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 (Peach=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.
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Acknowledgements
We thank all the study participants for their cooperation. For excellent technical assistance, we wish to acknowledge the laboratory personnel of the Institute of Clinical Molecular Biology and the members of the Popgen Biobank. This study was supported by the Deutsche Forschungsgemeinschaft (NE1191/1-1), the RESOLVE project (FP7-HEALTH-F4-2008-202047) and the Excellence Cluster ‘Inflammation at Interfaces’.
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Flachsbart, F., Möller, M., Däumer, C. et al. Genetic investigation of FOXO3A requires special attention due to sequence homology with FOXO3B. Eur J Hum Genet 21, 240–242 (2013). https://doi.org/10.1038/ejhg.2012.83
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DOI: https://doi.org/10.1038/ejhg.2012.83
