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POPH90014 Epidemiology 1: Assignment 1 Answer

Epidemiology 1 (POPH90014)


Assignment 1

Word limit:1500 words.  

You are permitted to exceed this count by 150 words.  If your assignment is longer than 1650 words, you will be penalized 10% for every 150 words you exceed it by.  For example, if your assignment is 1700 words, you will be penalized 10%, and if it is 2000 words, you will be penalized 30%.
Please include a word count.  
Some of the questions below tell you what not to include in the word count.  If a question has no such instructions, then include its answer in the word count.
Do not include any graphs or figures in your word count.

Notes on completing this assignment:

  • Create a new document.  Do not include a cover page and do not put your name on your assignment.
  • Don’t repeat the questions in your completed assignment.  Just number each answer.
  • Answer the questions in order.
  • Use 12-point font except in Table 1, where you should use 10-point.
  • For questions that require calculation, show formulae and all your working unless otherwise instructed.
  • Your answers should be brief.  You can use dot points where appropriate.
  • We use “contingent” marking, which means that if your answer to a question is wrong, we do not deduct marks for subsequent answers that make use of the first answer.
  • There is no need to cite the Victorian Cancer Registry, the ABS or the Global Cancer Observatory.

This assignment is about cancer of the cervix uteri (which we will refer to as cervical cancer), which is almost exclusively due to infection by certain types of the human papilloma virus (HPV).  Most HPV infections clear quickly, but some persistent infections can lead to the development of cervical cancer.

In 2007, Australia was the first country to introduce a vaccine to prevent HPV infection.  You can read about the vaccine here.  Using a combination of the vaccine and screening for HPV, the World Health Organization has set a goal to eliminate cervical cancer.

For the first part of the assignment, you will perform calculations using data on cervical cancer incidence from 2009-2013 obtained from the Victorian Cancer Registry. The Registry records details of all cancers diagnosed in Victoria.

We wish to compare incidence by an area-based measure of social disadvantage. The Australian Bureau of Statistics uses census data to construct indices of social disadvantage.  One of these, which we use here, is called the Index of Relative Social Disadvantage (IRSD). 

Table 1 shows data on number of cases of cervical cancer by quintile of social disadvantage.  We have restricted the table to the most and least disadvantaged quintiles and to women 25 years or older because there were few younger cases.

Table 1:Cervical cancer in Victoria from 2009-2013, by age and area-based quintile of social disadvantage.

Age
Quintile of Social Disadvantage
Rate ratio
Rate difference2
Most1

Least
Cases

Incidence Rate2

Cases

Incidence Rate2
25-34
33



31




35-44
48



33




45-54
42



30




55-64
34



24




65-74
26



13




75+
21



12




All ages3
204



143




Most disadvantaged quintile and least disadvantaged quintile

Per XXX

All ages 25+

The population data necessary to calculate the rates are given in Table 2.

Table 2:Female population in the most and least disadvantaged areas in Victoria, by year.

Age
2009
2010
2011
2012
2013

Most
Least
Most
Least
Most
Least
Most
Least
Most
Least
25-34
73296
87113
75387
88547
77392
89806
78290
93528
79410
97381
35-44
69918
89560
69476
90258
68981
90469
68885
91739
68536
92768
45-54
69216
81612
69195
82975
68844
83718
68621
84746
68787
86577
55-64
62901
62829
63782
64781
65286
65993
65473
67057
66327
68309
65-74
48222
35659
49566
37052
50688
38722
53219
41369
54920
43750
75+
53646
36750
55184
36690
56233
36620
57807
36293
59308
36587
All ages
377199
393523
382590
400303
387424
405328
392295
414732
397288
425372

Source: Australian Bureau of Statistics, custom table.

  1. Of the two measures of incidence –incidence rate and incidence proportion –incidence rate is the correct measure to use for these data.  Why? [1 mark]

[8 marks]

Do not include the answer to this question in the word count.

a. Copy Table 1 and paste it into your assignment answer document.  Fill in the blanks in the Table.

The denominators for the rates should be included in the columns immediately to the right of the “Cases” columns; these columns currently have no heading – you should add the correct heading. 

Add the unit for the incidence rates to the footnote (i.e., replace the XXX).  

Refer to the Canvas material on “Number of decimal places to report” when presenting the rates, rate ratios and rate differences.  

You are encouraged to use a spreadsheet program such as Microsoft Excel for the calculations. You can also use statistical software such as Stata or R if you wish.

For the rate ratios and rate differences, use the incidence rates for the least disadvantaged quintile as the reference.  

b) Below the table, show your full working for the incidence rate for women aged 25-34 in the most disadvantaged quintile.  

3. Which group had the higher incidence rates: women living in the most disadvantaged areas or women living in the least disadvantaged areas?[1 mark]

4. Describe the patterns of age-specific rates separately for the most and least disadvantaged women. 
You might find this easier if you draw a graph showing the age-specific rates.  If you choose to draw a graph, it will not be assessed, and you will not be penalised for not drawing a graph.[3 marks]

5. Describe and compare the patterns in the age-specific rate ratios and age-specific rate differences.  
Drawing graphs of the age-specific rate ratios and rate differences might help you see the patterns better, but the graphs will not be assessed.
 [4 marks]

6. We wish to use the rate differences to compare the rates for the most and least disadvantaged women.  What information would we lose if we ignore the age-specific rate differences and only use the crude rate difference (i.e., the all ages rate difference)? [2 marks]

7. Calculate the risk that a woman who was 25 years old in 2009 and living in the most disadvantaged areas would have been diagnosed with cervical cancer within 5 years.  Describe this risk in a sentence. Include only the sentence in your word count.[5 marks

8. What proportion of cervical cancer among the most disadvantaged women could have been prevented if they had the same incidence rate as the least disadvantaged women? Use the crude (i.e., all ages) rates in your calculation for this purpose.  Describe the result in a sentence. Include only the sentence in your word count.[3 marks]

Until 2017, women in Australia were recommended to have a Pap smear every two years as part of Australia’s national screening program for cervical cancer.  Examination of Pap smears identifies abnormalities of the cervix before they became cancer; treatment of these abnormalities prevents them from progressing to cancer.  It has been a very successful program.  (In 2017, Australia changed to five-yearly screening using a test to detect HPV infection.)

9. Figure 1 shows participation in the screening program in Victoria by quintile of social disadvantage.  In no more than 60 words, describe the association between level of social disadvantage and participation in the screening program and discuss whether this might account for some of the differences in incidence rates of cervical cancer by level of social disadvantage.  (Ignore differences in the time periods between Figure 1 and Table 1.)[4 marks]

Figure 1: Participation in cervical screening program in Victoria, 2006-2008, by quintile of social disadvantage.

Source: Victorian Cytology Service, Victorian Cervical Cytology Registry, Statistical Report 2011 (https://www.vcs.org.au/wp-content/uploads/2019/07/Statistical_Report_2011.pdf). Accessed 17 February 2020

10. You work in the cancer prevention section of the Victorian Department of Health and Human Services.  The Minister has asked for a 100-word briefing on socioeconomic disadvantage and the incidence of cervical cancer, and what can be done to reduce the inequality.  Write a summary to present to the Minister.[5 marks]

11. Based solely on the data used for Question 2 and your calculations for that question, can you conclude that social disadvantage causes cervical cancer? Explain your answer. 
[2 marks]

Smoking and cervical cancer

12. Smoking increases the risk of developing cervical cancer.  The rate ratio from cohort studies is 1.5.  About 15% of Australian women smoke cigarettes.  Calculate the proportion of cervical cancer in Australia that can be attributed to smoking cigarettes. Write a sentence describing your result. 
Include only the sentence in your word count.[3 marks]

13. Smoking makes it easier for women to become infected with HPV and when infected, for the infection to persist for a long time, which in turn leads to increased risk of cervical cancer.  Using only the information given in this question, does HPV infection confound the association between smoking and risk of cervical cancer? Should you adjust for HPV infection when assessing the association between smoking and cervical cancer? 
Explain your answer. Draw a DAG illustrating the relationships. [4 marks]

This part of the assignment is about the descriptive epidemiology of cervical cancer globally. The questions make use of data from the International Agency for Research on Cancer.  The data are held in the Global Cancer Observatory, which is an interactive web-based platform presenting global cancer statistics to inform cancer control and research.

The website is:  https://gco.iarc.fr/

Click on the Cancer Today button.

Use the map function

Use all age groups. Under cancer sites, select cervix uteri.  (Under indicators ASR = age-standardized incidence rates).  The word “World” means that the rates are standardised to the age distribution of the (hypothetical) world population. The age distribution is shown later in this document.

14. What region of the world stands out as having several countries with the highest age-standardized incidence rates of cervical cancer (( 26 per 100,000 person years)?  What regions have the lowest age-standardized incidence rates (i.e., < 7.3 per 100,000 person years)?  You can loosely think about these regions of the world: Australia and New Zealand, Western Europe, North America, Central and South America, Sub-Saharan Africa, the Middle East South and South East Asia, China.[3 marks]

15. Is the pattern generally similar for age-standardized mortality rates across regions of the world?[1 mark]

16. What are the crude and age-standardized rates for Uganda?[2 marks]

17. Use the sunburst function to display incident cases for cervical cancer.  As an epidemiologist, explain why this nice-looking figure can be misleading?  [2 marks]

18. Use the scatterplot function to plot the age-standardised incidence rates for cervical cancer (Y axis) against the Human Development Index (X axis).  (You can find information about the Human Development Index here.)  Paste the chart into your assignment.  Tools to download the chart are on the right of the plot.  Describe the relationship between the Human Development Index and the age-standardised incidence rate of cervical cancer in one sentence.[3 marks]

Click on the Cancer over time button.  

Use incidence data for the next two questions.

19. Perform an online analysis of “time trends” for these countries: Uganda Kampala, Brazil, USA, SEER 9 White, China 5 registries, India Chennai, Japan Miyagi, Italy 8 registries, UK England, and Australia Victoria.  Copy the graph and paste it into your assignment.  Describe the trends in no more than 70 words.[5 marks]

20. Now perform an online analysis of age-specific curves for Uganda Kampala, Brazil, USA, SEER 9 White, China 5 registries, India Chennai, Japan Miyagi, UK England, and Australia Victoria for the period 2010-12.  (It allows you to select multiple years by holding down the control key in Windows (command key on a Mac) and clicking the three years.)  
Copy the graph and paste it into your assignment.  (Right click the image, then click Copy Image, then go to your assignment and Paste it into your document.)
Describe the shape of the curves in no more than 70 words.[5 marks]

The figure below shows the Population Pyramid for Uganda in 2012 and for the World Standard Population (Std) used for the age standardisation.

Percentage of Population in Each age group

21. Explain why the crude and age-standardised incidence rates are so different for Uganda. You will need to refer to your answers to questions 16 and 20 to answer this question. Which measure is preferable when comparing rates across countries and why?[4 marks]

22. The crude rate for Victoria in 2012 was 7.4 per 100,000 person years and the age-standardised rate was 5.7 per 100,000 person years. What feature of the age-specific rates for Victoria contribute to the much smaller difference between the crude and age-standardised rates for Victoria than you saw for Uganda? 
 [2 marks]

Number of cases of any type of cancer due to HPV infection

You need to hunt on the website yourself for these data.  

23. How many cancer cases in 2018 does the International Agency for Research on Cancer state were due to human papilloma virus?[1 mark]

Quality of the data

24. What does IARC say about the quality of the data?  Which type of countries have lower quality data? [You might need to hunt to find this information on the website]
 [1 mark]

25. As mentioned in the introduction, the World Health Organization has a goal to eliminate cervical cancer.  In which parts of the world do the greatest challenges to elimination exist?  Draw on previous answers.  You can also draw on other sources to answer this question. Justify your answer.[6 marks]

Answer

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