GWAS is a widely used case-control approach to study genetic associations with different traits ranging from eye color to complex diseases. It has been used to discover genetic markers resulting in various genetic diseases such as Alzheimer’s disease and many other traits (BertramandTanzi2009),it has become a standard statistical approach to investigate genotype-phenotype relations.
Using ontologies, we can aggregate patient information over the structure of the ontology and thereby increase statistical power of the GWAS. We are able to test associations with classes in the ontology that have never been directly observed but which only arise through the ontology structure and hierarchy. We can also use the ontology to discriminate associations between sibling classes, thereby leading to more specific associations.
This method is used to find what makes one disease stand out from other similar diseases in an ontology. As normal the cases are the same as normal study, but the controls subset contains individuals that is a part of at least one of the super classes of the studied disease and does not have the disease itself. This result in the output will be more specified finding variants that is more prevalent in this disease than similar ones.
Here our studied class and all subclasses are in the case subset, while everyone else is part of the control subset
Here our studied class and all subclasses are in the case subset, while all subjects that is in the our class superclass and its sublclasses (except case subjects) is in the control subset. All other subjects not in these two subsets will be ignored.
Each study have a requirement of containing at least 100 cases. This is because the the fewer cases a study have the worse the quality is for that study.
Sometimes our settings for our GWAS will remove unfit cases to under our at least 100 cases rule. For gender filtering we do not apply this rule, as long as the total sum of cases is at least 100.
Yes, our links have been generated with text mining in litratre and have not been able to find all links with high enough confidence.
"Compare GWAS" does not make sure the plots exists, it only generates the right link. Please be sure that inputted code exists in our database.
For our GWAS we use Plink Version 1 , with the settings MAF: 0.01 and GENO: 0.1
As of now you can not, but we are working to implement this in the future
If you have further questions, please feel free to send me an email on: firstname.lastname@example.org