10cM Linkage Mapping Set v2 ABI

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Genome Coverage 400 Microsatellite markers
Dec 2002 Golden Path
Blue STR from CIDR panel Black Gaps
10cM - Linkage Mapping Set v2 ABI Median
intermarker distance 4.7 Mb Mean intermarker
distance 5.6 Mb Mean genetic gap
distance 8.9 cM Average Heterozygosity
0 .76
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Genome Coverage 11,555 SNPs
Dec 2002 Golden Path
Red at least 1 SNP per 100 kb Black Gaps
10K SNP Array - Affymetrix Median intermarker
distance 105 kb Mean intermarker distance
210 kb Mean genetic gap distance 0.32
cM Average Heterozygosity 0 .37
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Mapping Array Applications

• Genetic Linkage
• Loss of Heterozygosity
• Genetic Epidemiology
• Linkage Disequilibrium Mapping
• Association (100K 500K)
• DNA Copy Number Determination

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Candidate-gene VS whole-genome SNP association
studies
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Factors to be considered

• Marker informativeness - allele frequencies
• Distance between adjacent SNPs
• Location with respect to exons or regulatory
  elements
• Non-coding or coding
• Local linkage disequilibrium
• Haplotype tagging SNPs

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HapMap Project
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