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1. A first-generation linkage disequilibrium map of human chromosome 22

Elisabeth Dawson, Goncalo R. Abecasis, Suzannah Bumpstead, Yuan Chen, Sarah Hunt, David M. Beare, Jagjit Pabial, Thomas Dibling, Emma Tinsley, Susan Kirby, David Carter, Marianna Papaspyridonos, Simon Livingstone, Rocky Ganske, Elin Lõhmussaar, Jana Zernant, Neeme Tõnisson, Maido Remm, Reedik Mägi, Tarmo Puurand, Jaak Vilo, Ants Kurg, Kate Rice, Panos Deloukas, Richard Mott, Andres Metspalu, David R. Bentley, Lon R. Cardon & Ian Dunham

Nature 418: 544-548 (2002)

DNA sequence variants in specific genes or regions of the human genome are responsible for a variety of phenotypes such as disease risk or variable grug response. These variants can be investigated directly, or through their non-random associations with neighbouring markers (called linkage disequilibrium (LD)). Here are report measurement of LD along the complete sequence of human chromosome 22. Duplicate genotyping and analysis of 1,504 markers in Centre d’Etude du Polymorphisme Humain (CEPH) reference families at a median spacing of 15 kilobases (kb) reveals a highly variable pattern of LD along the chromosome, in whichextensive regions of nearly complete LD up to 804 kb in length are interspersed with regions of little or no detectable LD. The LD patterns are replicated in a panel of unrelated UK Caucasians. There is a strong correlation between high LD and low recombination frequency in the extant genetic map, suggesting that historical and contemporary recombination rates are similar. This study demostrates the feasibility of developing genome-wide maps of LD.

2. High-density genotyping and linkage disequilibrium in the human genome using chromosome 22 as a model

Maido Remm and Andres Metspalu
Current Opinion in Chemical Biology 6:24–30 (2002)

Technology and genetics have advanced to the point where genotyping thousands of individuals at thousands of marker locations around the whole human genome is possible. The whole-genome scan for detection of complex disease genes is a widely discussed topic. We review some of the recent high-density genotyping experiments and discuss related details, particularly the extent and variability of linkage disequilibrium. We also discuss the quality of single nucleotide polymorphisms.
(SNPs) in public databases and its consequences to the number of SNPs required for large-scale genotyping projects.