Mining Disease Susceptibility Genes through SNP Analyses and Expression Profiling Using MALDI-TOF Mass Spectrometry

Journal of Proteome Research

Volumn 3, Issue 2, 2004, Pages 218-227

  Tang, Kai ^a   Oeth, Paul ^a   Kammerer, Stefan ^a   Denissenko, Mikhail F ^a   Ekblom, Jonas ^a   Jurinke, Christian ^a   Van Den Boom, Dirk ^a   Braun, Andreas ^a   Cantor, Charles R ^a  

^a SEQUENOM INC   (United States)

Author keywords

Differential allele expression; Gene expression; MALDI; Mass spectrometry; Pharmacogenomics; Single nucleotide polymorphism

Indexed keywords

ALLELE; ANALYTIC METHOD; GENE EXPRESSION; GENETIC SUSCEPTIBILITY; GENETIC TRAIT; GENETIC TRANSCRIPTION; GENOME; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; PRIORITY JOURNAL; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; TECHNOLOGY;

ALLELES; CHEMOKINES; DNA, COMPLEMENTARY; DOSE-RESPONSE RELATIONSHIP, DRUG; GENETIC PREDISPOSITION TO DISEASE; GENOME; HUMANS; PHARMACOGENETICS; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEOME; PROTEOMICS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; TRANSCRIPTION, GENETIC;

EID: 10944262167     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr034080s     Document Type: Review

References (55)

1. Pandey, A.; Mann, M. Proteomics to study genes and genomes. Nature 2000, 405, 837-846.
2. Aebersold, R.; Mann, M. Mass spectrometry-based proteomics. Nature 2003, 422, 198-207.
3. Sali, A.; Glaeser, R.; Earnest, T.; Baumeister, W. From words to literature in structural proteomics. Nature 2003, 422, 216-225.
4. Hanash, S. Disease proteomics. Nature 2003, 422, 226-232.
5. Godovac-Zimmermann, J.; Brown, L. R. Perspectives for mass spectrometry and functional proteomics. Mass Spectrom Rev. 2001, 20, 1-57.
6. Bittner, M.; Meltzer, P.; Chen, Y.; Jiang, Y.; Seftor, E.; Hendrix, M.; Radmacher, M.; Simon, R.; Yakhini, Z.; Ben-Dor, A.; Sampas, N.; Dougherty, E.; Wang, E.; Marincola, F.; Gooden, C.; Lueders, J.; Glatfelter, A.; Pollock, P.; Carpten, J.; Gillanders, E.; Leja, D.; Dietrich, K.; Beaudry, C.; Berens, M.; Alberts, D.; Sondak, V. Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature 2000, 406, 536-540.
7. Golub, T. R.; Slonim, D. K.; Tamayo, P.; Huard, C.; Gaasenbeek, M.; Mesirov, J. P.; Coller, H.; Loh, M. L.; Downing, J. R.; Caligiuri, M. A.; Bloomfield, C. D.; Lander, E. S. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 1999, 286, 531-537.
8. Risch, N.; Merikangas, K. The future of genetic studies of complex human diseases. Science 1996, 273, 1516-1517.
9. Horikawa, Y.; Oda, N.; Cox, N. J.; Li, X.; Orho-Melander, M.; Hara, M.; Hinokio, Y.; Lindner, T. H.; Mashima, H.; Schwarz, P. E.; del Bosque-Plata, L.; Oda, Y.; Yoshiuchi, I.; Colilla, S.; Polonsky, K. S.; Wei, S.; Concannon, P.; Iwasaki, N.; Schulze, J.; Baier, L. J.; Bogardus, C.; Groop, L.; Boerwinkle, E. ; Hanis, C. L.; Bell, G. I. Genetic variation in the gene encoding calpain-10 is associated with type 2 diabetes mellitus. Nat. Genet. 2000, 26, 163-175.
10. Roth, C. M. Quantifying gene expression. Curr. Issues Mol. Biol. 2002, 4, 93-100.
11. Holden, A. L. The SNP consortium: summary of a private consortium effort to develop an applied map of the human genome. Biotechniques 2002, Suppl, 22-24, 26.
12. Judson, R.; Salisbury, B.; Schneider, J.; Windemuth, A.; Stephens, J. C. How many SNPs does a genome-wide haplotype map require? Pharmacogenomics 2002, 3, 379-391.
13. Karas, M.; Hillenkamp, F. Laser desorption ionization of proteins with molecular masses exceeding 10 000 daltons. Anal. Chem. 1988, 60, 2299-2301.
14. Jurinke, C.; van den Boom, D.; Cantor, C. R.; Koster, H. Automated genotyping using the DNA MassArray technology. Methods Mol. Biol. 2002, 187, 179-192.
15. Tang, K., Opalsky, D., Abel, K., van den Boom, D., Yip, P., Del Mistro, G., Braun, A., Cantor, C. R. Single nucleotide polymorphism analyses by MALDI-TOF MS. Int. J. Mass Spectrom. 2003, 226, 37-54.
16. Ding, C.; Cantor, C. R. A high-throughput gene expression analysis technique using competitive PCR and matrix-assisted laser desorption ionization time-of-flight MS. Proc. Natl. Acad. Sci. USA 2003, 100, 3059-3064.
17. Rodi, C. P.; Darnhofer-Patel, B.; Stanssens, P.; Zabeau, M.; van den Boom, D. A strategy for the rapid discovery of disease markers using the MassARRAY system. Biotechniques 2002, Suppl, 62-66, 68-69.
18. von Wintzingerode, F.; Bocker, S.; Schlotelburg, C.; Chiu, N. H.; Storm, N.; Jurinke, C.; Cantor, C. R.; Gobel, U. B.; van den Boom, D. Base-specific fragmentation of amplified 16S rRNA genes analyzed by mass spectrometry: a tool for rapid bacterial identification. Proc. Natl. Acad. Sci. USA 2002, 99, 7039-7044.
19. Hartmer, R.; Storm, N.; Boecker, S.; Rodi, C. P.; Hillenkamp, F.; Jurinke, C.; van den Boom, D. RNase T1 mediated base-specific cleavage and MALDI-TOF MS for high-throughput comparative sequence analysis. Nucleic Acids Res. 2003, 31, e47.
20. Böcker, S. SNP and mutation discovery using base-specific cleavage and MALDI-TOF mass spectrometry. Bioinformatics 2003, 19 Suppl 1, i44-i53.
21. Stanssens, P. Z., M.; Meersseman, G.; Remes, G.; Gansemans, Y.; Storm, N.; Hartmer, R.; Honisch, C.; Rodi, C. P.; Böcker, S.; van den Boom, D. High-throughput MALDI-TOF Discovery of Genomic Sequence Polymorphisms. 2003, submitted.
22. Braun, A.; Little, D. P.; Koster, H. Detecting CFTR gene mutations by using primer oligo base extension and mass spectrometry. Clin. Chem. 1997, 43, 1151-1158.
23. Tang, K., Allman, S. L., Jones, R. B., Chen, C. H. Quantitative analysis of biopolymers by matrix-assisted laser desorption. Anal. Chem. 1993, 65, 2164-2166.
24. Nelson, R. W., McLean, M. A., Hutchens, T. W. Quantitative determination of proteins by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anal. Chem. 1994, 66, 1408-1415.
25. Bucknall, M.; Fung, K. Y.; Duncan, M. W. Practical quantitative biomedical applications of MALDI-TOF mass spectrometry. J. Am. Soc. Mass Spectrom. 2002, 13, 1015-1027.
26. Mohlke, K. L.; Erdos, M. R.; Scott, L. J.; Fingerlin, T. E.; Jackson, A. U.; Silander, K.; Hollstein, P.; Boehnke, M.; Collins, F. S. High-throughput screening for evidence of association by using mass spectrometry genotyping on DNA pools. Proc. Natl. Acad. Sci. USA 2002, 99, 16 928-16 933.
27. Werner, M.; Sych, M.; Herbon, N.; Illig, T.; Konig, I. R.; Wjst, M. Large-scale determination of SNP allele frequencies in DNA pools using MALDI-TOF mass spectrometry. Hum. Mutat. 2002, 20, 57-64.
28. Ross, P.; Hall, L.; Haff, L. A. Quantitative approach to single-nucleotide polymorphism analysis using MALDI-TOF mass spectrometry. Biotechniques 2000, 29, 620-626, 628-629.
29. Storm, N.; Darnhofer-Patel, B.; van den Boom, D.; Rodi, C. P. MALDI-TOF mass spectrometry-based SNP genotyping. Methods Mol. Biol. 2003, 212, 241-262.
30. Barratt, B. J.; Payne, F.; Rance, H. E.; Nutland, S.; Todd, J. A.; Clayton, D. G. Identification of the sources of error in allele frequency estimations from pooled DNA indicates an optimal experimental design. Ann. Hum. Genet. 2002, 66, 393-405.
31. Sham, P.; Bader, J. S.; Craig, I.; O'Donovan, M.; Owen, M. DNA Pooling: a tool for large-scale association studies. Nat. Rev. Genet. 2002, 3, 862-871.
32. Jurinke, C.; Oeth, P.; van dem Boom, D. MALDI-TOF Mass spectrometry: a versatile tool for high performance DNA analysis. Mol. Biotech. 2003, in press.
33. Le Hellard, S.; Ballereau, S. J.; Visscher, P. M.; Torrance, H. S.; Pinson, J.; Morris, S. W.; Thomson, M. L.; Semple, C. A.; Muir, W. J.; Blackwood, D. H.; Porteous, D. J.; Evans, K. L. SNP genotyping on pooled DNAs: comparison of genotyping technologies and a semi automated method for data storage and analysis. Nucleic Acids Res. 2002, 30, e74.
34. Shifman, S.; Pisante-Shalom, A.; Yakir, B.; Darvasi, A. Quantitative technologies for allele frequency estimation of SNPs in DNA pools. Mol. Cell Probes 2002, 16, 429-434.
35. Cardon, L. R.; Bell, J. I. Association study designs for complex diseases. Nat. Rev. Genet. 2001, 2, 91-99.
36. Tabor, H. K.; Risch, N. J.; Myers, R. M. Opinion: Candidate-gene approaches for studying complex genetic traits: practical considerations. Nat. Rev. Genet. 2002, 3, 391-397.
37. Buetow, K. H.; Edmonson, M.; MacDonald, R.; Clifford, R.; Yip, P.; Kelley, J.; Little, D. P.; Strausberg, R.; Koester, H.; Cantor, C. R.; Braun, A. High-throughput development and characterization of a genomewide collection of gene-based single nucleotide polymorphism markers by chip-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Proc. Natl. Acad. Sci. USA 2001, 98, 581-584.
38. Bansal, A.; van den Boom, D.; Kammerer, S.; Honisch, C.; Adam, G.; Cantor, C. R.; Kleyn, P.; Braun, A. Association testing by DNA pooling: an effective initial screen. Proc. Natl. Acad. Sci. USA 2002, 99, 16 871-16 874.
39. Herbon, N.; Werner, M.; Braig, C.; Gohlke, H.; Dutsch, G.; Illig, T.; Altmuller, J.; Hampe, J.; Lantermann, A.; Schreiber, S.; Bonifacio, E.; Ziegler, A.; Schwab, S.; Wildenauer, D.; van den Boom, D.; Braun, A.; Knapp, M.; Reitmeir, P.; Wjst, M. High-resolution snp scan of chromosome 6p21 in pooled samples from patients with complex diseases. Genomics 2003, 81, 510-518.
40. Altshuler, D.; Hirschhorn, J. N.; Klannemark, M.; Lindgren, C. M.; Vohl, M. C.; Nemesh, J.; Lane, C. R.; Schaffner, S. F.; Bolk, S.; Brewer, C.; Tuomi, T.; Gaudet, D.; Hudson, T. J.; Daly, M.; Groop, L.; Lander, E. S. The common PPARgamma Pro12Ala polymorphism is associated with decreased risk of type 2 diabetes. Nat. Genet. 2000, 26, 76-80.
41. Hansen, L.; Hansen, T.; Vestergaard, H.; Bjorbaek, C.; Echwald, S. M.; Clausen, I. O.; Chen, Y. H.; Chen, M. X.; Cohen, P. T.; Pedersen, O. A widespread amino acid polymorphism at codon 905 of the glycogen-associated regulatory subunit of protein phosphatase-1 is associated with insulin resistance and hypersecretion of insulin. Hum. Mol. Genet. 1995, 4, 1313-1320.
42. Davies, H.; Bignell, G. R.; Cox, C.; Stephens, P.; Edkins, S.; Clegg, S. ; Teague, J.; Woffendin, H.; Garnett, M. J.; Bottomley, W.; Davis, N.; Dicks, E.; Ewing, R.; Floyd, Y.; Gray, K.; Hall, S.; Hawes, R.; Hughes, J.; Kosmidou, V.; Menzies, A.; Mould, C.; Parker, A.; Stevens, C.; Watt, S.; Hooper, S.; Wilson, R.; Jayatilake, H.; Gusterson, B. A.; Cooper, C.; Shipley, J.; Hargrave, D.; Pritchard-Jones, K.; Maitland, N.; Chenevix-Trench, G.; Riggins, G. J.; Bigner, D. D.; Palmieri, G.; Cossu, A.; Flanagan, A.; Nicholson, A.; Ho, J. W.; Leung, S. Y.; Yuen, S. T.; Weber, B. L.; Seigler, H. F.; Darrow, T. L.; Paterson, H.; Marais, R.; Marshall, C. J.; Wooster, R.; Stratton, M. R.; Futreal, P. A. Mutations of the BRAF gene in human cancer. Nature 2002, 417, 949-954.
43. Yuan, B. Z.; Zhou, X.; Durkin, M. E.; Zimonjic, D. B.; Gumundsdottir, K. ; Eyfjord, J. E.; Thorgeirsson, S. S.; Popescu, N. C. DLC-1 gene inhibits human breast cancer cell growth and in vivo tumorigenicity. Oncogene 2003, 22, 445-450.
44. Kirk, K. M.; Doege, K. J.; Hecht, J.; Bellamy, N.; Martin, N. G. Osteoarthritis of the hands, hips and knees in an Australian twin sample-evidence of association with the aggrecan VNTR polymorphism. Twin Res. 2003, 6, 62-66.
45. Freeman, D. J.; Griffin, B. A.; Holmes, A. P.; Lindsay, G. M.; Gaffney, D.; Packard, C. J.; Shepherd, J. Regulation of plasma HDL cholesterol and subfraction distribution by genetic and environmental factors: associations between the TaqI B RFLP in the CETP gene and smoking and obesity. Arterioscler. Thromb. 1994, 14, 336-344.
46. Heizmann, C.; Kirchgessner, T.; Kwiterovich, P. O.; Ladias, J. A.; Derby, C.; Antonarakis, S. E.; Lusis, A. J. DNA polymorphism haplotypes of the human lipoprotein lipase gene: possible association with high density lipoprotein levels. Hum. Genet. 1991, 86, 578-584.
47. Yamada, S.; Zhu, Q.; Aihara, Y.; Onda, H.; Zhang, Z.; Yu, L.; Jin, L.; Si, Y. J.; Nishigori, H.; Tomura, H.; Inoue, I.; Morikawa, A.; Yamagata, K.; Hanafusa, T.; Matsuzawa, Y.; Takeda, J. Cloning of cDNA and the gene encoding human hepatocyte nuclear factor (HNF)-3 beta and mutation screening in Japanese subjects with maturity-onset diabetes of the young. Diabetologia 2000, 43, 121-124.
48. Zhu, Q.; Yamagata, K.; Yu, L.; Tomura, H.; Yamada, S.; Yang, Q.; Yoshiuchi, I.; Sumi, S.; Miyagawa, J.; Takeda, J.; Hanafusa, T.; Matsuzawa, Y. Identification of missense mutations in the hepatocyte nuclear factor-3beta gene in Japanese subjects with late-onset Type II diabetes mellitus. Diabetologia 2000, 43, 1197-1200.
49. Becker-Andre, M.; Hahlbrock, K. Absolute mRNA quantification using the polymerase chain reaction (PCR). A novel approach by a PCR aided transcript titration assay (PATTY). Nucleic Acids Res. 1989, 17, 9437-9446.
50. Lockhart, D. J.; Dong, H.; Byrne, M. C.; Follettie, M. T.; Gallo, M. V.; Chee, M. S.; Mittmann, M.; Wang, C.; Kobayashi, M.; Horton, H.; Brown, E. L. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol. 1996, 14, 1675-1680.
51. Ding, C.; Cantor, C. R. Direct molecular haplotyping of long-range genomic DNA with M1-PCR. Proc. Natl. Acad. Sci. USA 2003, 100, 7449-7453.
52. Wutz, A.; Smrzka, O. W.; Schweifer, N.; Schellander, K.; Wagner, E. F.; Barlow, D. P. Imprinted expression of the Igf2r gene depends on an intronic CpG island. Nature 1997, 389, 745-749.
53. Constancia, M.; Pickard, B.; Kelsey, G.; Reik, W. Imprinting mechanisms. Genome Res. 1998, 8, 881-900.
54. Yan, H.; Yuan, W.; Velculescu, V. E.; Vogelstein, B.; Kinzler, K. W. Allelic variation in human gene expression. Science 2002, 297, 1143.
55. Little, D. P.; Braun, A.; O'Donnell, M. J.; Koster, H. Mass spectrometry from miniaturized arrays for full comparative DNA analysis. Nat. Med. 1997, 3, 1413-1416.