title: Conflicting results in SNP genotype assessment.
abstract: Single nucleotide polymorphisms (SNPs) are highly abundant in the genome and especially useful in the search for disease susceptibility genes via population-based association or linkage studies. Therefore, there is a strong need for high throughput and reliable methodologies to assess the SNP genotypes. Despite an unambiguous result of an SNP analysis, with the use of a commercial kit based on primer extension, subsequent sequencing analysis revealed that a proportion of the genotypes was not correctly assessed. The problem we have encountered may originate from specific structures in the genomic DNA sequence, rather than being a methodological problem.
authors.affiliation: Danish Centre for Molecular Gerontology, Institute of Human Genetics, University of Aarhus, Denmark. lotte@humgen.au.dk
authors.forename: Lise Lotte
authors.initials: LL
authors.lastname: Hansen
authors.forename: Bo Eskerod
authors.initials: BE
authors.lastname: Madsen
authors.forename: Kristina
authors.initials: K
authors.lastname: Pedersen
authors.forename: Carsten
authors.initials: C
authors.lastname: Wiuf
mesh_terms: D001483:Base Sequence; D001943:Breast Neoplasms / Q000235:genetics*; D017931:DNA Primers / Q000235:genetics; D005260:Female; D008040:Genetic Linkage; D005820:Genetic Testing / Q000379:methods* / Q000592:standards*; D005838:Genotype; D006801:Humans; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D011933:Reagent Kits, Diagnostic; D015203:Reproducibility of Results
chemical_list: D017931:DNA Primers; D011933:Reagent Kits, Diagnostic