Robust SNP genotyping by multiplex PCR and arrayed primer extension.

"specifically for discrepant genotype case 1 (coriell na18502 at snp rs3776720) we found a neighbouring snp (t/a) which is located at the 3' end of the anti-sense pcr primer site (5' cga tgt agg tga cac tag tat tgc agg cag acg tg a 3' - [additional file 6 ]) - this polymorphic site (30 bp downstream of rs3776720) is reported in dbsnp as rs6871885 with the a base (sense strand) being described as a rare allele (0 083) in sub-saharan african populations only (coriell na18502 is indeed a sub-saharan african yoruba and is heterozygote for this snp).; for discrepant genotype case 2 (coriell na18621 at snp rs12472674) we found a sequence variant (g/a) 52 bp downstream of snp rs12472674 located within the anti-sense pcr primer site (5' cga tgt agg tga cac tag ctc aat atg tta c ca caa 3' - [additional file 6 ]) - this variant (heterozygous in coriell na18621 - asian han chinese) has not been previously reported in dbsnp and may represent a novel polymorphism.; for the low quality genotype case 3 (coriell na19210 at snp rs4739199) we found a sequence variant (g/a) 45 bp downstream of snp rs4739199 located within the anti-sense pcr primer site (5' cga tgt agg tga cac tag tc c act tca tta ggt gaa 3' - [additional file 6 ]) - this variant (heterozygous in coriell na19210 - sub-saharan african yoruba) has also not been previously reported in dbsnp and may represent a novel polymorphism."

"Competing interests The author(s) declare that they have no competing interests."

"AcknowledgementsWe thank Tom Hudson, Martin Leboeuf, Alexandre Montpetit and Stephanie Roumy (McGill University and Genome Quebec Innovation Centre) for advice and access to HapMap genotype data and Coriell DNA samples. We are grateful to Colleen Nelson, Jamie Rosner, Bruce Dangerfield and Jonathan Ma at the Microarray Facility of The Prostate Centre at Vancouver General Hospital for microarray printing services used for this study [33], and we acknowledge BioData Ltd., Estonia [32] for access to APEX probe design software. We thank Teresa Feuchuk and Jo-Lynn Mervyn for administrative assistance, and Ruben Zamar, Will Welch, Rafeef Abugharbieh, Peter Paré and Bruce McManus for continued support. In addition, we would like to thank the reviewers of this manuscript for their helpful comments. This research was supported by funding from AllerGen NCE, the National Sanitarium Association (Canada), the British Columbia Lung Association, the Canadian Institutes of Health Research, and the Michael Smith Foundation for Health Research."