Conclusions
The Sequazyme Pinpoint assay has successfully typed hundreds of different loci in many different laboratories. Major advantages of the technique are that primer selection is extremely simple and a high percentage of selected primers successfully genotype. The primers need contain no special labels or groups, so they are inexpensive and easily obtainable. Because the PCR and primer extension protocols are solution-based and the extension protocol is universal, the assay does not involve any of the relatively high infrastructure costs of DNA chips. Because MALDI-TOF is largely artefact-free and high in resolution, the base-calling accuracy is extremely high. The ability to detect and quantitate low relative abundance of the minor allele in pooled samples is largely unique to mass spectrometry, due to its high resolution compared to electrophoretic, chromatographic, fluorescent, and isotopic techniques. The ability to process several thousand samples a day, together with the ability to internally multiplex, enables throughputs of about 20,000 alleles a day, suitable for most medium to high throughput genotyping laboratories. Future developments include further miniaturisation to lower reagent costs, faster lasers to support higher throughput MALDI-TOF, and associated robotic systems to provide greater throughput.
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References
Cargill M, Alshuler D, Ireland J, Sklar P, Ardlie K, Patil N, Lane CR, Lim EP, Kalyanaraman N, Nemesh j, Ziaugra L, Friedland L, Rolfe A, Warrington J, Lipshutz R, Daley GQ, Lander ES. Nature Genetics 22: 231, 1999
van Rensburg SJ, Potocnik FCV, deVilliers JNP, Kotze MJ, Taljaard JJP. Annals of New York Academy of Science 903: 200, 2000
Lutz CT, Foster PA, Noll WW, Voelkerding KV, Press RD, McGlennen RC, Kirschbaum NE. Clinical Chemistry 44: 1146, 1998
Hoogendoorn B, Owen MJ, Oefner PJ, Williams N, Austin J, O’Donovan MC. Hum.Gen. 104: 89, 1999
Nelson NC. Critical Reviews in Clinical Laboratory Sciences 35: 369, 1998
Greenwood AD, Burke DT. Genome Research 6: 336, 1996
Goelet P, Knapp MR, Anderson S. US Patent Number 5888819, 1999
Fahy E, Nazarbaghi R, Zomorrodi M, Herrnstadt C, Parker W, Davis RE, Ghosh S. Nucleic Acids Research 25: 3102, 1997
Ross PL, Hall L, Smirnov IP, Haff, LA. Nature Biotech. 16: 1347, 1998
Haff LA, Smirnov IP. Biochemical Mass Spectrometry 24: 901, 1996
Haff LA, Smirnov, IP. Biochemical Mass Spectrometry 1996, 901, 1998
Haff LA, Smirnov IP. Nucleic Acids Research 25: 3749, 1997
Haff LA, Smirnov IP. Genome Research 7: 378, 1997
Roskey M, Juhasz P, Smirnov IP, Takach EJ, Martin SA, Haff LA. Proc. Natl. Acad. Sci. USA 93: 4724, 1996
Fei Z, Smith LM. Rapid Communications in Mass Spectrometry 14: 950, 2000
Pieles U, Zurcher W, Schar M, Moser HE. Nucleic Acids Research 21: 3191, 1993
Zhu YF, Chung CN, Taranenko NI, Allman SL, Martin SA, Haff L, Chen CH. Rapid Communications in Mass Spectrometry 10: 383, 1996.
Li YCL, Cheng S, Chan T-WD. Rapid Communications in Mass Spectrometry 12: 993, 1998
Ross PL, Hall LR, Haff LA. BioTechniques 29: 620, 2000
Belgrader P, Marino, MM, Lubin M, Barany, F. Genome Science and Technology 1: 77. 2000
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Haff, L.A., Belden, A.C., Hall, L.R., Ross, P.L., Smirnov, I.P. (2001). SNP Genotyping by MALDI-TOF Mass Spectrometry. In: Nicholas Housby, J. (eds) Mass Spectrometry and Genomic Analysis. Focus on Structural Biology, vol 2. Springer, Dordrecht. https://doi.org/10.1007/0-306-47595-2_2
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