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A map of the human genome in linkage disequilibrium units.
Proc Natl Acad Sci U S A. 2005 Aug 16;102(33):11835-9.
A map of the human genome in linkage disequilibrium units.
Tapper W, Collins A, Gibson J, Maniatis N, Ennis S, Morton NE.
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Two genetic maps with additive distances contribute information about
recombination patterns, recombinogenic sequences, and discovery of
genes affecting a particular phenotype. Recombination is measured in
morgans (w) over a single generation in a linkage map but may cover
thousands of generations in a linkage disequilibrium (LD) map
measured in LD units (LDU). We used a subset of single nucleotide
polymorphisms from the HapMap Project to create a genome-wide map in
LDU. Recombination accounts for 96.8% of the LDU variance in
chromosome arms and 92.4% in their deciles. However, deeper analysis
shows that LDU/w, an estimate of the effective bottleneck time (t),
is significantly variable among chromosome arms because (i) the
linkage map is approximated from the Haldane function, then adjusted
toward the Kosambi function that is more accurate but still
exaggerates w for all chromosomes, especially shorter ones; (ii) the
non-pseudoautosomal region of the X chromosome is subject to
hemizygous selection; and (iii) at resolution less than approximately
40,000 markers per w, there are indeterminacies (holes) in the LD map
reflecting intervals of very high recombination. Selection and
stochastic variation in small regions must have effects, which remain
to be investigated by comparisons among populations. These
considerations suggest an optimal strategy to eliminate holes
quickly, greatly enhance the resolution of sex-specific linkage maps,
and maximize the gain in association mapping by using LD maps.
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