52-gene signature in peripheral blood identifies a genomic profile associated with increased risk of mortality and poor disease outcomes in idiopathic pulmonary fibrosis

A method of assessing a blood sample obtained from an individual, the method comprising:

• (a) obtaining RNA from a blood sample from an individual;
• (b) combining the RNA obtained in (a) with nucleic acid probes that hybridize to at least one of the following 52 genes:
• PLBD1, TPST1, C19orf59 (MCEMP1), IL1R2, HP, FLT3, S100A12, LCK, CAMK2D, NUP43, SLAMF7, LRRC39, ICOS, CD47, LBH, SH2D1A, CNOT6L, METTL8, ETS1, C2orf27A, P2RY10, TRAT1, BTN3A1, LARP4, TC2N, GPR183, MORC4, STAT4, LPAR6, C7orf58 (CPED1), DOCK10, ARHGAP5, HLA-DPA1, BIRC3, GPR174, CD28, UTRN, CD2, HLA-DPB1, ARL4C, BTN3A3, CXCR6, DYNC2LI1, BTN3A2, ITK, SNHG1, CD96, GBP4, S1PR1, NAP1L2, KLF12, and IL7R, thereby producing a combination;
• (c) maintaining the combination under conditions under which hybridization of RNA and nucleic acid probes occurs, thereby producing RNA-nucleic acid probe complexes;
• (d) measuring the number of RNA-nucleic acid probe complexes for each of the 52 genes;
• (e) producing an expression level for each of the genes based on the number of RNA-nucleic acid probe complexes measured in (d);
• (f) comparing the expression level of each gene with a gene-specific reference value, thereby producing a normalized expression level for each gene;
• (g) determining (i) if the normalized expression level of each of PLBD1, TPST1, C19orf59 (MCEMP1), IL1R2, HP, FLT3, and S100A12 is greater than the gene-specific reference value, wherein if the normalized expression level of a gene in the sample is greater than the gene-specific reference value, the gene is an upregulated gene and (ii) if the normalized expression level of each of LCK, CAMK2D, NUP43, SLAMF7, LRRC39, ICOS, CD47, LBH, SH2D1A, CNOT6L, METTL8, ETS1, C2orf27A, P2RY10, TRAT1, BTN3A1, LARP4, TC2N, GPR183, MORC4, STAT4, LPAR6, C7orf58 (CPED1), DOCK10, ARHGAP5, HLA-DPA1, BIRC3, GPR174, CD28, UTRN, CD2, HLA-DPB1, ARL4C, BTN3A3, CXCR6, DYNC2LI1, BTN3A2, ITK, SNHG1, CD96, GBP4, S1PR1, NAP1L2, KLF12, and IL7R is less than the gene-specific standard, wherein if the normalized expression level of a gene in the sample is less than the gene-specific standard, the gene is a downregulated gene;
• (h) calculating (i) the proportion of upregulated genes in the sample, thereby producing a proportion of upregulated genes and (ii) the proportion of downregulated genes in the sample, thereby producing a proportion of downregulated genes;
• (i) adding the normalized expression levels of the upregulated genes and multiplying the resulting sum by the proportion of upregulated genes calculated in (h)(i), thereby producing an up score;
• (j) adding the normalized expression levels of the downregulated genes and multiplying the resulting sum by the proportion of downregulated genes calculated in (h)(ii), thereby producing a down score;
• and
• (k) comparing the up score to a reference median up score and the down score to a reference median down score.