Single nucleotide polymorphic discrimination by an electronic dot blot assay on semiconductor microchips

Abstract

We have developed a rapid assay for single nucleotide polymorphism (SNP) detection that utilizes electronic circuitry on silicon microchips. The method was validated by the accurate discrimination of blinded DNA samples for the complex quadra-allelic SNP of mannose binding protein. The microchip directed the transport, concentration, and attachment of amplified patient DNA to selected electrodes (test sites) creating an array of DNA samples. Through control of the electric field, the microchip enabled accurate genetic identification of these samples using fluorescently labeled DNA reporter probes. The accuracy of this approach was established by internal controls of dual labeled reporters and by using mismatched sequences in addition to the wild-type and variant reporter sequences to validate the SNP-genotype. The ability to customize this assay for multiple genes has advantages over other existing approaches.

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Figure 1: Microchip image, assay overview, and MBP sequences.
Figure 2: Cy3/Cy5 images of a representative chip.
Figure 3: Quantification and scoring of blinded samples.
Figure 4: MBP blinded samples (allele D) and IL-1β T/T homozygote.

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Acknowledgements

The authors wish to thank Michael Heller, James O'Connell, Mark Collins, Elaine Weidenhammer, and Tina Nova for critical reading of the manuscript, and Daniel Raymond, Lori Westin, and Don Ackley for technical assistance.

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Correspondence to David J. Wu.

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Gilles, P., Wu, D., Foster, C. et al. Single nucleotide polymorphic discrimination by an electronic dot blot assay on semiconductor microchips. Nat Biotechnol 17, 365–370 (1999). https://doi.org/10.1038/7921

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