The national research network CONNECT-GENERATE (https://generate-net.de/connect-generate.html), funded by the Federal Ministry of Education and Research (BMBF), aims to improve the diagnosis and treatment of people with autoimmune brain diseases. Subproject 3 investigates the genetic basis of these diseases using modern genetic methods, such as genome-wide association studies, expression analyses (RNAseq), and microbiome sequencing. In the second funding period starting in 2023, we will use genome sequencing of patients to gain an even deeper insight into the genetics of brain inflammations. In addition to the genomes of the patients, comparative genomes of healthy controls of the same ethnicity are equally important. Through collaboration with the DZHK, we can use the pseudonymised control data already available there, which would otherwise have to be generated anew at great expense.