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A low-cost open-source SNP genotyping platform for association mapping applications

Stuart J Macdonald1*, Tomi Pastinen2, Anne Genissel13, Theodore W Cornforth14 and Anthony D Long1

  • * Corresponding author: Stuart J Macdonald

Author Affiliations

1 Department of Ecology and Evolutionary Biology, University of California Irvine, CA 92697-2525, USA

2 McGill University and Genome Québec Innovation Centre, 740 Docteur Penfield Avenue, Montreal, Québec H3A 1A4, Canada

3 Section of Evolution and Ecology, University of California Davis, Davis, CA 95616, USA

4 Institute of Neuroscience, 1254 University of Oregon, Eugene, Oregon 97403-1254, USA

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Genome Biology 2005, 6:R105  doi:10.1186/gb-2005-6-12-r105

Published: 2 December 2005


Association mapping aimed at identifying DNA polymorphisms that contribute to variation in complex traits entails genotyping a large number of single-nucleotide polymorphisms (SNPs) in a very large panel of individuals. Few technologies, however, provide inexpensive high-throughput genotyping. Here, we present an efficient approach developed specifically for genotyping large fixed panels of diploid individuals. The cost-effective, open-source nature of our methodology may make it particularly attractive to those working in nonmodel systems.