The present invention provides methods of detecting increased carcinoembryonic antigen-related cell adhesion molecule (CEACAM) protein expression in a biological sample from a patient with a loss of function mutation in a protein tyrosine phosphatase non-receptor type 2 (PTPN2) gene. The invention also provides methods of treating or preventing inflammatory bowel disease (IBD) in a patient with a loss of function mutation in a protein tyrosine phosphatase non-receptor type 2 (PTPN2) gene.