Characterization of a Novel Hyper-Variable Variable Number Tandem Repeat in the Dopamine Transporter Gene (SLC6A3)

The dopamine transporter gene, SLC6A3, has received substantial attention in genetic association studies of various phenotypes (hypertension, ADHD, substance use disorders, etc.). Although some variable number tandem repeats (VNTRs) present in SLC6A3 have been used as genetic markers in these association studies, results have not been consistent. We searched for unanalyzed VNTRs in SLC6A3 that might account for the heterogeneity of existing association study results. We used the Tandem Repeat Annotation Library (TRAL) to characterize the VNTR landscape of 64 unrelated long-read haplotype-phased SLC6A3 sequences. We further report sequence similarity of each repeat unit of the five VNTRs along with the correlations of SNP-SNP, SNP-VNTR and VNTR-VNTR alleles across the length of the gene. We present the discovery of a novel hyper-variable number tandem repeat (hyVNTR) in intron 8 of SLC6A3, which contains a range of 3.4-133.4 repeat copies and has a consensus sequence length of 38bp, with 84% G+C content. The 38-base repeat was predicted to form G-quadruplexes in silico and was confirmed by circular dichroism spectroscopy. Additionally, this hyVNTR contains multiple putative binding sites for PRDM9, which, in combination with low levels of linkage disequilibrium around the hyVNTR, suggests it is a recombination hotspot.