.T., Mast, A.L., Dahlberg, J.E., Kwiatkowski, R.W., de Arruda, M., Neri, B.P. and Lyamichev, V.I. (2000) Sensitive detection of DNA polymorphisms by the serial invasive signal amplification reaction. Proc. Natl Acad. Sci. USA, 97, 8272-8277.
7. Jeffreys, A.J., Mac Leod, A., Tamaki, K., Neil, D.L. and Monckton, D.G. (1991) Minisatellite repeat coding as a digital approach to DNA typing. Nature, 354, 204-209.
8. Whitcombe, D., Brownie, J., Gillard, H.L., Mc Kechnie, D., Theaker, J., Newton, C.R. and Little, S. (1998) A homogeneous fluorescence assay for PCR amplicons: its application to real-time, single-tube genotyping. Clin. Chem., 44, 918-923.
9. Howell, W.M., Jobs, M., Gyllensten, U. and Brookes, A.J. (1999) Dynamic allele-specific hybridization. A new method for scoring single nucleotide polymorphisms. Nat. Biotechnol., 17, 87-88.
10. Tyagi, S., Bratu, D.P. and Kramer, F.R. (1998) Multicolor molecular beacons for allele discrimination. Nat. Biotechnol., 16, 49-53.
11. Sauer, S., Lechner, D., Berlin, K., Lehrach, H., Escary, J.L., Fox, N. and Gut, I.G. (2000) A novel procedure for efficient genotyping of single nucleotide polymorphisms. Nucleic Acids Res., 28, e13.
12. Fei, Z. and Smith, L.M. (2000) Analysis of single nucleotide polymorphisms by primer extension and matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom., 14, 950-959.
13. Ronaghi, M., Uhlen, M. and Nyren, P. (1998) A sequencing method based on real-time pyrophosphate. Science, 281, 363-365.
14. Nyren, P., Karamohamed, S. and Ronaghi, M. (1997) Detection of singlebase changes using a bioluminometric primer extension assay. Anal. Biochem., 244, 367-373.
15. Ahmadian, A., Gharizadeh, B., Gustafsson, A.C., Sterky, F., Nyren, P., Uhlen, M. and Lundeberg, J. (2000) Single-nucleotide polymorphism analysis by pyrosequencing. Anal. Biochem., 280, 103-110.
16. Schmalzing, D., Belenky, A., Novotny, M.A., Koutny, L., Salas-Solano, O., El-Difrawy, S., Adourian, A., Matsudaira, P. and Ehrlich, D. (2000) Microchip electrophoresis: a method for high-speed SNP detection. Nucleic Acids Res., 28, e43.
17. Fan, J.B., Chen, X., Halushka, M.K., Berno, A., Huang, X., Ryder, T., Lipshutz, R.J., Lockhart, D.J. and Chakravarti, A. (2000) Parallel genotyping of human SNPs using generic high-density oligonucleotide tag arrays. Genome Res., 10, 853-860.
18. Gilles, P.N., Wu, D.J., Foster, C.B., Dillon, P.J. and Chanock, S.J. (1999) Single nucleotide polymorphic discrimination by an electronic dot blot assay on semiconductor microchips. Nat. Biotechnol., 17, 365-370.
19. Sosnowski, R.G., Tu, E., Butler, W.F., O'Connell, J.P. and Heller, M.J. (1997) Rapid determination of single base mismatch mutations in DNA hybrids by direct electric field control. Proc. Natl Acad. Sci. USA, 94, 1119-1123.
20. Boon, E.M., Ceres, D.M., Drummond, T.G., Hill, M.G. and Barton, J.K. (2000) Mutation detection by electrocatalysis at DNA-modified electrodes. Nat. Biotechnol., 18, 1096-1100.
21. Chen, J., Iannone, M.A., Li, M.S., Taylor, J.D., Rivers, P., Nelsen, A.J., Slentz-Kesler, K.A., Roses, A. and Weiner, M.P. (2000) A microspherebased assay for multiplexed single nucleotide polymorphism analysis using single base chain extension. Genome Res., 10, 549-557.
22. Lannone, M.A., Taylor, J.D., Chen, J., Li, M.S., Rivers, P., Slentz-Kesler, K.A. and Weiner, M.P. (2000) Multiplexed single nucleotide polymorphism genotyping by oligonucleotide ligation and flow cytometry. Cytometry, 39, 131-140.
23. Syvanen, A.C. (1999) From gels to chips: "minisequencing" primer extension for analysis of point mutations and single nucleotide polymorphisms. Hum. Mutat., 13, 1-10.
24. Landegren, U., Nilsson, M. and Kwok, P.Y. (1998) Reading bits of genetic information: methods for single-nucleotide polymorphism analysis. Genome Res., 8, 769-776.
25. Nollau, P. and Wagener, C. (1997) Methods for detection of point mutations: performance and quality assessment. IFCC Scientific Division, Committee on Molecular Biology Techniques. Clin. Chem., 43, 1114-1128.
26. Whitcombe, D., Newton, C.R. and Little, S. (1998) Advances in approaches to DNA-based diagnostics. Curr. Opin. Biotechnol., 9, 602-608.
27. Breen, G., Harold, D., Ralston, S., Shaw, D. and St Clair, D. (2000) Determining SNP allele frequencies in DNA pools. Biotechniques, 28, 464-466, 468, 470.
28. Campbell, D.A., Valdes, A. and Spurr, N. (2000) Making drug discovery a SN(i)P. Drug Discov. Today, 5, 388-396.
29. Okano, K., Uematsu, C., Matsunaga, H. and Kambara, H. (1998) Characteristics of selective polymerase chain reaction (PCR) using two-base anchored primers and improvement of its specificity. Electrophoresis, 19, 3071-3078.
30. Capaldi, S., Getts, R.C. and Jayasena, S.D. (2000) Signal amplification through nucleotide extension and excision on a dendritic DNA platform. Nucleic Acids Res., 28, e21.
31. Ronaghi, M. (2000) Improved performance of pyrosequencing using single-stranded DNA-binding protein. Anal. Biochem., 286, 282-288.
32. Hyman, E.D. (1988) A new method of sequencing DNA. Anal. Biochem., 174, 423-436.
33. Ronaghi, M., Karamohamed, S., Pettersson, B., Uhlen, M. and Nyren, P. (1996) Real-time DNA sequencing using detection of pyrophosphate release. Anal. Biochem., 242, 84-89.
34. Germer, S., Holland, M.J. and Higuchi, R. (2000) High-throughput SNP allele-frequency determination in pooled DNA samples by kinetic PCR. Genome Res., 10, 258-266.