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by: Samanta Aufderhar


Samanta Aufderhar
GPA 3.93


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Class Notes
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This 5 page Class Notes was uploaded by Samanta Aufderhar on Wednesday September 9, 2015. The Class Notes belongs to PHG 518 at University of Washington taught by Staff in Fall. Since its upload, it has received 25 views. For similar materials see /class/192363/phg-518-university-of-washington in Public Health Genetics at University of Washington.

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Date Created: 09/09/15
PHG 518 Exercise on Power In Class May 22 2008 Each person in the class is an independent PI on projects that are investigating the association of the risk of depression and gene X identi ed by a single biallelic tagSNP Each study is identi ed by a letter AJ To assess an overall genotypic association each PI compared the null model without the exposure the genotype classes for gene X with the genetic model additive model for the genotypes of gene X The likelihood ratio test comparing the likelihoods of these two models ie Chisquared test statistic with 1 degree of freedom was noted along with the pvalue associated with this test You look at a table with the following thresholds for a chisquared dfl test against the given type I error A Is your study a positive nding for a type I error at 005 0001 What did you compare to answer this question B Now we ask the PI s to release their ndings at type I error 005 Observed Positive finding Observed Negative finding at type I error 0001 Observed Positive nding Observed Negative finding C However we do not know whether these observed ndings were actually the truth Let s pretend that the following is the truth in theory Note we would never know this as fact in practice Now fill in the tables below Observed Positive Observed What is the estimated power for the above table at type I error 005 What is the accuracy of the type I error for the table how does it compare to a type I error 005 What is the estimated power for the above table at type I error 0001 What is the accuracy of the type I error for the table how does it compare to a type I error 0001 What would make my power estimates and type I error comparisons more reliable EPI518PHG 518 LD and Haplotype Inference In Class Exercise May 15 2008 Table 1 Haplotype and allele frequencies Locus 2 B b Locus 1 A 004 050 054 a 0 27 019 0 46 031 069 10 1 The table above provides hypothetical data showing allele and haplotype frequencies from a population sample a Using the notation presented in the slides state the values for pA pa pB pb pAB pAb p33 and pab forthis population sample b Describe in words what pA and pb represent 0 What is the most frequent haplotype in this sample The least frequent d Based on this data calculate D r and D between Locus 1 and Locus 2 2 Assume Locus 1 is the untyped disease causing SNP and Locus 2 is the SNP you are genotyping in your casecontrol study You have performed power calculations assuming that you had genotyped the disease causing allele These power calculations indicate a sample size of 500 cases and 500 controls Estimate the sample size you will actually need for your study Table 2 Genotype frequencies Locus 1 Geno types AA AT TT Total Locus CC 1077 427 46 1550 CG 409 170 13 592 genotypes 66 I 36 14 1 51 Total 1522 611 60 2193 3 Table 2 provides genotype data for 2193 individuals For example 1077 people were homozygous for the C allele at locus 1 and homozygous for the A allele at locus 2 a What is the allele frequency for the T allele at locus 1 b What is the allele frequency for the G allele at Locus 2 0 Based on the data in this table can you calculate the painNise LD between the the two loci lfyes do the calculations if no indicate what other information would you need


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