A second-generation combined linkage-physical map of the human genome. F. Chen1, C. He1, X. Kong1, W. Chen2, M. Hansen4, F.L. Hyland3, G.C. Kennedy2, S. Murray4, Y. Turpaz2, F.M. De La Vega3, J. Ziegle3, T.C. Matise1. 1) Genetics Dept, Rutgers Univ., Piscataway, NJ; 2) Affymetrix, Inc., Santa Clara, CA; 3) Applied Biosystems, Foster City, CA; 4) Illumina, Inc., San Diego, CA.
Accurate and comprehensive linkage maps are critical for the success of positional cloning projects and other genetic studies. We have constructed a second generation high-resolution genetic map that includes a much larger set of polymorphic markers (N=28,219) than the first version and is consistent with the latest genome assembly (NCBI Build 36). To build the new combined linkage-physical map, a set of SNP genotype data including 5,172 SNPs from the Affymetrix Human Mapping 10K Array, 3,506 SNPs from the Applied Biosystems SNPlex Human Linkage Mapping Set 4k, and 4,782 SNPs from the Illumina Linkage IV Panel were collected and integrated into our existing data set (N=14,759). In the initial mapping stage, only markers with known physical positions were used and were added to the map only if the results of linkage analysis were consistent with physical position. Markers with no physical position were added in later steps using only linkage information. The data were also cleaned by removal of genotypes that are likely to be erroneous, identified as those that lead to close double-recombination events. Then markers whose linkage positions did not originally match physical position were re-evaluated against the more complete map. Finally, Those markers which still had discordant positions were assigned to map intervals determined by linkage analysis. This map represents the most comprehensive linkage map ever constructed. The average map resolution is 0.17 cM (127kb) between neighboring markers, with 58 percent of neighboring markers showing no recombination events. This map is a valuable tool for obtaining map distances for linkage studies to identify genetic loci. It is disseminated via our MAP-O-MAT website (http://compgen.rutgers.edu/mapomat).