Haplotype architecture of the norepinephrine transporter gene SLC6A2 in four populations

Abstract

The norepinephrine transporter (NET) regulates levels of monoamine neurotransmitters integral to a variety of behaviors and autonomic functions. Two SLC6A2 polymorphisms have been used in genetic association studies, generating intriguing but nondefinitive results on traits such as hypertension and mood. One of these SLC6A2 variants is functional but rare. The other is common but not informative over the entire 48 kb SLC6A2 region and is insufficient to capture the functional diversity potentially contained within any SLC6A2 region. To elucidate SLC6A2 haplotype structure and define markers sufficient to capture haplotype diversity within detected haplotype blocks, 26 single-nucleotide polymorphisms (SNPs) were genotyped in 384 individuals evenly divided across Finnish Caucasian, US Caucasian, Plains American Indian, and African American populations. Three conserved blocks, 13.6, 12.5, and 25 kb in size and showing little evidence for historical recombination were observed in all populations. Haplotype diversity in block 1 and numbers of common haplotypes were highest in African Americans, among whom 5-6 optimal markers were sufficient to maximize diversity of each block. For other populations, 2-3 markers/block sufficed, but the optimal markers differed across populations. The SLC6A2 haplotype map and 25-marker panel (excluding the monomorphic one) is a comprehensive tool for genetic linkage studies on phenotypes related to NET function.

Detailed Analysis of Variants in FTO in Association with Body Composition in a Cohort of 70-Year-Olds Suggests a Weakened Effect among Elderly

“…More importantly, haplotype methods use the LD structure of the region and are more informative than single marker analyses when the causative variant has not been selected for genotyping. Also, haplotypes has been shown to, in general, be conserved across human populations [46], [47] and certain genes have a much conserved haplotype [48]. Our very dense haplotype map over the FTO gene could therefore be translatable to other populations and be of general interest.…”

Effects of Persisting Emotional Impact from Child Abuse and Norepinephrine Transporter Genetic Variation on Antidepressant Efficacy in Major Depression: A Pilot Study

“… 51 – 53 ) Furthermore, recently the combination of a child abuse history and carrying the TT polymorphism at rs5569 was demonstrated to significantly decreased antidepressant response in a sample of 308 patients, 54 ) and appears commonly polymorphic rather than being a rare variant of limited public health clinical utility. 55 , 56 )…”