ArticleLipids in health and disease2006
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.
Article in Lipids in health and disease, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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6 citing papers in PubMed, 18 citations in OpenAlex.
- Integrating next-generation sequencing with biochemical screening to optimize first-tier newborn screening systems.Human genomics · 2026Article
- An Asymptomatic Case With MEN1 Slipping Through Genetic Screening by SNV-dependent Allelic Dropout.Journal of the Endocrine Society · 2022Article
- Tumor cellularity as a quality assurance measure for accurate clinical detection of BRAF mutations in melanoma.Molecular diagnosis & therapy · 2014Article
- Clinical validation of KRAS, BRAF, and EGFR mutation detection using next-generation sequencing.American journal of clinical pathology · 2014Article
- Identification of gene mutations in autosomal dominant polycystic kidney disease through targeted resequencing.Journal of the American Society of Nephrology : JASN · 2012Article
- Modification of primers for GRHPR genotyping: avoiding allele dropout by single nucleotide polymorphisms and homology sequence.Urological research · 2008Article
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Authors and funding
7 authors at 3 institutions in 2 countries.
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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.
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