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Published online 5 March 2004

Nucleic Acids Research, 2004, Vol. 32, No. 4 e47
© 2004 Oxford University Press

SNPWaveTM: a flexible multiplexed SNP genotyping technology

Michiel J. T. van Eijk*, José L. N. Broekhof, Hein J. A. van der Poel, René C. J. Hogers, Harrie Schneiders, Judith Kamerbeek, Esther Verstege, Joris W. van Aart, Henk Geerlings, Jaap B. Buntjer, A. Jan van Oeveren and Pieter Vos

Keygene NV, Agro Business Park 90, PO Box 216, 6700 AE Wageningen, The Netherlands

*To whom correspondence should be addressed. Tel: +31 317 466866; Fax: +31 317 424939; Email: michiel.van-eijk{at}keygene.com

Scalable multiplexed amplification technologies are needed for cost-effective large-scale genotyping of genetic markers such as single nucleotide polymorphisms (SNPs). We present SNPWaveTM, a novel SNP genotyping technology to detect various subsets of sequences in a flexible fashion in a fixed detection format. SNPWave is based on highly multiplexed ligation, followed by amplification of up to 20 ligated probes in a single PCR. Depending on the multiplexing level of the ligation reaction, the latter employs selective amplification using the amplified fragment length polymorphism (AFLP®) technology. Detection of SNPWave reaction products is based on size separation on a sequencing instrument with multiple fluorescence labels and short run times. The SNPWave technique is illustrated by a 100-plex genotyping assay for Arabidopsis, a 40-plex assay for tomato and a 10-plex assay for Caenorhabditis elegans, detected on the MegaBACE 1000 capillary sequencer.


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