# Problem Set 1 Answers - Genetics 202 Problem Set One Answer...

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Genetics 202 Problem Set One Answer Key (40 points total) Problem 1: Which sized allele appears to segregate with the phenotype in this pedigree? (2 points) The 202 bp allele segregates with the disease phenotype. Making simple parametric assumptions, calculate the LOD score to determine whether there is statistical evidence of linkage between this SSRP and the phenotype. You can exclude the 2 individuals, for whom the other parent’s genotype isn’t available when doing your calculation. (4 points) Since there are 14 fully informative meoises (after using individuals 1 and 3 to formulate the hypothesis that the 202 bp allele is linked to the craniosynostosis causing mutation), the equation for calculating the odds ratio is (1- θ ) 14 /(0.5) 14 , which will be maximum when θ =0 at 16,384, which gives a LOD = log 10 (16,384)=4.2 Who are the two individuals you’ll be excluding? (2 points) Since both parents are not available for individuals 4 and 7, these two individuals can be excluded. Briefly describe the assumptions you made when calculating the LOD score with respect to (10 points, 2 each) The penetrance of the phenotype. I assumed complete penetrance. The phenocopy rate for the phenotype. I assumed a very low phenocopy rate. The allele frequencies at the marker locus in the general population. Since I didn’t consider individuals for whom both parents weren’t available, and every other parent to child transmission is fully informative, I didn’t bother with knowing the frequency of the 202 bp allele in the general population. However, if I wanted to include individuals 4 and 7 in my calculation, I would have needed to include the probability that their unavailable parents carried the 202 bp allele.

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