Conflicting results in SNP genotype assessment

Lise Lotte Hansen; Bo Eskerod Madsen; Kristina Pedersen; Carsten Wiuf

doi:10.2144/000112675

Conflicting results in SNP genotype assessment

Lise Lotte Hansen^*, Bo Eskerod Madsen, Kristina Pedersen, Carsten Wiuf

^*Corresponding author for this work

2 Citations (Scopus)

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.

Original language	English
Journal	BioTechniques
Volume	43
Issue number	6
Pages (from-to)	756-762
Number of pages	7
ISSN	0736-6205
DOIs	https://doi.org/10.2144/000112675
Publication status	Published - 1 Dec 2007
Externally published	Yes

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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.

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Conflicting results in SNP genotype assessment

Abstract

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