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Immune checkpoint inhibitors (ICIs) have yielded remarkable responses but often lead to immune-related adverse events (irAEs). Although germline causes for irAEs have been hypothesized, no individual variant associated with developing irAEs has been identified. We carried out a genome-wide association study of 1,751 patients on ICIs across 12 cancer types. We investigated two irAE phenotypes: (1) high-grade (3–5) and (2) all-grade events. We identified 3 genome-wide significant associations (
P
< 5 × 10
−8
) in the discovery cohort associated with all-grade irAEs: rs16906115 near
IL7
(combined
P
= 3.6 × 10
−11
; hazard ratio (HR) = 2.1); rs75824728 near
IL22RA1
(combined
P
= 3.5 × 10
−8
; HR = 1.8); and rs113861051 on 4p15 (combined
P
= 1.2 × 10
−8
, HR = 2.0); rs16906115 was replicated in 3 independent studies. The association near
IL7
colocalized with the gain of a new cryptic exon for
IL7
, a critical regulator of lymphocyte homeostasis. Patients carrying the
IL7
germline variant exhibited significantly increased lymphocyte stability after ICI initiation, which was itself predictive of downstream irAEs and improved survival.
A genome-wide association study in large cohorts of patients with different types of cancer treated with immune checkpoint inhibitors identifies genetic variants associated with immune-related adverse events.