Linkage disequilibrium and signatures of positive selection around LINE-1 retrotransposons in the human genome.

Journal Article (Journal Article)

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.

Full Text

Duke Authors

Cited Authors

  • Kuhn, A; Ong, YM; Cheng, C-Y; Wong, TY; Quake, SR; Burkholder, WF

Published Date

  • June 3, 2014

Published In

Volume / Issue

  • 111 / 22

Start / End Page

  • 8131 - 8136

PubMed ID

  • 24847061

Pubmed Central ID

  • PMC4050588

Electronic International Standard Serial Number (EISSN)

  • 1091-6490

Digital Object Identifier (DOI)

  • 10.1073/pnas.1401532111


  • eng

Conference Location

  • United States