Whole Exome Sequencing for the Identification of Mutations in CD8⁺ T-Cells

Advances in next-generation sequencing and in particular whole exome sequencing (WES) have provided an innovative opportunity to perform a mutational screening of the entire coding region of the genome down to the single base, enhancing the discovery of causal mutations important for disease treatment and management. Recently, the accumulation of germline mutations in expanded CD8⁺ T-cells has been found to have a pathogenic significance in autoimmune diseases such as rheumatoid arthritis, and, on the other hand, this type of mutations may act in combination with newly acquired somatic mutations modulating tumorigenesis, evolution, and cancer recurrence determining the clinical outcome. Therefore, we describe a protocol for identifying and characterizing germline single nucleotide variants (SNVs) and small deletions (Indels) from next-generation WES data of CD8⁺ T-cells coming from patients with autoimmune diseases and comparing them to matching control samples. Conversely, the same protocol can be applied for identifying and characterizing germline SNVs from CD8⁺ T-cells isolated from tumor samples with a non-favorable clinical outcome compared to those from patients with a favorable clinical outcome used as controls.