Methods for subtyping of head and neck squamous cell carcinoma

A method of detecting a group of biomarkers in a head and neck tissue sample obtained from a patient, the method comprising measuring the nucleic acid expression level of every biomarker in the group of biomarkers consisting of only ATP binding cassette subfamily C member 1 (ABCC1), ATP binding cassette subfamily C member 5 (ABCC5), actinin alpha 1 (ACTN1), amyloid beta precursor protein binding family B member 2 (APBB2), apolipoprotein L3 (APOL3), aquaporin 3 (AQP3), ATPase 13A4 (ATP13A4), ATPase H+ transporting V1 subunit D (ATP6V1D), calcium binding tyrosine phosphorylation regulated (CABYR), caspase 4 (CASP4), caveolin 1 (CAV1), corneodesmosin (CDSN), choline phosphotransferase 1 (CHPT1), carbohydrate sulfotransferase 7 (CHST7), class II major histocompatibility complex transactivator (CIITA), CKLF like MARVEL transmembrane domain containing 3 (CMTM3), collagen type VI alpha 1 chain (COL6A1), collagen type VI alpha 2 chain (COL6A2), cystatin A (CSTA), Cytochrome P450 family 26 subfamily A member 1 (CYP26A1), dehydrogenase/reductase 1 (DHRS1), E74 like ETS transcription factor 3 (ELF3), epithelial cell adhesion molecule (EPCAM), epithelial mitogen (EPGN), family with sequence similarity 171 member A1 (FAM171A1), family with sequence similarity 3 member B (FAM3B), striatin interacting protein 1 (FAM40A), filamin binding LIM protein 1 (FBLIM1), forkhead box A1 (FOXA1), follistatin like 3 (FSTL3), fucosyltransferase 6 (FUT6), glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (I blood group) (GCNT2), glutathione peroxidase 8 (putative) (GPX8), grainyhead like transcription factor 3 (GRHL3), gasdermin A (GSDMA), HLF, PAR bZIP transcription factor (HLF), interleukin 4 receptor (IL4R), inhibin beta A subunit (INHBA), KIAA1609, Kruppel like factor 5 (KLF5), prolyl 3-hydroxylase 1 (LEPRE1), latent transforming growth factor beta binding protein 3 (LTBP3), mal, T-cell differentiation protein 2 (MAL2), MAP7 domain containing 1 (MAP7D1), Meis homeobox 1 (MEIS1), MOB kinase activator 3B (MOBKL2B), mucin 4, cell surface associated (MUC4), nicotinamide N-methyltransferase (NNMT), NOP2/Sun RNA methyltransferase family member 7 (NSUN7), olfactomedin like 2B (OLFML2B), olfactomedin like 3 (OLFML3), prolyl 4-hydroxylase, transmembrane (P4HTM), POZ/BTB and AT hook containing zinc finger 1 (PATZ1), PBX homeobox 1 (PBX1), procollagen C-endopeptidase enhancer (PCOLCE), pleckstrin homology like domain family B member 1 (PHLDB1), placenta specific 8 (PLAC8), phospholipase D2 (PLD2), peroxisome proliferator activated receptor delta (PPARD), periplakin (PPL), protein kinase, X-linked (PRKX), RAB6B, member RAS oncogene family (RAB6B), ribosomal modification protein rimK like family member A (RIMKLA), serpin family E member 1 (SERPINE1), serpin family H member 1 (SERPINH1), sideroflexin 3 (SFXN3), SH3-containing guanine nucleotide exchange factor (SGEF), solute carrier family 31 member 2 (SLC31A2), SLC9A3 regulator 1 (SLC9A3R1), snail family transcriptional repressor 2 (SNAI2), transforming growth factor beta induced (TGFBI), tight junction protein 3 (TJP3), transmembrane protein 51 (TMEM51), transmembrane protease, serine 11A (TMPRSS11A), transmembrane protease, serine 11B (TMPRSS11B), transmembrane protease, serine 2 (TMRSS2), tetratricopeptide repeat domain 9 (TTC9), thioredoxin reductase 1 (TXNRD1), ubiquitin like modifier activating enzyme 7 (UBA7) and zinc finger DHHC-type containing 2 (ZDHHC2) in the head and neck tissue sample obtained from the patient using an amplification, a hybridization and/or a sequencing assay.