The present disclosure provides methods and compositions that find use in identifying presence of an advanced stage autoimmune liver disease (ALD) is a subject diagnosed as having ALD. Also provided here are methods and compositions that find use in monitoring effectiveness of treatment of an ALD patient receiving a treatment for the ALD. Also provided here are methods and compositions that find use in identifying subjects suffering from a relapse of ALD. The methods and compositions of the present disclosure also find use in facilitating treatment decisions for a subject having ALD.