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Filling missing genotypes using haplotypes

Filling missing genotypes using haplotypes. Haplotypes. The DNA content of the individual gametes that formed the individual Phasing – process of decomposing a genotype into its constituent haplotypes FastPhase does not use pedigree

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Filling missing genotypes using haplotypes

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  1. Filling missing genotypes using haplotypes

  2. Haplotypes • The DNA content of the individual gametes that formed the individual • Phasing – process of decomposing a genotype into its constituent haplotypes • FastPhase does not use pedigree • Paul VanRaden developed method that starts with the Gengler estimated gene contents

  3. How it works • The algorithm is iterative • Like an animal model, sums information from parent, progeny, and mate genotypes • The amount of information is in the denominator and direction of linkage in the numerator • Other haplotyping algorithms multiply probabilities and are based on likelihoods • Paternal or maternal origin is detected from observed or estimated parent genotypes

  4. How it works (cont.) • Missing genotypes are determined from parent, progeny, and mate genotypes at the same locus or at any nearby locus that is more informative.

  5. Simulation • 17,015 Holsteins • 1,479 Jerseys • 713 Brown Swiss • 1 Chromosome, 1000 SNP • Checked • Linkage – consecutive SNP • Parental assignment

  6. Simulation (Cont.) • Genotypes, linkages, and haplotypes were also estimated for: • 63,381 Holstein • 15,176 Jerseys • 3,969 Brown Swiss • 1,361 Holstein had call rate > 90% • Mostly dams of genotyped animals

  7. Accuracy • Estimates of genotype or haplotype accuracy needed with real data, true values are not available for comparison • The most popular sires and dams had 100% correctly called linkages and paternal alleles • Animals with fewer close relatives had somewhat fewer correct calls. • For each heterozygous marker, paternity correct if the allele identified as from sire actually was • Linkage correct if estimated phase matched true phase for each adjacent pair of heterozygous markers.

  8. Holstein Correct calls

  9. Low density panel • Success rate already sufficient to implement low-density genotyping methods of Habier • Correlations about 0.91 whether true or estimated haplotypes were between low & high density EBV

  10. Implications • Method for haplotyping large dairy populations available • Programming for X chromosome not yet done • Increased benefit form accurate mapping of SNP. • Will use UMD3. Some SNP still without location • Can impute missing parent genotypes to increase predictor population and confirm parentage

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