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More About LOD Scores

More About LOD Scores. 2012. a) Relatedness. Backcross, F 2 , Recombinant inbred lines Humans: Need to be able to compare maps between groups Need suitable families for analysis - large, multigenerational. The Centre d'Etude du Polymorphism Humain (CEPH). Form P. Form Q. 1%. 99%. 15%.

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More About LOD Scores

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  1. More About LOD Scores 2012

  2. a) Relatedness • Backcross, F2, Recombinant inbred lines • Humans: • Need to be able to compare maps between groups • Need suitable families for analysis - large, multigenerational

  3. The Centre d'Etude du Polymorphism Humain (CEPH)

  4. Form P Form Q 1% 99% 15% 85% 42% 58% b) Viability (polymorphism)

  5. c) Maintenance

  6. d) Size

  7. The LOD Score Method

  8. What is the inheritance of the two traits? • Nail-patella syndrome - (affected individuals indicated by filled symbols) - dominant • Blood Type - A and B codominant and each dominant to O

  9. Is this cross informative? • Yes - the phase of the alleles at the two loci can be determined by examining the genotypes of the grandchildren. Note: information from the grandparents is useful in determining this.

  10. What type of cross is this? • Essentially a test cross  - AB Npnp x OO npnp (an individual heterozygous at both loci crossed to an individual homozygous at both loci)

  11. Are there any linkage associations evident? • Yes - alleles A and Np appear to be linked. Why? Because the 2 alleles are typically present in the same individuals.

  12. Are there any recombinant individuals in the pedigree? 1, noted by the asterisk in the figure. Why? He has the A blood type allele but is not affected with Nail patella.

  13. What is the percent recombination? • 1/8, or 12.5%

  14. THE LOD SCORE METHOD:

  15. Z ( ) = log [(1 -  )n-rr/ (1/2)n] Z () = (n - r) log [2 (1 -  )] + r log (2  )

  16. Z () = (n - r) log [2 (1 -  )] + r log (2  ) Z (0.1) = (8 - 1) log [2 (1 – 0.1)] + 1 log (2 * 0.1) Z (0.1) = (7) log [2 (0.9)] + (1) log (0.2) Z (0.1) = (7) log [1.8] + (1) log (0.2)

  17. Z q1 = LOD score based on q1 Z q2 = LOD score based on another recombination frequency q2 Z q3 = LOD score based on q3, etc.

  18. Calculating LOD Scores

  19. Z () = (n - r) log [2 (1 -  )] + r log (2  ) Z () = (18 - 3) log [2 (1 - )] + 3 log (2 )

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