Long range linkage disequilibrium across the human genome

Evan Koch; Mickey Ristroph; Mark Kirkpatrick

doi:10.1371/journal.pone.0080754

Long range linkage disequilibrium across the human genome

PLoS One. 2013 Dec 12;8(12):e80754. doi: 10.1371/journal.pone.0080754. eCollection 2013.

Authors

Evan Koch¹, Mickey Ristroph¹, Mark Kirkpatrick¹

Affiliation

¹ Department of Integrative Biology, University of Texas, Austin, Texas, United States of America.

Abstract

Long-range linkage disequilibria (LRLD) between sites that are widely separated on chromosomes may suggest that population admixture, epistatic selection, or other evolutionary forces are at work. We quantified patterns of LRLD on a chromosome-wide level in the YRI population of the HapMap dataset of single nucleotide polymorphisms (SNPs). We calculated the disequilibrium between all pairs of SNPs on each chromosome (a total of >2×10(11) values) and evaluated significance of overall disequilibrium using randomization. The results show an excess of associations between pairs of distant sites (separated by >0.25 cM) on all of the 22 autosomes. We discuss possible explanations for this observation.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Genome, Human / genetics*
Haplotypes
Humans
Linkage Disequilibrium / genetics*
Polymorphism, Single Nucleotide / genetics

Grants and funding

Funding was from N.S.F. grant DEB-0819901 (www.nsf.gov) and the Miller Institute for Basic Research in Science (millerinstitute.berkeley.edu). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.