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Multiplexed genotyping with sequence-tagged molecular inversion probes

Nature Biotechnology volume 21, pages 673–678 (2003)Cite this article

Abstract

We report on the development of molecular inversion probe (MIP) genotyping, an efficient technology for large-scale single nucleotide polymorphism (SNP) analysis. This technique uses MIPs to produce inverted sequences, which undergo a unimolecular rearrangement and are then amplified by PCR using common primers and analyzed using universal sequence tag DNA microarrays, resulting in highly specific genotyping. With this technology, multiplex analysis of more than 1,000 probes in a single tube can be done using standard laboratory equipment. Genotypes are generated with a high call rate (95%) and high accuracy (>99%) as determined by independent sequencing.

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Figure 1: Selection for circularized padlock probes.
Figure 2: Molecular inversion probes.
Figure 3: Process flow and array image.
Figure 4: Assay performance.

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Acknowledgements

We thank K. Tran, T. Brundage, J. Patterson, E. Prakash and C. Bruckner for technical assistance and T. Jones and P. Oefner for helpful discussions. This work was supported by NIH HG00205. The work in Uppsala was supported by the Beijer and Wallenberg Foundations, the Research Councils of Sweden for natural science and for medicine, the Swedish Cancer Fund and Polysaccharide Research AB (Uppsala).

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  1. Paul Hardenbol, Maneesh Jain, Eugeni A Namsaraev, George A Karlin-Neumann, Hossein Fakhrai-Rad & Thomas D Willis

    Present address: ParAllele BioScience, 384 Oyster Point Blvd Suite 8, S., San Francisco, California, 94080, USA

Authors and Affiliations

  1. Stanford Genome Technology Center, Stanford University, 855 California Avenue, Palo Alto, 94304, California, USA

    Paul Hardenbol, Maneesh Jain, Eugeni A Namsaraev, George A Karlin-Neumann, Hossein Fakhrai-Rad, Mostafa Ronaghi, Thomas D Willis & Ronald W Davis

  2. Department of Genetics and Pathology, The Beijer Laboratory, Rudbeck Laboratory, Uppsala, Se-751 85, Sweden

    Johan Banér, Mats Nilsson & Ulf Landegren

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Correspondence to Mostafa Ronaghi.

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Competing interests

P.H., M.J., E.A.N., G.A.K.-N., H. F.-R. and T.D.W. are currently employed by ParAllele Bioscience (South San Francisco, California), a company that is commercializing the Molecular Inversion Probe Assay. M.R., U.L. and R.W.D. are shareholders of ParAllele Bioscience. J.B. and M.N. have no association with the company.

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Hardenbol, P., Banér, J., Jain, M. et al. Multiplexed genotyping with sequence-tagged molecular inversion probes. Nat Biotechnol 21, 673–678 (2003). https://doi.org/10.1038/nbt821

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