aj-grant
commented
2 weeks ago Hi Ange, Thanks for your message! Yes, the rint GWAS associations from the Neale lab were used. They were harmonised to be associated with increased BMI according to the Pulit results. The CHD associations should be the same as the CARDIOGRAMplusC4D results from 2015 (Nikpay et al., 2015) which can be accessed on the Cardiogram website. I expect the results should be very similar using the 2022 statistics as well.
Hopefully that clears things up, but let me know if not or if you have any further questions!
Andrew
Good afternoon,
I hope this email finds you well
My name is Ange, I am currently trying to reproduce BMI results from the Navmix paper. I have some questions with regard to it.
I have performed all the steps and tried to reproduce the results but keep having four clusters and one noise cluster. I have the same number of variants, but I think this may be due to different beta or se. So here are some questions : Did you use the raw or the rint gwas from the Neale lab (this is not clear in the paper) ? I have used raw, but I recognize that maybe you have used different datasets. Did you harmonize the file? I have noticed that Neale's lab effect alleles were not the same as the Pulit BMI effect alleles. As phenoscanner is not working, I was planning to use the Summary statistics of CARDIOGRAM 2022, I believe the results should be similar. Do you have any other ideas/suggestions to help me troubleshooting?
Best
Ange