Nicotine GWAS
The project is a genome-wide genotyping approach to analyse the genetics of nicotine dependence. We had 1800 samples genotyped for the 900,000 SNPs. In addition to the nicotine addiction, we also worked with Parkinson's disease whole-genome sequencing and RNAseq data from PPMI longitudinal cohort. Thi cohort enables to analyse genetic and lifestyle factors for getting Parkinson's disease.
Area of science
Medical And Health Sciences
Systems used
Zeus, Data
Applications used
PLINK, MELT, Rstudio, Tribes, TEtranscriptThe Challenge
The main challenges were to identify the genetic associations from the complex data. The aim of the project was to find genetic determinants for nicotine dependence and the smoking connection to complex diseases, like Parkinson’s disease. Data modelling was quite challenging
The Solution
We applied PLINK for general association analysis using case/control and linear modelling for quantitative data. We used RStudio for more detailed analysis as it is. really flexible for several modelling options
The Outcome
It worked very well. I got sufficient power to perform calculations and do analysis. I am very grateful for PAwsey team helping out with complex installations where I got stuck. Especially with the RStudio. I suggest to set up a server-based R studio version.
List of Publications from this project
Genetic interaction between two VNTRs in the MAOA gene is associated with the nicotine dependence.
Kõks G, Prans E, Ho XD, Duy BH, Tran HD, Ngo NB, Hoang LN, Tran HM, Bubb VJ, Quinn JP, Kõks S.
Exp Biol Med (Maywood). 2020 Apr 2:1535370220916888. doi: 10.1177/1535370220916888.
The Genetic Variations Associated With Time to Aseptic Loosening After Total Joint Arthroplasty.
Koks S, Wood DJ, Reimann E, Awiszus F, Lohmann CH, Bertrand J, Prans E, Maasalu K, Märtson A.
J Arthroplasty. 2020 Apr;35(4):981-988. doi: 10.1016/j.arth.2019.11.004. Epub 2019 Nov 12.
