Multiplex single nucleotide polymorphism genotyping by adapter ligation-mediated allele-specific amplification

Analytical Biochemistry

Volumn 355, Issue 2, 2006, Pages 240-248

  Wang, Wei peng ^a,b   Ni, Kun yi ^b   Zhou, Guo hua ^a,c  

^a HUADONG RESEARCH INSTITUTE FOR MEDICINE AND BIOTECHNICS   (China)

^b CHINA PHARMACEUTICAL UNIVERSITY   (China)

^c NANJING UNIVERSITY   (China)

Author keywords

Adapter; ALM ASA; CYP2D6; Genotyping; SNP

Indexed keywords

NUCLEOTIDES; POLYMERASE CHAIN REACTION; POLYMORPHISM;

ADAPTER; ALM-ASA; AUTOMATION DEVICES; CYP2D6; GENETIC POLYMORPHISMS; GENOTYPING; RESTRICTION FRAGMENT LENGTH POLYMORPHISMS; SINGLE-NUCLEOTIDE POLYMORPHISMS;

GENES;

CYTOCHROME P450 2D6; LIVER ENZYME;

ADAPTER LIGATION MEDIATED ALLELE SPECIFIC AMPLIFICATION; ARTICLE; GENETIC POLYMORPHISM; GENOME; GENOTYPE; HUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SINGLE NUCLEOTIDE POLYMORPHISM; TECHNIQUE;

EID: 33746309053     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2006.04.022     Document Type: Article

References (37)

1. Sachidanandam R., Weissman D., Schmidt S.C., Kakol J.M., Stein L.D., Marth G., Sherry S., Mullikin J.C., Mortimore B.J., Willey D.L., Hunt S.E., Cole C.G., Coggill P.C., Rice C.M., Ning Z., Rogers J., Bentley D.R., Kwok P.Y., Mardis E.R., Yeh R.T., Schultz B., Cook L., Davenport R., Dante M., Fulton L., Hillier L., Waterston R.H., McPherson J.D., Gilman B., Schaffner S., Van Etten W.J., Reich D., Higgins J., Daly M.J., Blumenstiel B., Baldwin J., Stange-Thomann N., Zody M.C., Linton L., Lander E.S., and Altshuler D. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409 (2001) 928-933
2. Zhao Z., and Boerwinkle E. Neighboring-nucleotide effects on single nucleotide polymorphisms: a study of 2.6 million polymorphisms across the human genome. Genome Res. 12 (2002) 1679-1686
3. Bourgeois S., and Labuda D. Dynamic allele-specific oligonucleotide hybridization on solid support. Anal. Biochem. 324 (2004) 309-311
4. Howell W.M., Jobs M., Gyllensten U., and Brookes A.J. Dynamic allele-specific hybridization: a new method for scoring single nucleotide polymorphisms. Nat. Biotechnol. 17 (1999) 87-88
5. Tyagi S., and Kramer F.R. Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. 14 (1996) 303-308
6. Newton C.R., Graham A., Heptinstall L.E., Powell S.J., Summers C., Kalsheker N., Smith J.C., and Markham A.F. Analysis of any point mutation in DNA: the amplification refractory mutation system (ARMS). Nucleic Acids Res. 17 (1989) 2503-2516
7. Zhou G.H., Shirakura H., Kamahori M., Okano K., Nagai K., and Kambara H. A gel-free SNP genotyping method: bioluminometric assay coupled with modified primer extension reactions (BAMPER) directly from double-stranded PCR products. Hum. Mutat. 24 (2004) 155-163
8. Chen X., Livak K.J., and Kwok P.Y. A homogeneous, ligase-mediated DNA diagnostic test. Genome Res. 8 (1998) 549-556
9. Baron H., Fung S., Aydin A., Bahring S., Luft F.C., and Schuster H. Oligonucleotide ligation assay (OLA) for the diagnosis of familial hypercholesterolemia. Nat. Biotechnol. 14 (1996) 1279-1282
10. Bakht S., and Qi X. Ligation-mediated rolling-circle amplification-based approaches to single nucleotide polymorphism detection. Expert Rev. Mol. Diagn. 5 (2005) 111-116
11. Ronaghi M., Uhlen M., and Nyren P. A sequencing method based on real-time pyrophosphate. Science 281 (1998) 363-365
12. Ronaghi M. Pyrosequencing sheds light on DNA sequencing. Genome Res. 11 (2001) 3-11
13. 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. Polymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes. Nat. Biotechnol. 17 (1999) 292-296
14. Olivier M. The Invader assay for SNP genotyping. Mutat. Res. 573 (2005) 103-110
15. Syvanen A.C. Toward genome-wide SNP genotyping. Nat. Genet. 37 Suppl. (2005) S5-S10
16. Hardenbol P., Baner J., Jain M., Nilsson M., Namsaraev E.A., Karlin-Neumann G.A., Fakhrai-Rad H., Ronaghi M., Willis T.D., Landegren U., and Davis R.W. Multiplexed genotyping with sequence-tagged molecular inversion probes. Nat. Biotechnol. 21 (2003) 673-678
17. Taylor J.D., Briley D., Nguyen Q., Long K., Iannone M.A., Li M.S., Ye F., Afshari A., Lai E., Wagner M., Chen J., and Weiner M.P. Flow cytometric platform for high-throughput single nucleotide polymorphism analysis. BioTechniques 30 (2001) 661-669
18. Gut I.G. DNA analysis by MALDI-TOF mass spectrometry. Hum. Mutat. 23 (2004) 437-441
19. Ross P., Hall L., Smirnov I., and Haff L. High level multiplex genotyping by MALDI-TOF mass spectrometry. Nat. Biotechnol. 16 (1998) 1347-1351
20. Elnifro E.M., Ashshi A.M., Cooper R.J., and Klapper P.E. Multiplex PCR: optimization and application in diagnostic virology. Clin. Microbiol. Rev. 13 (2000) 559-570
21. Li D., and Vijg J. Multiplex co-amplification of 24 retinoblastoma gene exons after pre-amplification by long-distance PCR. Nucleic Acids Res. 24 (1996) 538-539
22. Shuber A.P., Grondin V.J., and Klinger K.W. A simplified procedure for developing multiplex PCRs. Genome Res. 5 (1995) 488-493
23. Broude N.E., Zhang L., Woodward K., Englert D., and Cantor C.R. Multiplex allele-specific target amplification based on PCR suppression. Proc. Natl. Acad. Sci. USA 98 (2001) 206-211
24. Broude N.E., Driscoll K., and Cantor C.R. High-level multiplex DNA amplification. Antisense Nucleic Acid Drug Dev. 11 (2001) 327-332
25. Roberts R., Joyce P., and Kennedy M.A. Rapid and comprehensive determination of cytochrome P450 CYP2D6 poor metabolizer genotypes by multiplex polymerase chain reaction. Hum. Mutat. 16 (2000) 77-85
26. Shapero M.H., Zhang J., Loraine A., Liu W., Di X., Liu G., and Jones K.W. MARA: a novel approach for highly multiplexed locus-specific SNP genotyping using high-density DNA oligonucleotide arrays. Nucleic Acids Res. 32 (2004) e181
27. Zhou G., Kamahori M., Okano K., Chuan G., Harada K., and Kambara H. Quantitative detection of single nucleotide polymorphisms for a pooled sample by a bioluminometric assay coupled with modified primer extension reactions (BAMPER). Nucleic Acids Res. 29 (2001) e93
28. Suzuki M.T., and Giovannoni S.J. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62 (1996) 625-630
29. Garcia-Barcelo M., Chow L.Y., Chiu H.F., Wing Y.K., Lee D.T., Lam K.L., and Waye M.M. Genetic analysis of the CYP2D6 locus in a Hong Kong Chinese population. Clin. Chem. 46 (2000) 18-23
30. Garcia-Barcelo M., Chow L.Y., Lam K.L., Chiu H.F., Wing Y.K., and Waye M.M. Occurrence of CYP2D6 gene duplication in Hong Kong Chinese. Clin. Chem. 46 (2000) 1411-1413
31. Ji L., Pan S., Marti-Jaun J., Hanseler E., Rentsch K., and Hersberger M. Single-step assays to analyze CYP2D6 gene polymorphisms in Asians: Allele frequencies and a novel *14B allele in mainland Chinese. Clin. Chem. 48 (2002) 983-988
32. Ji L., Pan S., Wu J., Marti-Jaun J., and Hersberger M. Genetic polymorphisms of CYP2D6 in Chinese mainland. Chin. Med. J. (Engl.) 115 (2002) 1780-1784
33. Wang S.L., Lai M.D., and Huang J.D. G169R mutation diminishes the metabolic activity of CYP2D6 in Chinese. Drug Metab. Dispos. 27 (1999) 385-388
34. O'Dell S.D., Gaunt T.R., and Day I.N. SNP genotyping by combination of 192-well MADGE, ARMS, and computerized gel image analysis. BioTechniques 29 (2000) 500-506
35. Gaunt T.R., Hinks L.J., Rassoulian H., and Day I.N. Manual 768 or 384 well microplate gel "dry" electrophoresis for PCR checking and SNP genotyping. Nucleic Acids Res. 31 (2003) e48
36. Fan J.B., Chen X., Halushka M.K., Berno A., Huang X., Ryder T., Lipshutz R.J., Lockhart D.J., and Chakravarti A. Parallel genotyping of human SNPs using generic high-density oligonucleotide tag arrays. Genome Res. 10 (2000) 853-860
37. Gunderson K.L., Steemers F.J., Lee G., Mendoza L.G., and Chee M.S. A genome-wide scalable SNP genotyping assay using microarray technology. Nat. Genet. 37 (2005) 549-554