Biostatistics 1 Exam – Part 2, October 2014 Reference number: BIOSTATISTICS I: Introduction for epidemiologists, EXAM (part 2) Thursday 9th October 2014 09.00-11.00 Please write (PRINT) your name on this page only. (For the purpose of blinding, this front page will be separated during the grading of the exam.) Name: ……………………………………………………. Swedish personnummer: ………………………………… Reference Number: Please write the reference number on each page of the exam. Return your A4 page of hints and any other work with this exam script Good Luck! 1 Biostatistics 1 Exam – Part 2, October 2014 Reference number: Remember to write the reference number of your exam on each page of the exam; do not write your name. Please provide answers briefly and only in the space provided. When submitting this exam script, include your A4 page and any other pages showing your calculations. Q1 (12 points) In the paper “Is intestinal biopsy always needed for diagnosis of celiac disease” (Scoglio et al, Am Jour. of Gastroenterology, 2003), Figure 1 (below) describes a study of 181 patients undergoing biopsy for suspected celiac disease, 134 of whom were confirmed as celiac disease and 47 confirmed as not having celiac disease. Patients also had two serological tests (i.e. blood tests), one called TGA and one called AEA. From the last row in the Figure and using the biopsy result as gold-standard, complete the following for the AEA test: a) False positive rate: ________ (2 points) b) Sensitivity: _________ (2 points) c) PVP (Predictive value of a positive test: ____________ (3 points) d) If the two serological tests are combined and a patient diagnosed positive only if both tests are positive, then what is the i) Sensitivity: ________ (3 points) ii) Specificity: ________ (2 points) 2 Biostatistics 1 Exam – Part 2, October 2014 Reference number: Q2 (10 points) In 1867, Joseph Lister investigated the possible benefits of using carbolic acid as an operating room disinfectant. The following 2X2 table summarises the outcome of 75 amputations that he performed, where carbolic acid was used in 40 of these operations: Patient Survived Carbolic Acid Yes No Total Yes 34 6 40 No 19 16 35 Total 53 22 75 Grand Total (b) Compute the expected frequencies if there is no association between carbolic acid and survival and write these frequencies in parentheses in the cells of the table (3 points) (c) Conduct a significance test to see if there is a relationship between carbolic acid and survival: i) What Chi Square value do you get? __________ (3 points) ii) Provide an interval for the p-value using the tables on last page (____< p <_____) (2 points) iii) What do you conclude? ______________________________________(2 point) Q3. (10 points) A study was conducted in Uganda to estimate how delay in taking an infant to clinic affected the risk of them having symptoms that were consistent with both malaria and pneumonia (overlapping symptoms). Infants were categorised by age (1 = Up to 1 year, 2 = 1 to 2 years, 3 = Above 2 years). Stata gave the following output: . tab overlap agecat | agecat overlap | 1 2 3 | Total -----------+---------------------------------+---------- 0 | 1,031 555 363 | 1,949 1 | 649 283 142 | 1,074 -----------+---------------------------------+---------- Total | 1,680 838 505 | 3,023 . tabodds overlap agecat,or --------------------------------------------------------------------------- agecat | Odds Ratio chi2 P>chi2 [95% Conf. Interval] -------------+------------------------------------------------------------- 1 | 1.000000 . 2 | 0.810042 5.66 0.0173 0.680784 0.963841 3 | 0.621435 18.57 0.0000 0.499502 0.773133 --------------------------------------------------------------------------- Test of homogeneity (equal odds): chi2(2) = 20.29 Pr>chi2 = 0.0000 Score test for trend of odds: chi2(1) = 20.25 Pr>chi2 = 0.0000 3 Biostatistics 1 Exam – Part 2, October 2014 Reference number: (a) For any one of the age categories, show how the reported odds ratio was calculated from the numbers in the table (2 points). (b) Without doing any calculations, explain whether the Stata output provides evidence of an association between age and overlapping symptoms. ( 2 points) ________________________________________________________________________ (c) Compared to age category 1, explain whether there is evidence of a significant effect of (i) age category 2 ______________________________________________ (ii) age category 3 ________________________________________________ (2 points) (d) Is there evidence of a different OR for age categories 2 and 3 (vs. age-category 1). Explain. (2points) (e) Is there evidence of a trend with age: if not, explain why; if yes, explain the trend in words. (2 points) 4 Biostatistics 1 Exam – Part 2, October 2014 Reference number: Q4 (12 points) In the paper “Breast cancer incidence, case-fatality and breast cancer mortality in Danish women using hormone replacement therapy – a prospective observational study” (Int. Journal of Epi, 2005), Stahlberg et al report the number of breast cancer cases among HRT users and non-users in the Danish Nurse Cohort. From the information presented in the first two columns of Table 1at the bottom of this page, complete the following table: (a) Complete the following table: (3 points) HRT use Breast cancer Non-cases Total cases never past current (b) Calculate the crude OR of breast cancer among the current HRT-users, with the never-users as the reference group. (3 points) (c) Comparing your result in (b) with the published hazards ratios (HR), is there evidence of confounding? Explain why/why not. (3 points) _____________________________________________________________________________________ ______________________________________________________________________________________ (d) Explain whether the published study provides evidence that breast cancer risk is associated with a. Previous use ______________________________________________________ b. Current use: ______________________________________________________ (3 points) 5 Biostatistics 1 Exam – Part 2, October 2014 Reference number: Q5 (12 points) The following excerpt is taken from Table 2 of “Avoidance of sun exposure is a risk factor for all-cause mortality: results from the Melanoma in Southern Sweden cohort” (Jour of Internal Med, 2014) and reports the numbers of deaths among women with different sun-exposure habits. The score in the first column, which ranges from 0 to 4, is the number of “yes” answers to four questions regarding sunbathing. (a) Calculate the crude RR for exposure groups 1-2, using the non-exposed (group 0) as reference. RR (group 1-2):_________ (3 points) (b) State in words your interpretation of the RR value in (a): ______________________ __________________________________________________________________ (2 points) (c) The footnote in the table states that the estimates have been adjusted for a number of factors. Is there evidence that there was confounding by one or more of these factors? Explain. _____________________________________________________________________________ __________________________________________________________________ (4 points) (d) Is it more plausible to consider the variable “co-morbidity” (in the footnote) as a confounder, mediator or collider? Sketch a simple DAG to support your argument. (3 points) 6 Biostatistics 1 Exam – Part 2, October 2014 Reference number: Q6 (12 points) The table below reports the number of prostate cancers and the total person-time for French men aged 65 and older in 1979-1981 and in 1994-1996. (a) Calculate the age-specific incidence in each age group for 1979-1981 and write these values in the column provided in the table (state the units clearly). (4 points) (b) Apply the 1979-1981 incidence rates to the 1994-1996 population to find the expected number of prostate cancers in the rates had not changed during this time. (4 points) (c) If you learned that the total number of prostate cancers actually recorded in 1994-1996 was 26084, express this as a SIR relative to 1979-1981 (2 points) (d) Without performing any further calculations, show how you would construct a 95% confidence for the SIR in (c) (2 points) 1979-1981 1994-1996 Age Person- Prostate Incidence Person years cancers years 65-69 2,970,000 2021 3,764,000 70-74 2,640,000 3924 3,177,000 75-79 1,886,000 5297 1,659,000 80-84 985,000 4611 1,347,000 85+ 478,000 3273 1,003,000 7 Biostatistics 1 Exam – Part 2, October 2014 Reference number: 8 .