Methods and compositions for predicting and treating triple negative breast cancer

A kit for predicting a disease prognosis and/or a treatment outcome for a subject diagnosed with triple negative breast cancer (TNBC), the kit comprising:

• a) an isolated set of probes capable of detecting a panel of biomarkers comprising at least two biomarkers selected from the group consisting of ankyrin repeat domain 36 (ANKRD36), ankyrin repeat domain 36B pseudogene 2 (ANKRD36BP2), B-box and SPRY domain-containing (BSPRY), chromosome 12 open reading frame 65 (C12orf65), chromosome 2 open reading frame 49 (C2orf49), chromosome 1 open reading frame 198 (Clorf198), coiled-coil domain containing 114 (CCDC114), claudin 4 (CLDN4), CUE domain containing 1 (CUEDC1), outer dynein arm docking complex subunit 1 (ODAD1), cell growth regulator with EF-hand domain 1 (CGREF1), DEP domain containing 7 (DEPDC7), doublecortin like kinase 2 (DCLK2), diacylglycerol kinase (DGKH), disco interacting protein 2 homolog B (DIP2B), disrupted-in-schizophrenia 1 (DISC1), epithelial membrane protein 1 (EMP1), ERH mRNA splicing and mitosis factor (ERH), growth arrest and DNA damage inducible beta (GADD45B), glutaminase (GLS), grainyhead like transcription factor 1 (GRHL1), glycophorin C (GYPC), H2A histone family member X (H2AFX), HRas proto-oncogene (HRAS), intracellular adhesion molecule 1 (ICAM1), interphotoreceptor matrix proteoglycan 2 (IMPG2), potassium voltage-gated channel subfamily C member 3 (KCNC3), kruppel like factor 6 (KLF6), kruppel like factor 7 (KLF7), keratin 17 (KRT17), LON peptidase N-terminal domain and RING finger protein 2 (LONRF2), LPS responsive beige-like anchor protein (LRBA), leucine rich repeat, Ig-like and transmembrane domains 3 (LRIT3), leucine rich repeat containing 37B (LRRC37B), LSM11, U7 small nuclear RNA associated (LSM11), lysosomal trafficking regulator (LYST), metastasis associated lung adenocarcinoma transcript 1 (MALAT1), minichromosome maintenance complex component 3 associated protein antisense RNA 1 (MCM3AP_AS1), MICAL like 2 (MICALL2), MHC class I polypeptide-related sequence B (MICB), metallothionein 2A (MT2A), myelin expression factor 2 (MYEF2), NEDD4 binding protein 3 (N4BP3), neuroblastoma breakpoint family member 20 (NBPF20), NADH:
• Ubiquinone Oxidoreductase Core Subunit V2 (NDUFV2), neurogenic locus notch homolog protein 2 (NOTCH2), NADPH oxidase activator 1 (NOXA1), natriuretic peptide receptor 3 (NPR3), nuclear receptor subfamily 6 group A member 1 (NR6A1), P21 (RAC1) activated kinase 3 (PAK3), pantothenate kinase 3 (PANK3), par-6 family cell polarity regulator beta (PARD6B), peroxisomal biogenesis factor 1 (PEX1), piggyBac transposable element derived 4 (PGBD4), praja ring finger ubiquitin ligase 1 (PJA1), pleckstrin homology and FYVE domain containing 1 (PLEKHF1), purine nucleoside phosphorylase (PNP), protein tyrosine phosphatase receptor type A (PTPRA), protein phosphatase, Mg2+/Mn2+ dependent 1K (PPM1K), prickle planar cell polarity protein 1 (PRICKLE1), protein kinase AMP-activated non-catalytic subunit beta 2 (PRKAB2), PYD and CARD domain containing (PYCARD), RAS p21 protein activator 1 (RASA1), RASD family member 2 (RASD2), RAS guanyl releasing protein 1 (RASGRP1), rhophilin RHO GTPase binding protein 2 (RHPN2), Rab interacting lysosomal protein like 2 (RILPL2), roundabout guidance receptor 1 (ROBO1), RAR related orphan receptor A (RORA), Stromal cell derived factor 4 (SDF4), SERTA domain containing 4 (SERTAD4), shisa family member 5 (SHISA5), signal induced proliferation associated 1 like 2 (SIPA1L2), solute carrier family 22 member 20 (SLC22A20P), solute carrier family 24 member 3 (SLC24A3), solute carrier family 2 member 12 (SLC2A12), solute carrier family 39 member 10 (SLC39A10), solute carrier family 25 member 40 (SLC25A40), solute carrier family 43 member 1 (SLC43A1), solute carrier family 45 member 4 (SLC45A4), solute carrier family 6 member 20 (SLC6A20), spectrin beta, erthrocytic (SPTB), stromal antigen 3-like 3 (STAG3L3), sushi domain containing 3 (SUSD3), TATA-Box binding protein associated factor 10 (TAF10), t-complex-associated testis expressed 3 (TCTE3), transmembrane channel like 7 (TMC7), transmembrane and coiled-coil domain family 2 (TMCC2), transcriptional repressor GATA binding 1 (TRPS1), tubulin tyrosine ligase like 4 (TTLL4), tRNA-yW synthesizing protein 5 (TYW5), ubiquitin conjugating enzyme E2 W (UBE2 W), WD repeat, sterile alpha motif and U-box domain containing 1 (WDSUB1), N-protein N-terminal glutamine amidohydrolase (WDYHV1), N-terminal glutamine amidase 1 (NTAQ1), zinc finger BED-type containing 6 (ZBED6), zinc finger and BTB domain containing 46 (ZBTB46), zinc finger CCCH-type containing 13 (ZC3H13), zinc fingers and homeoboxes 2 (ZHX2), zinc finger protein 217 (ZNF217), zinc finger protein 233 (ZNF233), zinc finger protein 248 (ZNF248), zinc finger protein 469 (ZNF469), and zinc finger protein 785 (ZNF785);
• and
• b) instructions for use.