Clicker Question 1 Severe Malaria Case Trait Population Control Control Trait

Clicker question 1 severe malaria case trait

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Clicker Question #1??? Severe Malaria (Case: Trait +) Population Control (Control: Trait -) 251 313 1 33 (A) 313 (C) 125 (D) 33 (E) 1 126 malaria “cases” : 125 AA and 1 AS 173 population “controls” : 140 AA and 33 AS
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Odds Ratio Step 4. Calculate the odds ratio Total alleles a + c b + d P(exposure to one allele) P(exposure to alternate allele) Odds Ratio of Allele 1 = ad/bc P(exposure to one allele) P(exposure to alternate allele) a/(a+c) c/(a+c) b/(b+d) d/(b+d) = (a/c) (b/d) =
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4/17/18 10 19 Case: Trait + Control: Trait – Exposure + (Allele 1) a b Exposure – (Allele 2) c d Step 4. Calculate the odds ratio Total alleles a + c b + d Odds Ratio of Allele 2 for the Trait = cb/ad The OR for 1 allele, is just 1 over the OR for the other allele You may be asked to calculate for 1 allele or another, and for presence or absence of a trait a b c d Akerman et al. (2005) Annals of Human Genetics 69, 559-565 20 Odds ratio = ad/bc = (251*33)/(1*313) = 26.46 Step 4. Calculate odds ratio to measure impact of the allele Severe Malaria Population Control Number of A alleles 251 313 Number of S alleles 1 33 Severe malaria cases are ~26 times more likely to carry the A allele than the population controls Conversely, severe malaria cases are 26 times less likely to carry the S allele than the population controls (Odds ratio would be 1/26.46 or 0.04
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4/17/18 11 Step 5. Calculate the chi-square statistic 5a. Calculate the frequency of each allele in the population as a whole Total allele number = 564 “A” + 34 “S” = 598 alleles For whole population: f(A) = 564/598 = 0.943 f(S) = 34/598 = 0.057 (OBSERVED) Malaria (OBSERVED) Control Number of A alleles 251 313 Number of S alleles 1 33 564 34 598 21 Step 5. Calculate chi-square statistic to measure significance of result: 5b. Calculate expected values for allele numbers f(A) = 0.943 f(S) = 0.057 For expected numbers, assume the allele frequencies are the same in both groups (i.e. cases and controls). The expected allele number is the the population allele frequency times the total number of alleles in each group 22 Malaria Control Number of A alleles O: 251 O: 313 Number of S alleles O: 1 O: 33 E: 252*0.943 E: 252*0.057 E: 346*0.943 E: 346*0.057 252 346
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4/17/18 12 Step 5. Calculate chi-square statistic to measure significance of result: 5c: Calculate the final statistic 23 Malaria Control Number of A alleles O: 251 O: 313 Number of S alleles O: 1 O: 33 E: 238 E: 14 E: 326 E: 20 ! ! = ( ! ! ) !
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  • Spring '19
  • hoekstra
  • Genetics, vivax malaria

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