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Evaluation of approaches for identifying population informative markers from high density SNP Chips

Samantha Wilkinson1*, Pamela Wiener1, Alan L Archibald1, Andy Law1, Robert D Schnabel2, Stephanie D McKay2, Jeremy F Taylor2 and Rob Ogden3

Author Affiliations

1 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, Scotland, UK

2 Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA

3 Wildgenes Laboratory, Royal Zoological Society of Scotland, Edinburgh EH12 6TS, Scotland, UK

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BMC Genetics 2011, 12:45  doi:10.1186/1471-2156-12-45

Published: 13 May 2011

Additional files

Additional file 1:

Supplemental materials. Figure S1: A boxplot of the observed breed allele frequencies for the top ranked 50 SNP markers for each selection method. Figure S2: A plot of the percentage assignment success with cumulative number of top-ranked SNP markers at the 4 stringency threshold levels. The results of this individual assignment test is for the training set and hold-out set where the selection implemented was Wright's pairwise FST. Table S1: Type I (false positives) and II errors (false negatives). The table details the error rates that occurred in the individual assignment analysis, using pairwise Wright's FST at the lowest stringency threshold level (LLR > 0).

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Additional file 2:

Table S2. Top 500 SNP markers. The genetic markers are ranked by decreasing informativeness and the corresponding SNP discovery methods are listed with each SNP marker.

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