Authors: Carl D Soulsbury Graziella Iossa Keith J Edwards Philip J Baker Stephen Harris
Publish Date: 2006/09/28
Volume: 8, Issue: 3, Pages: 733-738
Abstract
Allelic dropouts are an important source of genotyping error particularly in studies using noninvasive sampling techniques This has important implications for conservation biology as an increasing number of studies are now using noninvasive techniques to study rare species or endangered populations Previously allelic dropout has typically been associated with PCR amplification of low quality/quantity template DNA However in this study we recorded high levels of allelic dropout 21–57 at specific loci amplified from a high quality DNA 631 ± 78 ng/μl source in the red fox Vulpes vulpes We designed a series of experiments to identify the sources of error Whilst we were able to show that the best method to identify allelic dropout was the dilution of template DNA prior to PCR amplification our data also showed two specific patterns 1 allelic dropouts occurred at specific loci 2 allelic dropouts occurred at specific pairwise combinations of alleles These patterns suggest that mechanisms other than low quantity template DNA are responsible for allelic dropout Further research on the causes of these patterns in this and other studies would further our understanding of genotyping errors and would aid future studies where allelic dropout may be a serious issueWe are grateful to the Natural Environment Research Council CDS Rotary Foundation of Rotary International Newby Trust Ltd and the Sir Richard Stapley Educational Trust GI the Biotechnology and Biological Sciences Research Council KJE the International Fund for Animal Welfare PJB and The Dulverton Trust SH for financial support We are also grateful to Jane Coghill of the University of Bristol Transcriptonics unit for processing the MegaBACE samples
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