Conflicting results in SNP genotype assessment

TY - JOUR

T1 - Conflicting results in SNP genotype assessment

AU - Hansen, Lise Lotte

AU - Madsen, Bo Eskerod

AU - Pedersen, Kristina

AU - Wiuf, Carsten

PY - 2007/12/1

Y1 - 2007/12/1

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=37349077842&partnerID=8YFLogxK

U2 - 10.2144/000112675

DO - 10.2144/000112675

M3 - Journal article

C2 - 18251251

AN - SCOPUS:37349077842

SN - 0736-6205

VL - 43

SP - 756

EP - 762

JO - BioTechniques

JF - BioTechniques

IS - 6

ER -