Universal Genetic Testing For Women With Newly Diagnosed

Assignment Task

A. This question relates to the following table extracted from an article by De Silva et al. entitled ‘Universal genetic testing for women with newly diagnosed breast cancer in the context of multidisciplinary team care’ published in the Medical Journal of Australia in 2023. Provide your answers to three decimal places. 

1. Use hand calculations to estimate the odds of having the pathogenic variant identified in those with a family history of breast cancer and the odds of having the pathogenic variant identified in those without a family history of breast cancer.

• The odds of having the pathogenic variant identified in those with a family history of breast cancer: (18/474) x 100 = 3.79% = 3.8%
• The odds of having the pathogenic variant identified in those without a family history of breast cancer: (11/474) x 100 = 2.32% = 2.3%

2. Using your results from (a) or otherwise:

• Calculate the pathogenic variant odds ratio and 95% confidence interval, that compares those with and without a family history of breast cancer. Provide an interpretation of these.

3. The pathogenic variant odds ratio:

• Perform a test that compares the odds of having the pathogenic variant in those with and without a family history of breast cancer. Ensure to state your hypotheses tested, your p-value and a conclusion. Is the p-value compatible with the confidence interval calculated in part (i)?

B. Use SPSS and the file bsn81.sav, together with hand calculations if needed, to produce the requested output and answer the following questions. Provide your answers to three decimal places.

i. The FEV/FVC (Forced Expiratory Volume/Forced Vital Capacity) ratio is a measure frequently used in the diagnosis of obstructive and restrictive lung disease. It is calculated by dividing the forced expiratory volume in the first one second (FEV) by the forced vital capacity (FVC) of the lungs. Calculate the FEV/FVC ratio and name it FEVFVCRatio (using Transform > Compute Variable). Produce a histogram that displays the distribution of this ratio and comment on the characteristics of the distribution of this ratio.

ii. Produce a scatterplot of FEVFVCRatio against AGE and calculate an appropriate statistic that quantifies the relationship between these two variables. Provide a single sentence describing the relationship between these two variables.

iii. Obtain the one-way ANOVA and appropriate post-hoc t-tests for comparing mean FEVFVCRatio across SMOKING groups (as a categorical variable). Present relevant output from SPSS and comment on the overall and pairwise tests and make a conclusion about differences in means based on this analysis (including pairwise estimates).

iv. Fit a multiple linear regression model (including main effects only) investigating the relationship between FEVFVCRatio and SMOKING (as a fixed factor) after adjusting for AGE (as a covariate) and SEX (as a fixed factor). Based on this model, provide an interpretation of the relationship between FEVFVCRatio and SMOKING, interpreting the estimates and 95% confidence intervals for the (adjusted) differences in means between the SMOKING groups. Include relevant SPSS output.

v. Are AGE and SEX confounders of the relationship between FEVFVC Ratio and SMOKING? Provid e an explanation using your analysis output/results.

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