Linkage disequilibrium and signatures of positive selection around LINE-1 retrotransposons in the human genome
Year: 2014
Type: article
Abstract: Insertions of the human-specific subfamily of LINE-1 (L1) retrotransposon are highly polymorphic across individuals and can critically influence the human transcriptome. We hypothesized that L1 insertions could represent genetic variants determining important human phenotypic traits, and performed an integrated analysis of L1 elements and single nucleotide polymorphisms (SNPs) in several human populations. We found that a large fraction of L1s were in high linkage disequilibrium with their surrounding genomic regions and that they were well tagged by SNPs. However, L1 variants were only partially captured by SNPs on standard SNP arrays, so that their potential phenotypic impact would be frequently missed by SNP array-based genome-wide association studies. We next identified potential phenotypic effects of L1s by looking for signatures of natural selection linked to L1 insertions; significant extended haplotype homozygosity was detected around several L1 insertions. This finding suggests that some of these L1 insertions may have been the target of recent positive selection.
Institutions: Agency for Science, Technology and Research, Institute of Molecular and Cell Biology, National University of Singapore, Singapore National Eye Center, Singapore Eye Research Institute, Duke-NUS Medical School, National University Health System, Howard Hughes Medical Institute, Stanford University
Language: English
Subfield: Plant Science
Domain: Life Sciences
Open Access status: green
Funder: Howard Hughes Medical Institute
OpenAlex ID: W2002508113