1. STANDARD Color-blindness (from Feller, Ch.5, Ex. 7). Let us assume that the frequencies of color-blindness are 5% and 0.25% of in men and women, respectively. What is the chance that a given color-blind person is a man?
2. STANDARD Let in population there are 2 alleles, M and N. Frequency of M, P(M)=0.1 Penetrances (conditional probability of having disease given genotype) are P(D|MM)=0.4, P(D|MN)=0.1, P(D|NN)=0.03.
   1. What is disease frequency in the population?
   2. What is frequency of mutant allele, M, in disease cases?
   3. What is frequency of mutant allele, M, in healthy people?
   4. What is the relative risk in carriers (versus population risk)?
   5. What is the relative risk in carriers (versus non-carrirs)?
3. A SNP has 2 alleles, G and A. The frequency of A is 0.2. HWE holds for the locus, however, calling occures differentially, e.g. 100% of AA genotypes are called, while among AG 5% of genotypes are not identified (fropped as missing) and among GG, 20% are not called.
   • STANDARDCompute genotypic frequencies resulting from such experiment.
   • STANDARDIn scored (called) data, what would be the expected genotypic frequencies under HWE?
4. HIGH Consider a SNP with alleles A and T, and a disease locus with alleles D and N. In a population, frequency of A-D haplotype is 0.07, frequency of A-N is 0.13, frequency of T-D is 0.03 and frequency of T-N is 0.77.
   1. STANDARD What is the frequency of the T allele?
   2. STANDARD What is the frequency of the D allele?
   3. STANDARD Is there linkage equilibrium between the SNP and the disease locus?
   4. STANDARD Assume that penetrances of genotypes DD, ND and NN are 0.55, 0.1 and 0.05. What is the disease frequency in the population?
   5. HIGH What is the probabilty of the disease in a person having SNP genotype (a) TT (b) AT (c) AA?