Sequencing and detection of polymorphisms in the 5' end of the human endogenous retroviral element, HRES-1

Fragments of the 5' long terminal repeat (LTR) of the human endogenous retroviral element, HRES-1, were amplified. Single strand conformation analysis of these fragments in combination with sequencing revealed two polymorphic nucleotides, namely a HindIII and an Eco571 polymorphic site. Moreover, a number of differences from the previously published HRES-1 LTR sequence were detected. The linkage pattern of the two polymorphisms suggested the existence of three allelic forms of HRES-1. The frequencies of the genotypes and alleles of HRES-1 were determined in 158 individuals. The detection of HRES-1 markers may be useful to study associations between this endogenous retrovirus and various diseases.