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

Publication ,  Journal Article
Kuhn, A; Ong, YM; Cheng, C-Y; Wong, TY; Quake, SR; Burkholder, WF
Published in: Proc Natl Acad Sci U S A
June 3, 2014

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.

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Published In

Proc Natl Acad Sci U S A

DOI

EISSN

1091-6490

Publication Date

June 3, 2014

Volume

111

Issue

22

Start / End Page

8131 / 8136

Location

United States

Related Subject Headings

  • Selection, Genetic
  • Retroelements
  • Polymorphism, Single Nucleotide
  • Phenotype
  • Long Interspersed Nucleotide Elements
  • Linkage Disequilibrium
  • Humans
  • Homozygote
  • Haplotypes
  • Genome-Wide Association Study
 

Citation

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Kuhn, A., Ong, Y. M., Cheng, C.-Y., Wong, T. Y., Quake, S. R., & Burkholder, W. F. (2014). Linkage disequilibrium and signatures of positive selection around LINE-1 retrotransposons in the human genome. Proc Natl Acad Sci U S A, 111(22), 8131–8136. https://doi.org/10.1073/pnas.1401532111
Kuhn, Alexandre, Yao Min Ong, Ching-Yu Cheng, Tien Yin Wong, Stephen R. Quake, and William F. Burkholder. “Linkage disequilibrium and signatures of positive selection around LINE-1 retrotransposons in the human genome.Proc Natl Acad Sci U S A 111, no. 22 (June 3, 2014): 8131–36. https://doi.org/10.1073/pnas.1401532111.
Kuhn A, Ong YM, Cheng C-Y, Wong TY, Quake SR, Burkholder WF. Linkage disequilibrium and signatures of positive selection around LINE-1 retrotransposons in the human genome. Proc Natl Acad Sci U S A. 2014 Jun 3;111(22):8131–6.
Kuhn, Alexandre, et al. “Linkage disequilibrium and signatures of positive selection around LINE-1 retrotransposons in the human genome.Proc Natl Acad Sci U S A, vol. 111, no. 22, June 2014, pp. 8131–36. Pubmed, doi:10.1073/pnas.1401532111.
Kuhn A, Ong YM, Cheng C-Y, Wong TY, Quake SR, Burkholder WF. Linkage disequilibrium and signatures of positive selection around LINE-1 retrotransposons in the human genome. Proc Natl Acad Sci U S A. 2014 Jun 3;111(22):8131–8136.
Journal cover image

Published In

Proc Natl Acad Sci U S A

DOI

EISSN

1091-6490

Publication Date

June 3, 2014

Volume

111

Issue

22

Start / End Page

8131 / 8136

Location

United States

Related Subject Headings

  • Selection, Genetic
  • Retroelements
  • Polymorphism, Single Nucleotide
  • Phenotype
  • Long Interspersed Nucleotide Elements
  • Linkage Disequilibrium
  • Humans
  • Homozygote
  • Haplotypes
  • Genome-Wide Association Study