Compositions and methods for cancer diagnosis and prognosis

A method for treating liver, kidney, breast, lung, or brain cancer in a human subject, wherein the human subject is identified as having liver, kidney, breast, lung, or brain cancer by a method comprising

• (a) determining the mRNA expression levels of 55 O-glycan-forming glycosyltransferases (OGFGTs) in a tumor sample from the human subject, wherein the tumor sample comprises liver, kidney, breast, lung, or brain cells and/or tissue, and wherein the 55 OGFGTs are:
• ST3GAL3, B3GNT3, C1GALT1C1, B3GNT6, CHST1, B4GALT5, B4GALT1, GALNT8, B4GALT3, GCNT7, B3GNT7, B4GALT2, FUT5, FUT4, GALNT4, ST3GAL1, ST3GAL2, FUT11, FUT2, FUT7, GALNT3, B3GNT2, GCNT2, FUT1, B4GALT4, FUT3, B3GNT5, CHST2, GALNT2, FUT9, GCNT4, B3GNT8, GALNT13, GALNT7, GALNT10, B3GNT9, GALNT6, C1GALT1, GALNT12, FUT10, B3GNT4, FUT6, B3GNT1, CHST4, ST3GAL4, GALNT5, ST3GAL6, GALNT1, GALNT9, GCNT1, GALNT14, GALNT11, ST6GALNAC1, GCNT3, and ST6GAL1;
• (b) analyzing the mRNA expression levels of the 55 OGFGTs determined in (a) with a classifier that can distinguish between cancer and non-cancer samples by comparing the mRNA expression level of each OGFGT in the tumor sample to a reference level;
• (c) identifying the human subject as having liver cancer, kidney cancer, breast cancer, lung cancer, or brain cancer;
• and
• (d) administering an anticancer treatment to the human subject identified as having liver cancer, kidney cancer, breast cancer, lung cancer, or brain cancer,
• wherein the anticancer treatment is selected from the group consisting of surgery, chemotherapy, radiation therapy, immunotherapy, gene therapy, and combinations thereof, and
• wherein the reference levels are:
• (a) the expression levels in a non-cancerous sample from the subject or the expression levels in a non-cancerous sample from one or more different subjects, wherein the non-cancerous sample is of the same tissue type as the sample from the subject;
• or (b) the expression levels in a cancerous sample from one or more different subjects, optionally wherein the cancerous sample is of the same tissue type as the sample from the subject.