Detection of single nucleotide polymorphisms using electrospray ionization mass spectrometry: Validation of a one-well assay and quantitative pooling studies

Journal of Mass Spectrometry

Volumn 37, Issue 10, 2002, Pages 1039-1050

  Zhang, Sheng ^a   Van Pelt, Colleen K ^a   Huang, Xian ^a   Schultz, Gary A ^a  

^a Advion BioSciences Inc   (United States)

Author keywords

Electrospray ionization mass spectrometry; Monolithic column; One well assay; Pooling study; Single nucleotide polymorphism

Indexed keywords

BIOASSAY; CHROMATOGRAPHIC ANALYSIS; DISEASES; DNA; DRUG PRODUCTS;

POLYMORPHISMS;

MASS SPECTROMETRY;

GENOMIC DNA; MAGNESIUM; NUCLEOTIDE DERIVATIVE; REAGENT;

ACCURACY; ANALYTIC METHOD; ARTICLE; AUTOMATION; CHEMICAL PROCEDURES; CHROMATOGRAPHY; CONTROLLED STUDY; COST EFFECTIVENESS ANALYSIS; DATA BASE; DISEASE PREDISPOSITION; DRUG RESPONSE; EVOLUTION; GENE FREQUENCY; GENE MAPPING; GENOTYPE; HUMAN; MASS SPECTROMETRY; PRIORITY JOURNAL; PURIFICATION; QUANTITATIVE ASSAY; SAMPLE; SENSITIVITY AND SPECIFICITY; SINGLE NUCLEOTIDE POLYMORPHISM; TIME; VALIDATION PROCESS;

EID: 0036772830     PISSN: 10765174     EISSN: None     Source Type: Journal    
DOI: 10.1002/jms.361     Document Type: Article

References (37)

1. Wang DG, Fan JB, Siao CJ, Berno A, Young P, Sapolsky R, Ghandour G, Perkins N, Winchester E, Spencer J, Kruglyak L, Stein L, Hsie L, Topaloglou T, Hubbell E, Robinson E, Mittmann M, Morris MS, Shen N, Kilburn D, Rioux J, Nusbaum C, Rozen S, Hudson TJ, Lander ES, et al. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 1998; 280: 1077.
2. Schafer AJ, Hawkins JR. DNA variation and the future of human genetics. Nature Biotechnol. 1998; 16: 33.
3. McCarthy JJ, Hilfiker R. The use of single-nucleotide polymorphism maps in pharmacogenomics. Nature Biotechnol. 2000; 18: 505.
4. Brookes AJ. The essence of SNPs. Gene 1999; 234: 177.
5. Landegren U, Nilsson M, Kwok PY. Reading bits of genetic information: methods for single-nucleotide polymorphism analysis. Genome Res. 1998; 8: 769.
6. Mancinelli L, Cronin M, Sadee W. Pharmacogenomics: the promise of personalized medicine. AAPS Pharmsci. 2000; 2: article 4.
7. Nebert DW. Pharmacogenetics and pharmacogenomics: why is this relevant to the clinical geneticist? Clin. Genet. 1999; 56: 247.
8. Head SR, Parikh K, Rogers YH, Bishai W, Goelet P, Boyce-Jacino MT. Solid-phase sequence scanning for drug resistance detection in tuberculosis. Mol. Cell Probes 1999; 13: 81.
9. Gut IG. Automation in genotyping of single nucleotide polymorphisms. Hum. Mutat. 2001; 17: 475.
10. Shi MM. Enabling large-scale pharmacogenetic studies by high-throughput mutation detection and genotyping technologies. Clin. Chem. 2001; 47: 164.
11. Bray MS, Boerwinkle E, Doris PA. High-throughput multiplex SNP genotyping with MALDI-TOF mass spectrometry: practice, problems and promise. Hum. Mutat. 2001; 17: 296.
12. Morin PA, Saiz R, Monjazeb A. High-throughput single nucleotide polymorphism genotyping by fluorescent 5′ exonuclease assay. Biotechniques 1999; 27: 538.
13. Lyamichev V, Mast AL, Hall JG, Prudent JR, Kaiser MW, Takova T, Kwiatkowski RW, Sander TJ, de Arruda M, Arco DA, Neri BP, Brow MA. Polymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes. Nature Biotechnol. 1999; 17: 292.
14. Ahmadian A, Gharizadeh B, Gustafsson AC, Sterky F, Nyren P, Uhlen M, Lundeberg J. Single-nucleotide polymorphism analysis by pyrosequencing. Anal. Biochem. 2000; 280: 103.
15. Syvanen AC. From gels to chips: 'minisequencing' primer extension for analysis of point mutations and single nucleotide polymorphisms. Hum. Mutat. 1999; 13: 1.
16. Kuppuswamy MN, Hoffmann JW, Kasper CK, Spitzer SG, Groce SL, Bajaj SP. Single nucleotide primer extension to detect genetic diseases: experimental application to hemophilia B (factor IX) and cystic fibrosis genes. Proc. Natl. Acad. Sci. USA 1991; 88: 1143.
17. Nyren P, Pettersson B, Uhlen M. Solid phase DNA minisequencing by an enzymatic luminometric inorganic pyrophosphate detection assay. Anal. Biochem. 1993; 208: 171-5.
18. Nikiforov TT, Rendle RB, Goelet P, Rogers YH, Kotewicz ML, Anderson S, Trainor GL, Knapp MR. Genetic Bit Analysis: a solid phase method for typing single nucleotide polymorphisms. Nucleic Acids Res. 1994; 22: 4167.
19. Pastinen T, Partanen J, Syvanen AC. Multiplex, fluorescent, solid-phase minisequencing for efficient screening of DNA sequence variation. Clin. Chem. 1996; 42: 1391.
20. Chen X, Kwok PY. Homogeneous genotyping assays for single nucleotide polymorphisms with fluorescence resonance energy transfer detection. Genet. Anal. 1999; 14: 157.
21. Cai H, White PS, Torney D, Deshpande A, Wang Z, Marrone B, Nolan JP. Flow cytometry-based minisequencing: a new platform for high-throughput single-nucleotide polymorphism scoring. Genomics 2000; 66: 135.
22. Hoogendoorn B, Owen MJ, Oefner PJ, Williams N, Austin J, O'Donovan MC. Genotyping single nucleotide polymorphisms by primer extension and high performance liquid chromatography. Hum. Genet. 1999; 104: 89.
23. Haff LA, Smirnov IP. Single-nucleotide polymorphism identification assays using a thermostable DNA polymerase and delayed extraction MALDI-TOF mass spectrometry. Genome Res. 1997; 7: 378.
24. Griffin TJ, Smith LM. Single-nucleotide polymorphism analysis by MALDI-TOF mass spectrometry. Trends Biotechnol. 2000; 18: 77.
25. Sauer S, Lechner D, Berlin K, Lehrach H, Escary JL, Fox N, Gut IG. A novel procedure for efficient genotyping of single nucleotide polymorphisms. Nucleic Acids Res. 2000; 28: E13.
26. Germer S, Holland MJ, Higuchi R. High-throughput SNP allele-frequency determination in pooled DNA samples by kinetic PCR. Genome Res. 2000; 10: 258.
27. Breen G, Harold D, Ralston S, Shaw D, St Clair D. Determining SNP allele frequencies in DNA pools. Biotechniques 2000; 28: 464.
28. Ross P, Hall L, Haff LA. Quantitative approach to single-nucleotide polymorphism analysis using MALDI-TOF mass spectrometry. Biotechniques 2000; 29: 620.
29. Wolford JK, Blunt D, Ballecer C, Prochazka M. High-throughput SNP detection by using DNA pooling and denaturing high performance liquid chromatography (DHPLC). Hum. Genet. 2000; 107: 483.
30. Sasaki T, Tahira T, Suzuki A, Higasa K, Kukita Y, Baba S, Hayashi K. Precise estimation of allele frequencies of single-nucleotide polymorphisms by a quantitative SSCP analysis of pooled DNA. Am. J. Hum. Genet. 2001; 68: 214.
31. Wasson J, Skolnick G, Love-Gregory L, Permutt MA. Assessing allele frequencies of single nucleotide polymorphisms in DNA pools by pyrosequencing technology. Biotechniques 2002; 32: 1144.
32. Neve B, Froguel P, Corset L, Vaillant E, Vatin V, Boutin P. Rapid SNP allele frequency determination in genomic DNA pools by pyrosequencing. Biotechniques 2002; 32: 1138.
33. Zhang S, Van Pelt CK, Schultz GA. Electrospray ionization mass spectrometry-based genotyping: an approach for identification of single nucleotide polymorphisms. Anal. Chem. 2001; 73: 2117.
34. Schultz GA, Corso TN, Prosser SJ, Zhang S. A fully integrated monolithic microchip electrospray device for mass spectrometry. Anal. Chem. 2000; 72: 4058.
35. Huang X, Zhang S, Schultz GA, Henion J. Surface-alkylated polystyrene monolithic columns for peptide analysis in capillary liquid chromatography-electrospray ionization mass spectrometry. Anal. Chem. 2002; 74: 2336.
36. Van Pelt CK, Corso TN, Schultz GA, Lowes S, Henion J. A four-column parallel chromatography system for isocratic or gradient LC/MS analyses. Anal. Chem. 2001; 73: 582.
37. Shah VP, Midha KK, Dighe S, McGilveray IJ, Skelly JP, Yacobi KA, Layloff T, Viswanathan CT, Cook CE, McDowall RD, Pittman KA, Spector S. Analytical methods validation: bioavailability, bioequivalence, and pharmacokinetic studies. J. Pharm. Sci. 1992; 81: 309.