How to cite Gene ATLAS?
If you find Gene ATLAS useful, use the following publication to cite this work when you use it: Oriol Canela-Xandri, Konrad Rawlik and Albert Tenesa. An atlas of genetic associations in UK Biobank. Nature Genetics (2018). 50, 1593–1599.
What is the Effect Allele?
The effect size column reports the average effect on the trait of the reported Effect Allele. That is, the average effect on the phenotype, y, is,
y = n * b,
where n is the number of copies of the reported Effect Allele and b the effect size reported in the database. The allele reported in the results for download is also the Effect Allele.
In the new database update with white participants,the reported Effect Allele is the same as in the previous version with white-British, but we have changed the name from reference allele to effect allele to avoid further confusion.
Which are the units of the reported effects?
For the traits that are unit-dependent (e.g. height, BMI), we kept the same units used in the UK Biobank database. For some of the quantitative traits, we repeated the analysis performing a Normal Rank transformation of the phenotypes. These can be found here.
What are the Normal Rank phenotypes?
For the non-binary phenotypes that have more than 500 different values, we repeated the analysis, but by transforming the phenotype using a Normal Rank transformation. The results for these phenotypes are available in the downloads section.
Which are the differences between the previous release and the new one?
The analyses of the first release were performed on 408,455 white-British individuals. On the second release we increased the analyzed sample size to 452,264 individuals of white ancestry. In addition, for the second analysis we corrected for the polygenic effect using a Leave-One-Chromosome-Out (LOCO) approach for the Linear Mixed Model, whereas on the first analyses, we used a schema where the Genetic Relationship Matrices were computed using odd chromosomes when analyzing variants in the even chromosomes and vice versa.
Where I can find the results from the previous release?
You can download the files here.
How is the reported MAF computed?
The reported MAF was computed in the whole population used for the analysis. Please, note that for some phenotypes (i.e. gender specific phenotypes), the MAF may be slightly different from the reported ones. Especially for variants with low MAF.
How is the reported HWE computed?
The HWE statistic was computed on the unrelated white-British individuals as defined by UK Biobank.