Genetic Risk Factors for Heart Disease

Frequently Asked Questions:

Please check here frequently for updates.

1. February 26, 2008:

   In the subjects.txt data file, IDs 231 and 304 are missing a genotype each. We are told that missing data is denoted by a ‘.’, however these two rows (shown below) do not indicate that data is missing. 231 hifat F 36 31.1 2 0 GG 304 hicarb2 M 51 26.2 3 0 GG Since both SNPs have alleles A and G, we are unsure which of the two SNPs is missing its genotype.

   For both of these subjects, the genotype is missing for position 238.

   The data description indicates that the PUFA measurement is derived from the 3-day food records. Since this record was completed on multiple occasions both before the trial started and during the trial, we are wondering if the PUFA “during” measurement relates to one particular 3-day food record completion during the trial period, or if it is a summary over each of the times the 3-day food record was completed during the trial period. If so, would you be able to provide information about the type of summary measure (e.g. average over observed time points)?

   Subjects filled out 3-day food records twice before the clinical trial started, and then 5 times while on their dietary treatment (corresponding to the 5 on-treatment times when there were blood cholesterol measurements). The pre dietary measurements are averages of the 2 pre-trial food records, and the during dietary measurements are averages of the 5 on-treatment measurements.

   Could you describe a little bit about the locations of the recruiting centres? Are these large, ethnically diverse populations? Are they the same centres as given in the Fontaine-Bisson paper referenced on the case study webpage? Are the participants of different ethnic backgrounds? If so, is information available on ethnicity?

   The centres are Sherbrooke, Montreal, Toronto, London, Edmonton. Ethnicity was not recorded.

   In general, do the two references now given on the case study webpage describe the collection of the data we have been provided (ie, the recruitment of participants, the dietary intervention etc)?

   Yes. Both references and the case study involve analyses of data collected as part of the same clinical trial.

2. March 17, 2008:

   Does the week 0 in the Lipids data set match the ‘pre’ period in the Dietary data set? I.e. are the weeks 4,12,26,39,52 on the ‘during’ period?

   Yes. The pre measure in the dietary data set is the average of the results from 2 3-day food records (at week 0 and one week before that) and the during dietary measurements are the average of results from 3-day records taken during the year that they are on the dietary treatment (weeks 4, 12, 26, 39, 52 are weeks in that year)

   It looks like the diet treatment may be a counfounder, but not of main interest.

   I agree. The dietary treatments likely caused changes in PUFA (and other dietary components) which you can see by comparing the pre/during values in the dietary intake file.

3. April 14, 2008:

   The variable Statins indicates some patients took cholesterol-lowering medication. Is this before the clinical trial or during the trial?

   The patients who are indicated as taking statins were on the same dose throughout the entire period of the enrollment in the trial. The other patients took no statins during that period.

   We are not sure if haplotype analysis is the main interest. However, we didn’t find LD between the two SNPs, and we would like to know how far away the two SNPs are from each other and whether haplotype analysis is necessary.

   I think the SNPs are in the promoter region of the same gene, so they are quite close to one another. Haplotype analysis is not necessary, but might be interesting if there is something there.

4. May 12, 2008:

   References in the Fontaine-Bisson paper indicate that the -308A allele has been shown to have higher transcription rates of TNF-alpha, so that the AA and GA genotypes result in increased TNF-alpha production relative to the GG. This seems to contradict the information in the “Related Studies” section of the case studies web page.

   The case studies web page has an error (reduced/increased were transcribed) (now corrected on the page). Thank you for discovering it.

5. May 15, 2008:

   Do we need to submit our final report? Do we need to present during the case study session? If so, how long is our presentation and in what kind of form? E.g., present to all the participants or just to the judges? Is the evaluation only based on the poster if there is no presentation?

   Your posters will be up all day Monday. You only need to be with your poster during the scheduled session in the afternoon. Anyone interested will talk to you about your poster during that session and you can talk to each other to compare notes on methodologies used and results found. The judges will also ask you questions during that session. The evaluation is based on the poster; the questions are for clarification about the poster.