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Mixing Different SNP Densities

Mixing Different SNP Densities. New Haplotyping Program findhap.f90. Begin with population haplotyping Divide chromosomes into segments List haplotypes by genotype match Similar to FastPhase, IMPUTE (Kent) End with pedigree haplotyping Detect crossover, fix noninheritance

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Mixing Different SNP Densities

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  1. Mixing Different SNP Densities

  2. New Haplotyping Programfindhap.f90 • Begin with population haplotyping • Divide chromosomes into segments • List haplotypes by genotype match • Similar to FastPhase, IMPUTE (Kent) • End with pedigree haplotyping • Detect crossover, fix noninheritance • Impute nongenotyped ancestors

  3. Haplotyping Tests – Real Data • Half of young animals assigned 3K • Proven bulls, cows all had 50K • Dams imputed using 50K and 3K • Half of ALL animals assigned 3K • Could 3K CDDR genotypes help? • 10,000 proven bulls yet to genotype • Should cows with 3K be predictors?

  4. Correlations of 3K and PA with 50KHalf ofYOUNG animals had 3K PTA, half 50K PTA

  5. Using 3K as Reference Genotypes Half ofALL animal NM$ were from 3K, half 50K

  6. Simulated 500K Genotypes • Linkage in base population • Similar to actual linkage reported by: • Villa-Angulo et al, 2009 BMC Genetics 10:19 • De Roos et al, 2008 Genetics 179:1503 • Underlying linkage corresponds to D’ • Three subsets of mixed 50K and 500K: • Only 1,586 (young) of 33,414 had 500K • Also bulls > 99% REL, total 3,726 • Also bulls > 90% REL, total 7,398

  7. Results from 500K Simulation

  8. Polygenic Effect and DGV • Should direct genomic value (DGV) include the polygenic effect? • CAN, FRA, and NLD include it • USA DGV includes only SNP effects • Advantage: DGV would contain all genetic variance • Disadvantage: Polygenic effects of clones differ (treated as full sibs)

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