May 17, 2012

Genetic investigation of FOXO3A requires special attention due to sequence homology with FOXO3B

European Journal of Human Genetics : EJHG
Friederike FlachsbartAlmut Nebel

Abstract

Our study demonstrates that the genetic investigation of forkhead box O3A gene (FOXO3A), a validated human longevity gene, is greatly hampered by the fact that its exonic regions have 99% sequence homology with the FOXO3B pseudogene. If unaccounted for, this high degree of homology can cause serious genotyping or sequencing errors. Here, we present an experimental set-up that allows reliable data generation for the highly homologous regions and that can be used for the evaluation of assay specificity. Using this design, we exemplarily showed FOXO3A-specific results for two single-nucleotide polymorphisms (SNPs) (rs4945816 and rs4946936) that are significantly associated with longevity in our centenarian-control sample (P(each)=0.0008). Because both SNPs are located in the 3' untranslated region of FOXO3A, they could be of functional relevance for the longevity phenotype. Our experimental set-up can be used for reliable and reproducible data generation for further sequencing and genotyping studies of FOXO3A with the aim of discovering new SNPs of functional relevance.

Mentioned in this Paper

FOXO3B gene
Sequencing
Pseudogenes
FOXO3A protein, human
FOXO3 gene
Nucleotides
Longevity
Forkhead Transcription Factors
Genetic Polymorphism
Assay

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