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Identification and functional characterization of three novel alleles for the serotonin transporter-linked polymorphic region

Abstract

A promoter polymorphism in the serotonin transporter gene (5-HTTLPR) has been reported to confer relative risk for phenotypes (depression/anxiety) and endophenotypes (amygdala reactivity). In this report, we identify and characterize three rare 5-HTTLPR alleles not previously described in the human literature. The three novel alleles were identified while genotyping 5-HTTLPR in a family-based attention deficit hyperactivity disorder clinical population. Two of the novel alleles are longer than the common 16-repeat long (L) allele (17 and 18 repeats) and the third is significantly smaller than the 14-repeat short (S) allele (11 repeats). The sequence and genetic architecture of each novel allele is described in detail. We report a significant decrease in the expression between the XL17 (17r) allele and the LA (16r) allele. The XS11 (11r) allele showed similar expression with the S (14r) allele. A 1.8-fold increase in expression was observed with the LA(16r) allele compared with the LG (16r) allele, which replicates results from earlier 5-HTTLPR expression experiments. In addition, transcription factor binding site (TFBS) analysis was performed using MatInspector (Genomatix) that showed the presence or absence of different putative TFBSs between the novel alleles and the common L (16r) and S (14r) alleles. The identification of rare variants and elucidation of their functional impact could potentially lead to understanding the contribution that the rare variant may have on the inheritance/susceptibility of multifactorial common diseases.

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Acknowledgements

This study was funded by Avera McKennan Hospital and University Health Center through a partnership with South Dakota State University and the University of South Dakota. We extend a special thanks to Dr Scott R Whittemore (University of Louisville School of Medicine) for his generosity in supplying the RN46A cell line for the expression experiments.

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Correspondence to G E Davies.

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Ehli, E., Hu, Y., Lengyel-Nelson, T. et al. Identification and functional characterization of three novel alleles for the serotonin transporter-linked polymorphic region. Mol Psychiatry 17, 185–192 (2012). https://doi.org/10.1038/mp.2010.130

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