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. 2014 Oct 29;6(1):23. doi: 10.1186/1868-7083-6-23

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© Jones et al.; licensee BioMed Central Ltd. 2014

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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The 4qA BSS analysis does not amplify from 10A176T or 4A166 alleles. (A) The 4qA BSS assay (upper panel) is specific for 4qA sequences (present in sample 17A) and does not amplify the non-permissive 10A176T or 4A166 alleles present in samples 27A and 27B. BSS PCR using oligonucleotide primers that do not distinguish between 4A and 10A176T (lower panel) amplifies robustly from all three samples. (B) Sequence analysis of the products from samples 27A and 27B confirmed their origins as being from a 10A176T allele. The lack of a detectable CpG at position #55 but the presence of a CpG at position #16 identifies these as derived from a chromosome with a 10A176T haplotype. Expected CpGs, based on predicted sequence composition of the unconverted region amplified, are listed in numerical order. Red boxes indicate methylated CpGs, blue boxes indicate unmethylated CpGs, and white boxes indicate no CpG detected at the expected site.