Effects of exon-intron boundary and secondary SNP on assay success rate in 96-plex validation. (A) The flanking regions of failed SNP assays that contain predicted exon-intron boundaries. Three out of five failed assays contained predicted exon-intron boundaries (marked with asterisk) which occur within oligonucloetide binding site; (B) The flanking regions of successful assays containing predicted exon-intron boundary (marked with asterisk) which are outside of oligonucloetide binding site in six out of seven assays; (C) SNP flanking region of failed assay indicating a secondary SNP (in single quotes) in LSO binding site; (D) Clustering profiles of assays containing a potential secondary SNP in flanking region; The two types of oligonucleotides, namely ASO and LSO were highlighted in green and red, respectively.
Wong et al. BMC Genomics 2012 13:726 doi:10.1186/1471-2164-13-726