Question

3. Consider a disease that is affected by many risk factors, including genetics. In a genome- wide association study, researchers determined the genotype of 1000 affected individuals at 100,000 SNPs. They previously determined the genotypes of 10,000 random individuals at these SNPs, so they have good estimates of the allele frequencies in the general population. a. At a SNP on chromosome 4, the two alleles are A and C. The A allele has a frequency of 0.4 in the general population. What are the expected genotype frequencies in the general population? b. What is the null hypothesis about the genotype frequencies among the 1000 affected individuals? c. In the 1000 affected individuals, the following genotype counts are observed: АЛ. 154 AC: 502 CC: 344 Calculate the chi-square value, to describe the distance between these observations and your expected genotype counts. (This is easiest with a calculator. Show your work.) d. If chi-square values greater than 5.9 correspond to p-values less than 0.05 in this case, can we conclude that the SNP is significantly associated with the disease?

Answer 1

Please look in the image for solution.