Platform and sample type independent single sample classifier for treatment decision making in pancreatic ductal adenocarcinoma cancer

A method for treating a subject diagnosed with pancreatic ductal adenocarcinoma (PDAC), the method comprising:

• (a) obtaining nucleic acid expression levels for each of the following genes in a biological sample comprising PDAC cells isolated from the subject:
• GPR87, KRT6A, BCAR3, PTGES, ITGA3, C16orf74, S100A2, KRT5, REG4, ANXA10, GATA6, CLDN18, LGALS4, DDC, SLC40A1, CLRN3, KRT15, KRT17, TFF1, PLA2G10, CDH17, DCBLD2 and TSPAN8, wherein the nucleic acid expression levels were determined using an amplification, hybridization or sequencing assay on the biological sample;
• (b) performing a pair-wise comparison of the nucleic acid expression levels for each gene pair in either Gene Pairs 1-8 or Gene Pairs A-H, wherein Gene Pairs 1-8 and Gene Pairs A-H are as follows:
• GENE
• GENE
• GENE
• PAIR
• A
• B
• Coefficient
• 1
• GPR87
• REG4
• 1.994
• 2
• KRT6A
• ANXA10
• 2.031
• 3
• BCAR3
• GATA6
• 1.618
• 4
• PTGES
• CLDN18
• 0.922
• 5
• ITGA3
• LGALS4
• 1.059
• 6
• C16orf74
• DDC
• 0.929
• 7
• S100A2
• SLC40A1
• 2.505
• 8
• KRT5
• CLRN3
• 0.485
• A
• GPR87
• REG4
• 3.413
• B
• KRT6A
• ANXA10
• 3.437
• C
• KRT17
• LGALS4
• 2.078
• D
• S100A2
• TFF1
• 2.651
• E
• C16orf74
• DDC
• 0.901
• F
• KRT15
• PLA2G10
• 2.677
• G
• PTGES
• CDH17
• 2.911
• H
• DCBLD2
• TSPAN8
• 1.903
• (c) calculating a Raw Score for the biological sample, wherein the calculating comprises:
• (i) assigning a value of 1 for each Gene Pair from either Gene Pairs 1-8 or Gene Pairs A-H for which Gene A of the Gene Pair has a higher nucleic acid expression level than Gene B of the Gene Pair, and a value of 0 for each Gene Pair from either Gene Pairs 1-8 or Gene Pairs A-H for which Gene A of the Gene Pair has a lower nucleic acid expression level than Gene B of the Gene Pair;
• (ii) multiplying each assigned value by the coefficient listed above for each Gene Pair from either Gene Pairs 1-8 or Gene Pairs A-H to calculate eight individual Gene Pair scores from either Gene Pairs 1-8 or Gene Pairs A-H;
• and
• (iii) adding a sum of the eight individual Gene Pair scores from either Gene Pairs 1-8 or Gene Pairs A-H to a respective baseline effect for either Gene Pairs 1-8 or Gene Pairs A-H to calculate a Raw Score for the biological sample, wherein the respective baseline effect is −6.815 for Gene Pairs 1-8 and −12.414 for Gene Pairs A-H, wherein if the calculated Raw Score is greater than or equal to 0, the tumor subtype is determined to be a basal-like subtype, and if the calculated Raw Score if less than 0, the tumor subtype is determined to be a classical subtype;
• (d) administering a treatment to the subject based on the subtype assigned, wherein:
• (i) if the assigned subtype is a basal-like subtype, the treatment strategy comprises gemcitabine;
• and
• (ii) if the assigned subtype is a classical subtype, the treatment comprises FOLFIRINOX.