Conflicting results in SNP genotype assessment.
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.
Hansen
Lise Lotte
LL
Danish Centre for Molecular Gerontology, Institute of Human Genetics, University of Aarhus, Denmark. lotte@humgen.au.dk
Madsen
Bo Eskerod
BE
Pedersen
Kristina
K
Wiuf
Carsten
C
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
D017931:DNA Primers; D011933:Reagent Kits, Diagnostic