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. 2005 Aug 16;102(33):11835-9.
doi: 10.1073/pnas.0505262102. Epub 2005 Aug 9.

A map of the human genome in linkage disequilibrium units

W Tapper  1 , A Collins, J Gibson, N Maniatis, S Ennis, N E Morton
Affiliations

A map of the human genome in linkage disequilibrium units

W Tapper et al. Proc Natl Acad Sci U S A. .

Abstract

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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Figures

Fig. 1.
Fig. 1.
The relationship in the human genome between LDU and linkage in w in chromosome arms (red) and deciles (blue).
Fig. 2.
Fig. 2.
A graph showing variation among chromosome arms for the ratio of the LD map in LDU/w to the physical map in Mb/w.
Fig. 3.
Fig. 3.
The declining density of holes with marker density among chromosome arms.
Fig. 4.
Fig. 4.
A graph of chromosome 19 for LDU/Mb (blue) and centimorgans (cM)/Mb (red) against the physical scale in Mb.
Fig. 5.
Fig. 5.
A graph of chromosome 19 for centimorgans (cM)/Mb in males (blue) and females (red) against the physical scale in Mb.
Fig. 6.
Fig. 6.
A graph of chromosome 19 for centimorgans (cM) in males (blue) and females (red) against the physical map in Mb.
See this image and copyright information in PMC

References

    1. Kong, X., Murphy, K., Raj, T., He, C., White, P. S. & Matise, T. C. (2004) Am. J. Hum. Genet. 75, 1143-1148. - PMC - PubMed
    1. Jeffreys, A. J., Kauppi, L. & Neumann, R. (2001) Nat. Genet. 29, 217-222. - PubMed
    1. International HapMap Consortium (2003) Nature 426, 789-796. - PubMed
    1. Maniatis, N., Collins, A., Xu, C.-F., McCarthy, L. C., Hewett, D. R., Tapper, W., Ennis, S., Ke, X. & Morton, N. E. (2002) Proc. Natl. Acad. Sci. USA 99, 2228-2233. - PMC - PubMed
    1. Maniatis, N., Morton, N. E., Gibson, J., Xu, C.-F., Hosking, L. K. & Collins, A. (2005) Hum. Mol. Genet. 14, 145-153. - PubMed

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