Methods for evaluating COPD status
The invention in some aspects provides methods of determining the likelihood that a subject has COPD based on the expression of informative-genes. In other aspects, the invention provides methods for determining an appropriate diagnostic intervention plan for a subject based on the expression of informative-genes. Related compositions and kits are provided in other aspects of the invention.
1. A method for processing a biological sample of a subject, comprising:
(a) obtaining said biological sample from a bronchial epithelium of said subject;
(b) subjecting a first portion of said biological sample to histological or cytological testing that indicates that said first portion of said biological sample is free of detectable cancer cells;
(c) upon identifying that said first portion of said biological sample is free of detectable cancer cells, using nucleic acid hybridization, amplification, or sequencing to generate a first data set with a level of gene expression products of a plurality of genes comprising PCDH7 and PTPRH from a second portion of said biological sample, which gene expression products are differentially expressed as compared to a reference;
(d) processing said first data set to obtain a second data set comprising a COPD risk-score for said biological sample; and
(e) outputting a report having said COPD risk score.
2. The method of claim 1 , wherein (c) comprises using probes having sequence complementarity with gene expression products of said plurality of genes comprising PCDH7 and PTPRH.
3. The method of claim 1 , wherein said subject exhibits one or more symptoms of COPD or has a lesion that is observable by computer aided tomography or chest x-ray.
4. The method of claim 3 , wherein, prior to subjecting said first portion of said biological sample to histological or cytological testing, said subject has not been diagnosed with COPD.
5. The method of claim 1 , wherein said COPD risk-score is (i) a combination of weighted gene expression product levels or (ii) a sum of weighted gene expression product levels.
6. The method of claim 5 , wherein said weighted expression levels are weighted by their relative contribution to predicting increased likelihood of having COPD.
7. The method of claim 1 , further comprising determining a treatment course based on said COPD risk-score.
8. The method of claim 6 , wherein said subject is either: (i) a candidate for a COPD therapy and/or an invasive lung procedure based on said COPD risk score indicating that said subject has a relatively high likelihood of having COPD; or (ii) not a candidate for a COPD therapy or an invasive lung procedure based on said COPD risk-score indicating that said subject has a relatively low likelihood of having COPD.
9. The method of claim 1 , wherein said biological sample is obtained using bronchial brushing, broncho-alveolar lavage, or a bronchial biopsy.
10. The method of claim 1 , wherein said plurality of genes comprises at least 3 additional genes selected from the group consisting of: CCDC81, CEACAM5, C12orf36, B3GNT6, PLAG1, PDE7B, CACHD1, EPB41L2, FRMD4A, PRKCE, ZNF483, DPYSL3, TNS3, FMNL2, GALE, CNTN3, HSD17B13, PTPRM, HLF, PROS1, PLA2G4A, KAL1, TCN1, DPP4, GPR98, KCNA1, CABLES1, PEG10, PPP1R9A, POLA2, C17orf37, ABCC4, CA8, CYP2A13, SETBP1, ANKS1B, CHP, THSD4, MPDU1, CD109, STK32A, HHLA2, AMMECR1, NPAS3, GXYLT2, KLF12, CA12, C21orf121, SH3BP4, FABP6, GUCY1B3, FUT3, STX10, FTO, CNTN4, ATP8A1, GMDS, ZNF671, WBPS, MYOSB, FLRT3, SCGB1A1, SNTB1, C16orf89, PRKD1, ANXA6, YIPF1, ATP10B, HNK, ABHD2, DNAH5, GGT7, FBN1, PRSS12, TMPRSS4, AM1GO2, TMEM54, or CAPRIN2.
11. The method of claim 1 , wherein said COPD risk-score is a combination of weighted gene expression product levels.
12. The method of claim 1 , wherein said COPD risk-score is a sum of weighted gene expression product levels.