Presence of recombination hotspots throughout SLC6A3

The human dopamine transporter gene SLC6A3 is involved in substance use disorders (SUDs) among many other common neuropsychiatric illnesses but allelic association results including those with its classic genetic markers 3’VNTR or Int8VNTR remain mixed and unexplainable. To better understand the genetics for reproducible association signals, we report the presence of recombination hotspots based on sequencing of the entire 5’ promoter regions in two small SUDs cohorts, 30 African Americans (AAs) and 30 European Americans (EAs). Recombination rate was the highest near the transcription start site (TSS) in both cohorts. In addition, each cohort carried 57 different promoter haplotypes out of 60 and no haplotypes were shared between the two ethnicities. A quarter of the haplotypes evolved in an ethnicity-specific manner. Finally, analysis of five hundred subjects of European ancestry, from the 1000 Genome Project, confirmed the promoter recombination hotspots and also revealed several additional ones in non-coding regions only. These findings provide an explanation for the mixed results as well as guidance for selection of effective markers to be used in next generation association validation (NGAV), facilitating the delineation of pathogenic variation in this critical neuropsychiatric gene.人类多巴胺转运蛋白基因（dopamine transporter gene）SLC6A3 参与物质使用障碍（Substance Use Disorders, SUDs）及多种其他常见神经精神疾病的病理过程，但针对该基因经典遗传标记3’可变数目串联重复序列（3’VNTR）或内含子8可变数目串联重复序列（Int8VNTR）的等位基因关联研究结果始终存在矛盾且无法得到合理解释。为更好地解析可重复关联信号的遗传学机制，本研究对两个小型物质使用障碍队列（分别纳入30名非裔美国人（African Americans, AAs）与30名欧洲裔美国人（European Americans, EAs））的全5’启动子区域进行测序，据此报道了该区域存在重组热点（recombination hotspot）。两个队列中，转录起始位点（Transcription Start Site, TSS）附近的重组率均为最高。此外，在60种预设启动子单倍型（haplotype）中，每个队列各携带57种不同的单倍型，且两个族裔群体间无共享单倍型；其中四分之一的单倍型以族裔特异性的方式演化。最后，对来自千人基因组计划（1000 Genome Project）的500名欧洲血统受试者的分析验证了该启动子区域的重组热点，同时还在非编码区域中发现了额外的数个重组热点。本研究结果既为此前的矛盾关联结果提供了合理解释，也为下一代关联验证（Next Generation Association Validation, NGAV）中有效遗传标记的筛选提供了指导，有助于阐明这一关键神经精神疾病相关基因中的致病性变异（pathogenic variation）。