Diagnostic and prognostic methods for lung disorders using gene expression profiles from nose epithelial cells

Abstract

The present invention provides methods for diagnosis and prognosis of lung cancer using expression analysis of one or more groups of genes, and a combination of expression analysis from a nasal epithelial cell sample. The methods of the invention provide far less invasive method with a superior detection accuracy for lung cancer when compared to any other currently available method for lung cancer diagnostic or prognosis. The invention also provides methods of diagnosis and prognosis of other lung diseases, such as lung cancer.

1 . A method of diagnosing lung cancer in an individual comprising the steps of:
 a) measuring a biological sample comprising nasal epithelial tissue from the individual for the expression of at least 20 gene transcripts from Table 6;   b) comparing the expression of the at least one gene transcripts to a control sample of those transcripts from individuals without cancer, wherein increased expression of the gene transcripts as indicated by a negative score in the last column of Table 6 and/or decreased expression of the gene transcripts as indicated by a positive score in the last column of Table 6 is indicative of the individual having lung cancer.   
     
     
         2 . The method of  claim 1 , wherein at least 40 gene transcripts are measured, wherein at least 60 gene transcripts are measured, or at least 70 gene transcripts are measured. 
     
     
         3 - 4 . (canceled) 
     
     
         5 . The method of  claim 1 , wherein the gene transcript measured is set forth in Table 5. 
     
     
         6 . The method of  claim 1 , wherein the gene transcript measured is set forth in Table 7. 
     
     
         7 . The method of  claim 1 , wherein the gene transcript measured is set forth in Table 1 wherein the measurement of the gene transcript relative to the control uses the third column of Table 1 setting forth direction of expression in lung cancer to determine if the individual has lung cancer. 
     
     
         8 . The method of  claim 7 , wherein the transcript measured is at least Table 3. 
     
     
         9 . The method of  claim 7 , wherein the transcript used is at least the transcripts set forth in Table 4. 
     
     
         10 . A method of diagnosing a lung disease in an individual exposed to air pollutant comprising the steps of
 a) measuring expression profile of a gene group in a nasal epithelial sample from a test individual; and   b) comparing the expression profile of the test individual to an expression profile of a first control individual exposed to similar air pollutant who does not have the lung disease and the expression profile of a second control individual exposed to similar air pollutants who has the lung disease, wherein similarity of the expression profile of the test individual with the expression profile of the first control rather than that of the second control is indicative of the test individual being not affected with the lung disease and wherein similarity of the expression profile of the test individual with the expression profile of the second control individual rather than that of the first control individual is indicative of the test individual being affected or at high risk of developing the lung disease.   
     
     
         11 . The method of  claim 7 , wherein the gene group comprises at least 30, sequences of genes selected from the group consisting with GenBank identification Nos. NM_003335; NM_000918; NM_006430.1; NM_001416.1; NM_004090; NMJD06406.1; NM_003001.2; NMJ)0131θ; NMJ)06545.1; NM_021145.1; NM_002437.1; NMJ)06286; NMJXH003698 /// NMJ)01003699 /// NMJJ02955; NMJ)O1 123 /// NM_006721; NMJ)24824; NMJ)04935.1; NM_002853.1; NM_019067.1; NM_024917.1; NM_020979.1; NM_005597.1; NM_007031.1; NM_009590.1; NM 020217.1; NM_025026.1; NMJ) 14709.1; NMJ)14896.1; AF010144; NMJ)05374.1; NM JJ01696; NM J)05494 /// NMJ)58246; NM_006534 /// NM_181659; NM_006368; NM_002268 /// NMJ)32771; NMJH4033; NMJ)16138; NM_007048 /// NM_194441; NMJ)06694; NMJ)00051 /// NM_138292 /// NM_138293; NM_000410 /// NM_139002 /// NMJ39003 /// NM_139004 /// NM_139005 /// NMJ 39006 /// NMJ 39007 /// NMJ 39008 /// NMJ 39009 /// NMJ 39010 /// NMJ39011; NM_004691; NMJ) 12070 /// NMJ 39321 /// NMJ39322; NM_006095; A1632181; AW024467; NMJ)21814; NMJ)05547.1; NMJ203458; NM_015547 /// NMJ47161; AB007958.1; NM_207488; NM_005809 /// NMJ 81737 /// NMJ 81738; NM_016248 /// NM J 44490; AK022213.1; NM_005708; NM_207102; AK023895; NM_144606 /// NMJ44997; NM_018530; AK021474; U43604.1; AU1 47017; AF222691; NM_0151 16; NMJ)01005375 /// NM_001005785 /// NM_001005786 /// NM_004081 /// NM_020363 /// NM_020364 /// NMJ)20420; AC004692; NM_001014; NM_000585 /// NMJ 72174 /// NMJ 72175; NM_054020 /// NMJ72095 /// NMJ 72096 /// NMJ 72097; BE466926; NMJ1I 8011; NMJ124077; NM_012394; NM_019011 /// NM_207111 /// NM_207116; NMJ)17646; NM_021800; NM_016049; NM_014395; NMJ114336; NMJ) 18097; NMJ) 19014; NMJ124804; NMJ) 18260; NM_018118; NMJH4128; NM_024084; NM_005294; AF077053; NM_138387; NMJ124531; NM_000693; NM_018509; NMJ)33128; NMJ120706; A1523613; and NM_014884. 
     
     
         12 . The method of  claim 1 , wherein the gene group comprises:
 a) sequences of genes selected from the group consisting of genes with GenBank identification Nos. NM_007062.1; NM_001281.1; BC000120.1; NM_014255.1; BC002642.1; NM_000346.1; NMJ106545.1; BG034328; NM_021822.1; NM_021069.1; NMJ) 19067.1; NM_017925.1; NMJ) 17932.1; NM_030757.1; NM_030972.1; AF126181.1; U93240.1; U90552.1; AF151056.1; U85430.1; U51007.1; BC005969.1; NM_002271.1; AL566172; AB014576.1; BF218804; AK022494.1; AA1 14843; BE467941; NM_003541.1; R83000; AL161952.1; AK023843.1; AK021571.1; AK023783.1; AU147182; AL0801 12.1; AW971983; A1683552; NM_024006.1; AK026565.1; NM_014182.1; NM_021800.1; NM_016049.1; NM1019023.1; NM_021971.1; NMJM4128.1; AK025651.1; AA133341; and AF1 98444.1;   b) sequences of genes selected from the group consisting of genes with GenBank identification Nos. NM_007062.1; NM_001281.1; BC002642.1; NM_000346.1; NM_006545.1; BG034328; NM_019067.1; NM_017925.1; NM_017932.1; NM_030757.1; NM_030972.1; NM_002268 /// NM_032771; NM_007048 /// NM_194441; NM_006694; U85430.1; NM_004691; AB014576.1; BF218804; BE467941; R83000; AL161952.1; AK023843.1; AK021571.1; AK023783.1; AL080112.1; AW971983; A1683552; NM_024006.1; AK026565.1; NM_014182.1; NM_021800.1; NM_016049.1; NM_021971.1; NM_014128.1; AA133341; and AF198444.1;   c) sequences of genes selected from the group consisting of genes with GenBank or Unigene identification Nos. NM_030757.1; R83000; AK021571.1; NM_014182.1; NM_17932.1; U85430.1; AI683552; BC002642.1; AW024467; NM_030972.1; BC021135.1; AL161952.1; AK026565.1; AK023783.1; BF218804; NM_001281.1; NM_024006.1; AK023843.1; BC001602.1; BC034707.1; BC064619.1; AY280502.1; BC059387.1; AF135421.1; BC061522.1; L76200.1; U50532.1; BC006547.2; BC008797.2; BC000807.1; AL0801 12.1; BC033718.1 /// BC046176.1 ///BC038443.1; NM_000346.1; BC008710.1; Hs.288575 (UNIGENE ID); AF020591.1; BC000423.2; BC002503.2; BC008710.1; BC009185.2; Hs.528304 (UNIGENE ID) U50532.1; BC0139232; BC031091; NM_007062; Hs.249591 (Unigene ID); BC075839.1 /// BC073760.1; BC072436.1 ///BC004560.2; BC001016.2; Hs.286261 (Unigene BD); AF348514.1; BC005023.1; BC066337.1 ///BC058736.1 /// BC050555.1; Hs.216623 (Unigene ID); BC072400.1; BC041073.1; U43965.1; BC021258.2; BC016057.1; BC016713.1 /// BC014535.1 /// AF237771.1; BC000360.2; BC007455.2; BC000701.2; BC010067.2; BC023528.2 /// BC047680.1; BC064957.1; Hs. 156701 (Unigene ID); BC030619.2; BC008710.1; U43965.1; BC066329.1; Hs.438867 (Unigene ID); BC035025.2 /// BC050330.1; BC023976.2; BC074852.2 /// BC074851.2; Hs.445885 (Unigene ID); BC008591.2 /// BC050440.1 ///; BC048096.1; AF365931.1; AF257099.1; and BC028912.1;   d) genes with GenBank or Unigene identification Nos: NM_003335; NM_001319; NM 021145.1; NM_001003698 /// NM_001003699 ///; NM_002955; NM_002853.1; NM_019067.1; NM_024917.1; NM_020979.1; NM_005597.1; NM_007031.1; NM_009590.1; NM_020217.1; NM_025026.1; NM_014709.1; NM_014896.1; AF010144; NM_005374.1; NM_006534 /// NM 181659; NM_014033; NM_016138; NM_007048 /// NM_194441; NM_000051 /// NM_138292 /// NM_138293; NM_000410 /// NMJ 39002 /// NM_139003 /// NM_139004 /// NM_139005 /// NM_139006 /// NM_139007 /// NM_139008 /// NM_139009 /// NM_139010 /// NM_139011 NMJH2070 /// NMJ 39321 /// NMJ39322; NM_006095; AI632181; AW024467; NM_021814; NM_005547.1; NM_203458; NM_015547 /// NM_147161; AB007958.1; NM_207488; NM_005809 /// NM_181737 /// NM_181738; NM_016248 /// NM_144490; AK022213.1; NM_005708; NM_207102; AKO23895; NM_144606 /// NMJ 44997; NMJH8530; AK021474; U43604.1; AU147017; AF222691.1; NM_0151 16; NM_001005375 /// NM_001005785 /// NM_001005786 /// NM_004081 /// NM_020363 /// NM_020364 /// NM_020420; AC004692; NM_001014; NM_000585 /// NM_172174 /// NMJ 72175; NM_054020 /// NM_172095 /// NMJ 72096 /// NMJ 72097; BE466926; NMjD 18011; NM_024077; NM_019011 /// NM_207111 /// NM_207116; NMJ) 17646; NMJ) 14395; NMJ) 14336; NMJ) 18097; NMJ)19014; NMJ324804; NM_018260; NM_018118; NM_014128; NM_024084; NMJ305294; AF077053; NM_000693; NM_033128; NM_020706; AJ523613; and NMJD14884, and wherein decrease in expression of at least 5 of these genes is indicative of the individual being affected with a lung disease;   e) sequences of genes selected from the group consisting of genes with GenBank or Unigene identification Nos NM_030757.1; R83000; AK021571.1; NM_1 7932.1; U85430.1; AI683552; BC002642.1; AW024467; NMJB0972.1; BC021135.1; AL161952.1; AK026565.1; AK023783.i; BF218804; AK023843.1; BC001602.1; BC034707.1; BC064619.1 AY280502.1; BC059387.1; BC061522.1; U50532.1; BC006547.2; BC008797.2; BC000807.1: AL080112.1; BC033718.1 ///BC046176.1 ///; BC038443.1; Hs.288575 (UNIGENE ID); AF020591.1; BC002503.2; BC009185.2; Hs.528304 (UNIGENE ID); U50532.1; BC013923.2; BC031091; Hs.249591 (Unigene ED); Hs.286261 (Unigene ID); AF348514.1; BC066337.1 /// BC058736.1 /// BC050555.1; Hs.216623 (Unigene ED); BC072400.1; BC041073.1; U43965.1; BC021258.2; BC016057.1; BC016713.1 ///BC014535.1 /// AF237771.1; BC000701.2; BC010067.2: Hs.156701 (Unigene DD); BC030619.2; U43965.1; Hs.438867 (Unigene ED); BC035025.2 /// BCO50330.1; BC074852.2 /// BC074851.2; Hs.445885 (Unigene ID); AF365931.1; and AF257099.1, and wherein decrease in expression of at least 5 of these genes is indicative of the individual being affected with a lung disease;   f) sequences of genes selected from the group consisting of genes with GenBank or Unigene identification Nos BF218804; AK022494.1; AA1 14843; BE467941; NM_003541.1; R83000; AL161952.1; AK023843.1; AK021571.1; AK023783.1; AU147182; AL080112.1; AW971983; A1683552; NM_024006.1; AK.026565.1; NM_014182.1; NM_021800.1; NM_016049.1 NM_019023.1; NM_021971.1; NM_014128.1; AK025651.1; AA133341; and AF 198444.1, and wherein decrease in expression of at least 5 of these genes is indicative of the individual being affected with a lung disease;   g) sequences of genes selected from the group consisting of genes with GenBank or Unigene identification Nos NM_000918; NM_006430.1; NM_001416.1; NM_004090; NM_006406.1; NM 003001.2; NM_006545.1; NM_002437.1; NM_006286; NM_001 123 /// NM_006721; NM_024824; NM_004935.1; NM_001696; NM_005494 /// NM_058246; NM_006368; NM_002268 /// NM_032771; NM_006694: NM_004691; NM_012394; NM_021800; NM_016049; NM_138387; NM_024531; and NM_018509, and wherein increase in expression of at least 5 of these genes is indicative of the individual being affected with a lung disease; or   h) sequences of genes selected from the group consisting of genes with GenBank or Unigene identification Nos NM_014182.1; NM_001281.1; NM_024006.1; AF135421.1; L76200.1; NM 000346.1; BC008710.1: BC000423.2 BC008710.1; NM_007062; BC075839.1 /// BC073760.1 BC072436.1 /// BC004560.2; BC001016.2; BC005023.1; BC000360.2: BC007455.2; BC023528.2 ///BC047680.1; BC064957.1; BC008710.1; BC066329.1; BC023976.2; BC008591.2 /// BC050440.1 /// BC048096.1; and BC028912.1, and wherein increase in expression of at least 5 of these genes is indicative of the individual being affected with a lung disease.   
     
     
         13 - 19 . (canceled) 
     
     
         20 . The method of  claim 5 , wherein the group comprises sequences of genes selected from the group consisting of genes with GenBank or Unigene identification Nos NM 007062.1; NM_001281.1; BC000120.1; NM_014255.1; BC002642.1; NM_000346.1; NM_006545.1; BG034328; NM 021822.1; NM_021069.1; NM_019067.1; NM_017925.1; NM_017932.1; NM_030757.1; NM_030972.1; AF126181.1; U93240.1; U90552.1; AF151056.1; U854301; U51007.1; BC005969.1; NM_002271.1; AL566172; and AB014576.1, and wherein increase in expression of at least 5 of these genes is indicative of the individual being affected with a lung disease. 
     
     
         21 . The method of  claim 1 , wherein the group comprises 5-9 sequences of genes selected from group 1 and group 2, group 1 consisting of genes with GenBank or Unigene identification Nos. NM_003335; NM_001319; NM_021145.1; NM_001003698 /// NM_001003699 ///; NM_002955; NM_002853.1; NM O 19067.1; NM_024917.1; NM_020979.1; NM_005597.1; NM_007031.1; NM_009590.1; NM_020217.1; NM_025026.1; NM_014709.1; NM_014896.1; AFO 10144; NM_005374.1; NM_006534 /// NM_181659; NM_014033; NM_016138; NM_007048 /// NM_194441; NM_000051 /// NM_138292 /// NMJ 38293; NM_000410 /// NM_1 39002 /// NM_139003 /// NMJ 39004 /// NMJ 39005 /// NM_139006 /// NM_139007 /// NMJ 39008 /// NM_139009 /// NM_139010 /// NMJ 39011; NM_012070 /// NMJ 39321 /// NM_139322; NM_006095; A1632181; AW024467; NM_021814; NMJD05547.1; NM_203458; NMJU5547 /// NM_147161; AB007958.1; NM_207488; NM_005809 /// NM_181737 /// NMJ81738; NM_016248 /// NM_144490; AK022213.1; NMJD05708; NM_207102; AK023895; NM_144606 /// NM_144997; NM_018530; AK021474; U43604.1; AU47017; AF222691.1; NM_015116; NMJ301005375 /// NM_OO 1005785 /// NM_001005786 /// NM_004081 /// NM_020363 /// NM_020364 /// NM_020420; AC004692; NM_001014; NM_000585 /// NM_172174 /// NM_172175; NM_054020 /// NM_172095 /// NMJ 72096 /// NM_172097; BE466926; NM_018011; NM_024077; NM_019011 /// NM_207111 /// NM_207116; NMJD17646; NM_014395; NM_014336; NM_018097; NM_019014; NMJD24804; NM_018260; NM_018118; NM_014128; NMJD24084; NM_005294; AF077053; NM_000693; NM_033128; NM_020706; AI523613; and NM_014884, and group 2 consisting of genes with GenBank or Unigene identification Nos. NM_000918; NM_006430.1; NM_00 1416.1; NM_004090; NM_006406.1; NM_003001.2; NM_006545.1; NM_002437.1; NM_006286; NM_001123 /// NM_006721; NMJD24824; NM_004935.1; NMJDO1 696; NM_005494 /// NMJD58246; NM_006368; NM_002268 /// NM_032771; NM_006694; NMJD04691; NM J) 12394; NM_021800; NM_016049; NMJ 38387; NM_024531; and NM_01 8509, and a group of at least 20 genes selected from group 3 and group 4, group 3 consisting of genes with GenBank or Unigene identification Nos BF218804; AK022494.1; AA1 14843; BE467941; NM_003541.1; R83000; AL161952.1; AK023843.1; AK021571.1; AK023783.1; AU147182; AL080112.1; AW971983; A1683552; NM_024006.1; AK026565.1; NM_014182.1; NM_021800.1; NM_016049.1; NM_019023.1; NM_021971.1; NM_014128.1; AK025651.1; AA133341; and AFI 98444.1 and group 4 consisting of genes with GenBank or Unigene identification Nos. NM_007062.1, NM_001281.1; BCOOO 120.1; NMJ) 14255.1; BC002642.1; NMJD00346.1; NMJD06545.1; BG034328; NMJD21822.1; NMJD21069.1; NM_019067.1; NMJ) 17925.1; NMJD 17932.1; NM_030757.1; NMJD30972.1; AF126181.1; U93240.1; U90552.1; AF151056.1; U85430.1; U51007.1; BC005969.1; NM_002271.1; AL566172; and ABO 14576.1. 
     
     
         22 . The method of  claim 20 , wherein decrease in the expression of any one of the group 1 genes and increase in the expression of any one of the group 2 genes, and decrease of the group 3 genes and increase of the group 4 genes is indicative of the individual being affected with a lung disease. 
     
     
         23 . The method of  claim 1 , wherein the group comprises 5-9 sequences of genes selected from group 5 and group 6, group 5 consisting of genes with GenBank or Unigene identification Nos. NM_030757.1; R83000; AK021571.1; NMJ7932.1; U85430.1; A1683552; BC002642.1; AW024467; NMJB0972.1; BC021 135.1; AL161952.1; AK026565.1; AK023783.1; BF218804; AK023843.1; BC001602.1; BC034707.1, BC064619.1; AY280502.1; BC059387.1; BC061522.1; U50532.1; BC006547.2; BC008797.2; BC000807.1; AL080112.1; BC033718.1 /// BC046176.1 ///; BC038443.1; Hs.288575 (UNIGENE ID); AF020591.1; BC002503.2; BC009185.2; Hs.528304 (UNIGENE ID); U50532.1; BC013923.2; BC031091; Hs.249591 (Unigene ID); Hs.286261 (Unigene BD); AF348514.1; BC066337.1 /// BC058736.1 /// BC050555.1; Hs.216623 (Unigene ED); BC072400.1; BC041073.1; U43965.1; BC021258.2; BCO 16057.1; BCO 6713.1 ///BC014535.1 /// AF237771.1; BC000701.2; BC010067.2; Hs.156701 (Unigene ID); BC030619.2; U43965.1; Hs.438867 (Unigene ID); BC035025.2 /// BC050330.1; BC074852.2 /// BC074851.2; Hs.445885 (Unigene ID); AP365931.1; and AP257099.1, and group 6 consisting of genes with GenBank or Unigene identification Nos. NM_014182.1; NM_001281.1; NM_024006.1; AF 135421.1; L76200.1; NM_000346.1; BC008710.1; BC000423.2; BC008710.1; NM_007062; BC075839.1 ///BC073760.1; BC072436.1 /// BC004560.2; BC001016.2; BC005023.1; BC000360.2; BC007455.2; BC023528.2 /// BC047680.1; BC064957.1; BC008710.1; BC066329.1; BC023976.2; BC008591.2 /// BC050440.1 ///; BC048096.1; and BC028912.1, and a group of at least 20 genes selected from group 3 and group 4, group 3 consisting of genes with GenBank or Unigene identification Nos BF218804; K022494.1; AA114843; BE467941; NM_003541.1; R83000; AL161952.1, AK023843.1; AK021571.1; AK023783.1; AU147182; AL080112.1; AW971983; A1683552; NM_024006.1; AK026565.1; NM_014182.1; NM_021800.1; NM_016049.1; NM_019023.1; NM_021971.1; NM_014128.1; AK025651.1; AA133341; and AF198444.1 and group 4 consisting of genes with GenBank or Unigene identification Nos. NM_007062.1; NM_001281.1; BCOOO1 20.1; NM_014255.1; BC002642.1; NM_000346.1; NM_006545.1; BG034328; NM_021822.1; NM_021069.1; NM_019067.1; NM_017925.1; NM_017932.1; NM_030757.1; NM_030972.1; AF126181.1; U93240.1; U90552.1; AF151056.1; U85430.1; U51007.1; BC005969.1; NM_002271.1; AL566172; and AB014576.1, wherein decrease in the expression of the group 5 genes and increase in the expression of the group 6 genes, and decrease the group 3 genes and increase of the group 4 genes is indicative of the individual being affected with a lung disease. 
     
     
         24 . The method of  claim 1 , wherein the transcripts are selected from the group consisting of transcripts encoding CYP1B1; AKR1 B1 O; CYP1 B1; CYP1A1; CYP1B1; CEAC AM5; ALDH3A1; SLC7A11; AKR1C2; NQO1; NQO1; GPX2; MUC5AC; AKR1C2; MUC5AC; AKR1C1; CLDN1O; AKR1C3; NQO1; SLC7A1 1; HGD /// LOC642252; AKR1C1; PIR; CYP4F11; TCN1; TM4SF1; KRT14; ME1; CBR1; ADH7; SPDEF; ME1; CXCL14; SRPX2; UPK1 B; TRIM16 /// TRIM16L ///LOC653524; KLF4; TXN; TKT; DEFB1; CSTA; CEACAM6; TALDO1; CA 12; GCLM; PGD; TXNRD1; CEACAM6; GCLC; GPC 1; TFF1; CABYR; CA12; UPK1B; GALNT6; TKT; TSPAN8; UGT1 A1O /// UGT1 A8 /// UGT1 A7 /// UGT1 A6 /// UGT1 A; SPDEF; MSMB; ANXA3; MUC5AC; CTGF; IDS; CA12; FTH1; HN1; DPYSL3; GMDS; UGT1A1O /// UGT1A8 /// UGT1A7 /// UGT1A6 /// UGT1A; ABHD2; GCLC; GALNT7; MSMB; HTATIP2; UGT1 A1O /// UGT1 A8 /// UGT1 A7 ///UGT1 A6 /// UGT1A; S1OOA1O; DAZ1 /V/DAZ3 /// DAZ2 /// DAZ4; IDS; PRDX1; CYP4F3; UGT1A1O /// UGT1A8 /// UGT1A7 /// UGT1A6 /// UGT1A; AGR2; S1OOP; NDUF A7; MAFG; ZNF323; AP2B1; UGT1A6; NKX3-1; SEPX1; CTSC; GCNT3; GULP1; LOC283677; SMPDL3A; SLC35A3; WBP5; TARS; EIF2AK3; C11orf32; GALNT12; VPS13D; BCL2L13; IMPA2; GMDS; AZGP1; PLCE1; FOLH1; NUDT4 /// NUDT4P1; TAGLN2; GNE; TSPAN13; GALNT3; HMGN4; SCP2; PLA2G10; GULPI; DIAPH2; RAP1GAP; FTH1; LYPLA1; CREB3L1; AKR1B1; RAB2; SCGB2A1; KIAA0367; ABCC1; TPARL; ABHD2; TSPAN1; DHRS3; ABCC1; FKBPI1; TTC9; GSTM3; S100A14; SLC35AI; ENTPD4; P4HB; AGTPBP1; NADK; B4GALT5; CCPG1; PTP4A1; DSG2; CCNG2; CPNE3; SEC31L1; SLC3A2; ARPC3; CDC14B; SLC17A5; HIST1H2AC; CBLB; HIST1H2BK; TOMIL1; TIMP1; ABCB6; GFPT1; TIAM1; SORL1; PAM; NADK; RND3; XPOT; SERINC5; GSN; HIGD1A; PDIA3; C3orf14; PRDX4; RAB7; GPR153; ARLI; IDS; GHITM; RGC32; TMED2; PTS; GTF3C1; IDH1; LAMP2; ACTL6A; RAB1 IA; COX5A; APLP2; PTK9; UBE2J1; TACSTD2; PSMD14; PDIA4; MTMR6; FA2H; NUDT4; TBC1D16; PIGP; CCDC28A; AACS; CHP; TJP2; EFHD2; KATNB1; SPA17; TPBG; GALNT1; HSP90B1; TMED1O; SOD1; BECN1; C14orf1; COPB2; TXNDC5; SSR4; TLE1; TXNL1; LRRC8D; PSMB5; SQSTM1; ETHE1; RPN2; TIPARP; CAP1; LOC92482; FKBP1A; EDEM1; CANX; TMEM59; GUK1; LOC57228; SPINT2; C20orf1 11; ECOP; JTB; REXO2; UFD1L; DDX17; SSH3; TRIOBP; GGA1; FAM53C; PPP3CC; SFRS14; ACTN1; SPEN; CYP2J2; TLE2; ProSAPiP1; PFTK1; PCDH7; FLNB; SIX2; CD81; ZNF331; AMACR; GNB5; CUGBP1; EDD1; TLR5; MGLL; CHST4; SERPINI2; PPAP2B; BCL1IA; STEAP3; SYNGR1; CRYM; RUTBC1; PARVA; NFIB; TCF7L1; MAGI2; CCDC81; COL9A2; CNKSR1; NCOR2; INHBB; PEX1 4; TSP AN9; RAB6B; GSTM5; FLJ10159; TNS1; MT2A; TNFSF 13 /// TNFSF12-TNFSF13; 1-Mar; ELF5; JAG2; FLJ23191; PHGDH; CYP2F1; TNS3; GAS6; CD302; PTPRM; CCND1; TNFSF13 /// TNFSF12-TNFSF13; ADCY2; CCND2; MT1X; SNED1; SFRS14; ANXA6; HNMT; AK1; EPOR; EPAS1; PDE8B; CYFIP2; SLIT1; ACCN2; KALI; MT1E; MT1F; HLF; SITPEC; JAG2; HSPA2; LOC650610; KRT15; SORD; ITM2A; PECI; HPGD; CKB; HLF; CYP2A6 /// CYP2A7 /// CYP2A7P1 /// CYP2A13; C14orf132; MT1G; FGFR3; PROS1; FAM107A; MT1X; FXYD1; MT1F; CX3CL1; CX3CL1; CYP2A6; HLF; SLIT2; BCAM; FMO2; MT1H; FLRT3; PRG2; TMEM45A; MMP1O; C3 /// LOC653879; CYP2W1; FABP6; SCGB1A1; MUC5B /// LOC649768; FAM107A; SEC14L3; 210524_x_at; 213169_at; 212126_at; 4351 1_s_at; 213891_s_at; 212233_at; and 217626_at. 
     
     
         25 . The method of  claim 1 , wherein the transcripts are selected from the group consisting of AACS; ABHD2; ADCY2; ADH7; ALDH3AI; AP2B1; APLP2; ARHE; ARL1; ARPC3; ASM3A; AZGP1; C1 4orf1; C1orfS; CANX; CAP1; CCND2; CCNG2; CEACAM5; CEACAM6; CHP; CLDN1O; COX5A; CPNE3; CPR8; CTSC; CYPI A1; CYP2F1; CYP4F11; CYP4F3; DAZ4; DCL-I; DKFZP434J214; DPYSL3; ERP70; FKBP1 1; FKBP1A; FLJ13052; FOLH1; FTH1; GALNT1; GALNT12; GALNT3; GALNT7; GCLM; GCNT3; GFPT1; GMDS; GNE; GRP58; GSN; HGD; HIST1H2BK; HMGN4; HTATIP2; IDS; IMPA2; JTB; KATNB1; KDELR3; KIAA0227; KIAA0367; KIAA0905; KLF4; LAMP2; LOC92689; LRRC5; MEL; MSMB; MT1G; MUC5B; NKX3-1; NQO1; NUDT4; OASIS; P4HB; PDEF; PIR; PLA2G10; PPP3CC; PRDX4; RAB1 IA; RAB2; RAP1GA1; RGC32; RNP24; S1OOA1O; SCGB2A1; SDR1; SEPX1; SLC17A5; SLC35A1; SLC7A11; TACSTD2; TAGLN2; TCN1; T1MP1; TKT; TM4SF13; TM4SF3; TMP21; TXNDC5; UBE2J1; UGT1A1O; UPK1B; CYP1B1 and 203369 x at. 
     
     
         26 . The method of  claim 1 , wherein the transcripts are selected from the group consisting of transcripts encoding for AACS; ABHD2; ADCY2; ADH7; ALDH3A1; AP2B1; APLP2; ARHE; ARL1; ARPC3; ASM3A; AZGP1; C14orf1; C1orfS; CANX; CAP1; CCND2; CCNG2; CEACAM5; CEACAM6; CHP; CLDN1O; COX5A; CPNE3; CPR8; CTSC; CYP1A1; CYP2F1; CYP4F11; CYP4F3; DAZ4; DCL-I; DKFZP434J214; DPYSL3; ERP70; FKBP1 1; FKBP1A; FLJ13052; FOLH1; FTH1; GALNT1; GALNT12; GALNT3; GALNT7; GCLM; GCNT3; GFPT1; GMDS; GNE; GRP58; GSN; HGD; HIST1H2BK; HMGN4; HTAT1P2; IDS; IMPA2; JTB; KATNB1; KDE LR3; KIAA0227; KIAA0367; KIAA0905; KLF4; LAMP2; LOC92689; LRRC5; ME1; MSMB; MT1G; MUC5B; NKX3-1; NQO1; NUDT4; OASIS; P4HB; PDEF; PIR; PLA2G10; PPP3CC; PRDX4; RAB1 IA; RAB2; RAP1GA1; RGC32; RNP24; S1OOA1O; SCGB2A1; SDR1; SEPX1; SLC17A5; SLC35A1; SLC7A11; TACSTD2; TAGLN2; TCN 1; TIMP 1; TKT; TM4SF13; TM4SF3; TMP21; TXNDC5; UBE2J1; UGT1A1O; UPK1B; CYP1B1 and 203369_x_at. 
     
     
         27 . The method of  claim 1 , wherein the transcripts are selected from the group consisting of transcripts encoding for MUC1; CD164; MUC16; MUC4; MUC5AC; CYP2A6; CYP2B7P1; CYP4B1; POR; CYP2F1; DNAI2; DYNLT1; DNALI1; DNAI1; DNAH9; DNAH7; DYNC1I2; DYNC1H1; DYNLL1; DYNLRB1; ESD; GSTM2; GSTM1; GSTK1; GSTA1; GPX4; GPX1; MGST2; GSTP1; GSS; GSTO1; KRT19; KRT7; KRT8; KRT18; KRT1O; KRT1O; KRT17; KRT5; KRT15; MAP1A; MAPRE1; EML2; MAST4; MACF1; ALDH3A1; ALDH1A1; ALDH3B1; ALDH3B1; ALDH3A2; ALDH1L1; ALDH9A1; ALDH2; K-ALPHA-I; TUBB3; TUBGCP2; TBCA; TUBB2A; TUBA4; TUBB2C; TUBA3; TUBA6; K-ALPHA-I; TUBB; TUBA6; TUBA1; TUBB; K-ALPHA-I; 76P; TUBB3; and TUBB2C.