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Diseases and Disease Groups

Diseases and Disease Groups are an important mechanism in EVAdb. Through use of these features, the system is able to assemble control groups for each query. By default, on each query for autosomal variants the set of variants is checked against summary statistics relating to the disease group that the original sample is part of. To count the number of occurences of a variant in the database, the current disease group is excluded to allow for finding of variants that are rare with respect to the general population (we would expect a disease causing mutation to be more prevalent in the disease group).

Parents

In many cases, not only the case is sequenced but also the parents. Such trio-analysis cases can be handled through the use of diseases as well. If desired, it is possible to have parents and samples in different disease groups to have parents as controls. Alternatively, they can be set to the same disease group so parents are not included in frequency filters for the case.

As such, each sample must be annotated with a disease when it is created. Diseases can be created in the admin application, by using the New disease form.

Field Example Description
Name Mitochondriopathy Name of the disease (used to reference it)
Symbol MT Short hand dispayed in some results tables
OmimID 590050 (If available) OmimID corresponding to the disease
Disease group Mitochondrial disease Disease group

Disease groups can not be modified through the application. They are hard-coded within the database.

Disease group table

The disease groups are preset in the mariadb database. The default data is included in the exomehg19_diseasegroup.dmp dump. The disease groups can be changed by modifying the table exomehg19.diseasegroup. By default, it is set by calling the following mysql statement.

INSERT INTO `diseasegroup`
VALUES
  (1,'Neurological disorder'),
  (2,'Developmental disorder'),
  (3,'Eye disease'),
  (4,'Controls'),
  (5,'Mitochondrial disease'),
  (6,'Tumor'),
  (7,'Immunological disorder'),
  (8,'Heart disease'),
  (9,'Lung disease'),
  (10,'Dermatological disease');

The available disease groups are:

  1. Neurological disorder
  2. Developmental disorder
  3. Eye disease
  4. Controls
  5. Mitochondrial disease
  6. Tumor
  7. Immunological disease
  8. Heart disease
  9. Lung disease
  10. Dermatological disease