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Allelic drop-out may occur with a primer binding site polymorphism for the commonly used RFLP assay for the -1131T>C polymorphism of the Apolipoprotein AV gene
- Source :
- Lipids in Health and Disease, Vol 5, Iss 1, p 11 (2006)
- Publication Year :
- 2006
- Publisher :
- BMC, 2006.
-
Abstract
- Abstract Apolipoprotein AV (ApoAV) gene variant, -1131T>C, is associated with increased triglyceride concentrations in all ethnic groups studied. An MseI based RFLP analysis is the most commonly used method for genotyping this SNP. We genotyped a large cohort comprising 1185 Asian Indians and 173 UK Caucasians for -1131T>C using an ARMS-PCR based tetra-primer method. For quality control, we re-genotyped approximately 10% random samples from this cohort utilizing the MseI RFLP, which showed a 2.9% (3/102) genotyping error rate between the two methods. To investigate further, we sequenced the 900 bp region around the -1131T>C polymorphism in 25 Asian Indians and 15 UK Caucasians and found a number of polymorphisms including the -987C>T polymorphism. Further analysis of the -987C>T SNP showed a higher rare allele frequency of 0.23 in Asian Indians (n = 158) compared to 0.09 in the UK Caucasians (n = 157). This SNP is located 4 bp from the 3' end of the RFLP forward primer and is in weak linkage disequilibrium with -1131T>C variant (r2 = 0.084 and D' = 1). Repeated RFLP analysis of seven subjects heterozygous for -987C>T (seven times), showed discordant results with the sequence at -1131T>C SNP nearly one third (15/49) of the time. We conclude that presence of -987C>T polymorphism in the forward primer of the MseI RFLP assay may lead to allelic drop-out and generate unforeseen errors in genotyping the -1131T>C polymorphism. Our results also emphasise the need for careful quality control in all molecular genetic studies, particularly while transferring genotyping methods between various ethnic groups.
- Subjects :
- Nutritional diseases. Deficiency diseases
RC620-627
Subjects
Details
- Language :
- English
- ISSN :
- 1476511X
- Volume :
- 5
- Issue :
- 1
- Database :
- Directory of Open Access Journals
- Journal :
- Lipids in Health and Disease
- Publication Type :
- Academic Journal
- Accession number :
- edsdoj.7e4b504214084b7486b8081aac2d8c73
- Document Type :
- article
- Full Text :
- https://doi.org/10.1186/1476-511X-5-11