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. 1999 Aug 31;96(18):10016-20.
doi: 10.1073/pnas.96.18.10016.

Chip-based genotyping by mass spectrometry

K Tang  1 , D J Fu, D Julien, A Braun, C R Cantor, H Köster
Affiliations

Chip-based genotyping by mass spectrometry

K Tang et al. Proc Natl Acad Sci U S A. .

Abstract

Silicon chips with immobilized target DNAs were used for accurate genotyping by mass spectrometry. Genomic DNAs were amplified with PCR, and the amplified products were covalently attached to chip wells via N-succinimidyl (4-iodoacetyl)aminobenzoate (SIAB) chemistry. Primer annealing, extension, and termination were performed on a 1-microl scale directly in the chip wells in parallel. Diagnostic products thus generated were detected in situ by using matrix-assisted laser desorption ionization mass spectrometry. This miniaturized method has the potential for accurate, high-throughput, low-cost identification of genetic variations.

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Figures

Figure 1
Figure 1
Schematic overview of PCR product immobilization, PROBE reaction, and MALDI-MS on a chip.
Figure 2
Figure 2
Mass spectra for genotyping of HPA-2 showing a homozygous sample (Upper) and a heterozygous sample (Lower). The primer was extended by one base for the 163T allele and three bases for the 163M allele. The unextended primer (P) was present in both cases.
Figure 3
Figure 3
Scanning electron microscopy of one recrystallized matrix spot formed by dispensing 3 nl of matrix twice.
Figure 4
Figure 4
Mass spectrum for genotyping of HPA-1 showing a heterozygous sample 33L/33P. A recycled HPA-1 chip was used to perform the PROBE reaction and MALDI-MS.
Figure 5
Figure 5
Mass spectrum for genotyping of HPA-4 showing a homozygous sample 143R. The template DNA was amplified by using universal primers listed in Table 1 before covalent attachment onto the chip surface.
See this image and copyright information in PMC

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