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Unformatted text preview: Sketch out a genealogy for this sample. The E-M Algorithm 1. In a study of the ACE gene, an Alu insertion deletion (I/D) and a nearby C/T single nucleotide polymorphism were genotyped in randomly sampled individuals. The following genotypic counts are found: C/C C/T T/T I/I 25 I/D 40 10 D/D 15 10 a) Describe the E-M procedure for estimating two marker haplotype frequencies, including relevant equations. b) Use the E-M algorithm to estimate haplotype frequencies p IC , p IT , p DC and p DT for the two markers. c) Compare the likelihood of the observed counts assuming linkage equilibrium between markers and using the haplotype frequencies estimated by E-M. Comment on your result. d) Estimate D and for this marker pair. e) Is there evidence for ancestral recombination between the I/D polymorphism and the C/T mutation in this population? Would the I/D polymorphism be a suitable surrogate for the C/T SNP in an association study?...
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This note was uploaded on 12/26/2011 for the course BIO 666 taught by Professor Staff during the Fall '06 term at University of Michigan.
- Fall '06