Different Real Time PCR approaches for the fine quantification of SNP's alleles in DNA pools: Assays development, characterization and pre-validation

Journal of Biochemistry and Molecular Biology

Volumn 38, Issue 5, 2005, Pages 555-562

  Mattarucchi, Elia ^a   Marsoni, Milena ^a   Binelli, Giorgio ^a   Passi, Alberto ^a   Curto, Francesco Lo ^a   Pasquali, Francesco ^a   Porta, Giovanni ^a  

^a UNIVERSITY OF INSUBRIA   (Italy)

Author keywords

DNA pools genotyping; Pre validation; Real time PCR; Single nucleotide polymorphism; SNP

Indexed keywords

EID: 32644449506     PISSN: 12258687     EISSN: 12258687     Source Type: Journal    
DOI: 10.5483/bmbrep.2005.38.5.555     Document Type: Article

References (18)

1. Alizadeh, M., Bernard, M., Danic, B., Dauriac, C., Birebent, B., Lapart, C., Lamy, T., Le Prise, P. Y., Beauplet, A., Bories, D., Semana, G. and Quelvennec, E. (2002) Quantitative assessment of ematopoietic chimerism after bone marrow transplantation by Real-Time quantitative polymerase chain reaction. Blood 99, 4618-4625.
2. Breen, G., Harold, D., Ralston, S., Shaw, D. and St Clair, D. (2000) Determining SNP allele frequencies in DNA pools. Biotechniques 28, 464-470.
3. Elmaagacli, A. H. (2002) Real-Time PCR for monitoring minimal residual disease and chimerism in patients after allogeneic transplantation. Int. J. Hematol. 76, 204-205.
4. Fredriksson, M., Barbany, G., Liljedahl, U., Hermanson, M., Kataja, M. and Syvanen A. C. (2004) Assessing hematopoietic chimerism after allogeneic stem cell transplantation by multiplexed SNP genotypi using microarrays and quantitative analysis of SNP alleles. Leukemia 18, 255-266.
5. 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.
6. Glaab, W. E. and Skopek, T. R. (1999) A novel assay for allelic discrimination that combines the fluorogenic 5' nuclease polymerase chain reaction (TaqMan) and mismatch amplification mutation assay. Mutat. Res. 430, 1-12.
7. Horwitz, W. (1995) Protocol for the design, conduct and interpretation of method performance studies. Pure Apl. Chem. 61, 331-343.
8. Kay, S. and Van den Eede, G. (2001) The limit of GMO detection. Nat. Biotechnol. 19, 405-406.
9. Livak, K. J. and Schmittgen, T. D. (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25, 402-408.
10. Newton, C. R., Graham. A., Heptinstall, L. E., Powell, S. J., Summers, C., Kalsheker, N., Smith, J. C. and Markham, A. F. (1989) Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acids Res. 17, 2503-2516.
11. Norton, N., Williams, N. M., O'Donovan, M. C. and Owen M. J. (2004) DNA pooling as a tool for large-scale association studies in complex traits. Ann. Med. 36, 146-152.
12. Pont-Kingdon, G. and Lyon, E. (2003) Rapid detection of aneuploidy (trisomy 21) by allele quantification combined with melting curves analysis of single-nucleotide polymorphism loci. Clin. Chem. 49, 1087-1094.
13. Punia, P., Cane, P., Teo, C. and Saunders, N. (2004) Quantitation of hepatitis B lamivudine resistant mutants by real-time amplification refractory mutation system PCR. J. Hepatol. 40, 986-992.
14. Ranade, K., Chang, M. S., Ting, C. T., Pei, D., Hsiao, C. F., Olivier, M., Pesich, R., Hebert, J., Chen, Y. D., Dzau, V. J., Curb, D., Olshen, R., Risch, N., Cox, D. R. and Botstein, D. (2001) High-throughput genotyping with single nucleotide polymorphisms. Genome Res. 11, 1262-1268.
15. Risch, N. J. (2000) Searching for genetic determinants in the new millennium. Nature 405, 847-856.
16. Rutledge, R. G. and Cote, C. (2003) Mathematics of quantitative kinetic PCR and the application of standard curves. Nucleic Acids Res. 31, 93.
17. Schwarz, G., Baumler, S., Block, A., Felsenstein, F. G. and Wenzel, G. (2004) Determination of detection and quantification limits for SNP allele frequency estimation in DNA pools using Real Time PCR. Nucleic Acids Res. 32, 24.
18. Schwarz, G., Baumler, S., Block, A., Felsenstein, F. G. and Wenzel, G. (2004) Quantitative technologies for allele frequency estimation of SNPs in DNA pools. Mol. Cell. Probes. 16, 429-434.