SpringerProtocols: Abstract: Automated Genotyping Using the DNA MassArray™ Technology

Automated Genotyping Using the DNA MassArray™ Technology

By: Christian Jurinke², Dirk van den Boom², Charles R. Cantor³, Hubert Köster³

Abstract

Full Text

Download PDF (290K)

The ongoing progress in establishing a reference sequence as part of the Human Genome Project (1) has revealed a new challenge: the large-scale identification and detection of intraspecies sequence variations, either between individuals or populations. The information drawn from those studies will lead to a detailed understanding of genetic and environmental contributions to the etiology of complex diseases.

Affiliation(s): (2) SEQUENOM GmbH, Hamburg, Germany
(3) SEQUENOM Inc., San Diego, CA

Book Title: DNA Arrays: Methods and Protocols

Series: Methods in Molecular Biology | Volume: 170 | Pub. Date: Mar-16-2001 | Page Range: 103-116 | DOI: 10.1385/1-59259-234-1:103

Subject: Genetics/Genomics

References

Download References

1.	Collins, F. S., Patrinos, A., Jordan, E., Chakravarti, A., Gesteland, R., Walters, L., and the members of DOE and NIH planning groups. (1998) New goals for the U.S. human genome project: 1998–2003. Science 282, 682–689.

2.	Botstein, D., White, D. L., Skolnick, M., and Davis, R. W. (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 32, 314–331.

3.	Weber, J. L. and May, P. E. (1989) Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am. J. Hum. Genet. 44, 388–396.

4.	Collins, F. S., Guyer, M. S., and Chakravarti, A. (1997) Variations on a theme: Cataloging human DNA sequence variation. Science 278, 1580–1581.

5.	Kruglyak, L. (1997) The use of a genetic map of biallelic markers in linkage studies. Nat. Genet. 17, 21–24.

6.	Nickerson, D. A., Taylor, S. L., Weiss, K. M., Clark, A. G., Hutchinson, R. G., Stengard, J., Salomaa, V., Vartiainen, E., Boerwinkle, E., Sing, C.F. (1998) DNA sequence diversity in a 9.7-kb region of the human lipoprotein lipase gene. Nature Genet. 19, 233–240.

7.	Sun, G. L., Diaz, O., Salomon, B., von Bothmer, R. (1999) Genetic diversity in Elymus caninus as revealed by isozyme, RAPD, and microsatellite markers. Genome 42, 420–431.

8.	Gusella, J. F., Wexler, N. S., Conneally, P. M., Naylor, S. L., Anderson, M. A., Tanzi, R. E., Watkins, P. C., Ottina, K., Wallace, M. R., and Sakaguchi, A. Y. (1983) A polymorphic DNA marker genetically linked to Huntigton’s disease. Nature 306, 234–238.

9.	Risch, N. and Merikangas, K. (1996) The future of genetic studies of complex human diseases. Science 273, 1516–1517.

10.	Risch, N. and Teng, J. (1998) The relative power of family-based and case-control designs for linkage disequilibrium studies of complex human diseases. Genome Res. 8, 1273–1288.

11.	Larrey, D., Berson, A., Habersetzer, F., Tinel, M., Castot, A., Babany, G., Letteron, P., Freneaux, E., Loeper, J., and Dansette, P. (1989) Genetic predisposition to drug hepatotoxicity: role in hepatitis caused by amineptine, a tricyclic antidepressant. Hepatology 10, 168–173.

12.	Collins, F. S., Brooks, L. D., and Chakravarti, A. (1998) A DNA polymorphism discovery resource for research on human genetic variation. Genome Res. 8, 1229–1231.

13.	Christopoulos, T. K.(1999) Nucleic acid analysis. Anal. Chem. 71, 425R–438R.

14.	Hacia, J. G. (1999) Resequencing and mutational analysis using oligonucleotide microarrays. Nat. Genetics Suppl. 21, 42–47.

15.	Karas, M. and Hillenkamp, F. (1988) Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal. Chem. 60, 2299–2301.

16.	Wu, K. J., Steding, A., and Becker, C. H. (1993) Matrix-assisted laser desorption time-of-flight mass spectrometry of oligonucleotides using 3-Hydroxypicolinic acid as an ultraviolet-sensitive matrix. Rapid Commun. Mass Spectrom. 7, 142–146.

17.	Tang, K., Fu, D., Kötter, S., Cotter, R. J., Cantor, C. R., and Köster, H. (1995) Matrix-assisted laser desorption/ionization mass spectrometry of immobilized duplex DNA probes. Nucleic Acids Res. 23, 3126–3131.

18.	Jurinke, C., van den Boom, D., Jacob, A., Tang, K., Wörl, R., and Köster, H. (1996) Analysis of ligase chain reaction products via matrix assisted laser desorption/ionization time-of-flight mass spectrometry. Anal. Biochem. 237, 174–181.

19.	Jurinke, C., Zöllner, B., Feucht, H.-H., Jacob, A., Kirchhübel, J., Lüchow, A., van den Boom, D., Laufs, R., and Köster, H. (1996) Detection of Hepatitis B virus DNA in serum samples via nested PCR and MALDI-TOF mass spectrometry. Genet. Anal. 13, 67–71.

20.	Pieles, U., Zurcher, W., Schar, M., and Moser, H. E. (1993) Matrix-assisted laser desorption ionization time-of-flight mass spectrometry: a powerful tool for the mass and sequence analysis of natural and modified oligonucleotides. Nucleic Acids Res. 21, 3191–3196.

21.	Köster, H., Tang, K., Fu, D. J., Braun, A., van den Boom, D., Smith, C. L., Cotter, R. J., and Cantor, C. R. (1996) A strategy for rapid and efficient DNA sequencing by mass spectrometry. Nat. Biotechnol. 14, 1123–1129.

22.	Fu, D. J., Tang, K., Braun, A., Reuter, D., Darnhofer-Demar, B., Little, D. P., O’Donnell, M. J., Cantor, C. R., and Köster, H. (1998) sequencing exons 5 to 8 of the p53 gene by MALDI-TOF mass spectrometry. Nature Biotechnol. 16, 381–384.

23.	Berkenkamp, S., Kirpekar, F., and Hillenkamp, F. (1998) Infrared MALDI mass spectrometry of large nucleic acids. Science 281, 260–262.

24.	Braun, A., Little, D. P., and Köster, H. (1997) Detecting CFTR gene mutations by using primer oligo base extension and mass spectrometry. Clin. Chem. 43, 1151–1158.

25.	Braun, A., Little, D. P., Reuter, D., Muller-Mysock, B., and Köster, H. (1997) Improved analysis of microsatellites using mass spectrometry. Genomics 46, 18–23.

Comments (Loading...)

Post comment/View all comments