A Map of the Human Genome in Linkage Disequilibrium Units

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 i...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS 2005-08, Vol.102 (33), p.11835-11839
Main Authors: Tapper, W., Collins, A., Gibson, J., Maniatis, N., Ennis, S., Morton, N. E.
Format: Article
Language:English
Subjects:
Biological Sciences
Chromosome Mapping
Chromosomes
Chromosomes, Human, Pair 19 - genetics
Female
Genetic linkage
Genetic mapping
Genome, Human
Genomics
Haplotypes
Human genetics
Humans
Linkage disequilibrium
Linkage Disequilibrium - genetics
Male
Medical research
Optimization
Polymorphism, Single Nucleotide - genetics
Quantitative genetics
Recombination, Genetic - genetics
Selection, Genetic
Sex Characteristics
Sex chromosomes
Statistical variance
Time Factors
X chromosome
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Summary: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 nonpseudoautosomal region of the X chromosome is subject to hemizygous selection; and (iii) at resolution less than ≈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.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.0505262102