Combinatorial analysis of linkage disequilibrium networks:
A comparison of genetic reference panels - R2 0.1

Correlation: [ Higher ]
[ 0.1 ] [ 0.15 ] [ 0.2 ] [ 0.25 ] [ 0.3 ] [ 0.35 ] [ 0.4 ] [ 0.45 ] [ 0.5 ] [ 0.55 ] [ 0.6 ] [ 0.65 ] [ 0.7 ] [ 0.75 ] [ 0.8 ] [ 0.85 ] [ 0.9 ] [ 0.95 ]

BXD

AXB

LXS

test

CC

test

Standard Inbreds w/o WD

test

Standard Inbreds w/ WD

test


Linkage disequilibrium is the statistical association of allele distributions at multiple loci. In this analysis linkage disequilibrium was estimated using mutual information of pair-wise SNP genotype distributions typed at over 10,000 loci in six populations. Most SNPs are in low level LD with other loci. For each strain panel, LD networks anchored to the same 20 randomly chosen locations were plotted, each in a different color, to reveal the chromosomal distribution of linked loci. In general, for two progenitor RI populations, LD is intra-chromosomal but LD blocks are quite large, leading to low precision in genetic analysis. In more diverse populations, LD blocks are smaller, but in Standard Inbred strains, small LD networks are pervasive with high inter-chromosomal linkage, leading to low accuracy in genetic analysis. In the Collaborative Cross, LD occurs in smaller, intra-chromosomal blocks that are not linked to other chromosomes, leading to high precision and high accuracy.