US2010292094A1PendingUtilityA1

Method of diagnosing neoplasms

53
Assignee: CLINICAL GENOMICS PTY LTDPriority: Oct 23, 2007Filed: Oct 23, 2008Published: Nov 18, 2010
Est. expiryOct 23, 2027(~1.3 yrs left)· nominal 20-yr term from priority
G01N 2800/06C12Q 2600/16C12Q 2600/112G01N 33/5753C12Q 2600/158C12Q 1/6886
53
PatentIndex Score
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Claims

Abstract

The present invention relates generally to nucleic acid molecules, the RNA and protein expression profiles of which are indicative of the onset, predisposition to the onset and/or progression of a neoplasm. More particularly, the present invention is directed to nucleic acid molecules, the expression profiles of which are indicative of the onset and/or progression of a large intestine neoplasm, such as an adenoma or an adenocarcinoma. The expression profiles of the present invention are useful in a range of applications including, but not limited to, those relating to the diagnosis and/or monitoring of colorectal neoplasms, such as colorectal adenocarcinomas. Accordingly, in a related aspect the present invention is directed to a method of screening a subject for the onset, predisposition to the onset and/or progression of a neoplasm by screening for modulation in the expression profile of one or more nucleic acid molecule markers.

Claims

exact text as granted — not AI-modified
1 - 30 . (canceled) 
     
     
         31 . A method of screening for the onset or predisposition to the onset of a large intestine neoplasm or monitoring the progress of a neoplasm in an individual, said method comprising measuring the level of expression of one or more genes or transcripts selected from: 
       
         
           
                 
                 
               
                     
                 
                   (i) 
                   the gene, genes or transcripts detected by Affymetrix probeset IDs: 
                 
                 
                 
                 
                 
               
                     
                   201563_at 
                   204702_s_at 
                   205828_at 
                 
                     
                   201328_at 
                   221577_x_at 
                   205886_at 
                 
                     
                   201341_at 
                   221922_at 
                   205890_s_at 
                 
                     
                   201416_at 
                   60474_at 
                   205910_s_at 
                 
                     
                   201417_at 
                   222696_at 
                   205941_s_at 
                 
                     
                   201468_s_at 
                   223447_at 
                   206224_at 
                 
                     
                   201506_at 
                   223970_at 
                   206976_s_at 
                 
                     
                   201656_at 
                   225541_at 
                   207173_x_at 
                 
                     
                   201925_s_at 
                   225835_at 
                   207457_s_at 
                 
                     
                   201926_s_at 
                   226360_at 
                   208079_s_at 
                 
                     
                   202286_s_at 
                   227174_at 
                   208712_at 
                 
                     
                   202718_at 
                   227475_at 
                   209218_at 
                 
                     
                   202831_at 
                   228303_at 
                   209309_at 
                 
                     
                   202833_s_at 
                   228653_at 
                   209752_at 
                 
                     
                   202935_s_at 
                   228754_at 
                   209773_s_at 
                 
                     
                   202936_s_at 
                   228915_at 
                   209774_x_at 
                 
                     
                   203124_s_at 
                   229215_at 
                   209792_s_at 
                 
                     
                   203256_at 
                   231832_at 
                   209875_s_at 
                 
                     
                   203313_s_at 
                   231941_s_at 
                   209955_s_at 
                 
                     
                   203510_at 
                   232176_at 
                   210052_s_at 
                 
                     
                   203860_at 
                   232252_at 
                   210511_s_at 
                 
                     
                   203895_at 
                   232481_s_at 
                   210559_s_at 
                 
                     
                   203896_s_at 
                   234331_s_at 
                   210766_s_at 
                 
                     
                   203961_at 
                   235210_s_at 
                   211506_s_at 
                 
                     
                   203962_s_at 
                   235976_at 
                   212281_s_at 
                 
                     
                   204259_at 
                   236894_at 
                   212344_at 
                 
                     
                   204351_at 
                   238017_at 
                   212353_at 
                 
                     
                   204401_at 
                     
                   212354_at 
                 
                     
                   204404_at 
                   238984_at 
                   213905_x_at 
                 
                     
                   204855_at 
                   241031_at 
                   214022_s_at 
                 
                     
                   204885_s_at 
                   200660_at 
                   214974_x_at 
                 
                     
                   205174_s_at 
                   200832_s_at 
                   215091_s_at 
                 
                     
                   205366_s_at 
                   200903_s_at 
                   217430_x_at 
                 
                     
                   205470_s_at 
                   201014_s_at 
                   217996_at 
                 
                     
                   205513_at 
                   201112_s_at 
                   218507_at 
                 
                     
                   205765_at 
                   201195_s_at 
                   218963_s_at 
                 
                     
                   205825_at 
                   201261_x_at 
                   218984_at 
                 
                     
                   205927_s_at 
                   201292_at 
                   219787_s_at 
                 
                     
                   205983_at 
                   201338_x_at 
                   219911_s_at 
                 
                     
                   206239_s_at 
                   201479_at 
                   221729_at 
                 
                     
                   206286_s_at 
                   201577_at 
                   221730_at 
                 
                     
                   207158_at 
                   201601_x_at 
                   221731_x_at 
                 
                     
                   207850_at 
                   201666_at 
                   221923_s_at 
                 
                     
                   209369_at 
                   202310_s_at 
                   37892_at 
                 
                     
                   210445_at 
                   202311_s_at 
                   222449_at 
                 
                     
                   210519_s_at 
                   202404_s_at 
                   222450_at 
                 
                     
                   211429_s_at 
                   202431_s_at 
                   222549_at 
                 
                     
                   212063_at 
                   202504_at 
                   222608 s_at 
                 
                     
                   212070_at 
                   202779_s_at 
                   223062_s_at 
                 
                     
                   212190_at 
                   202859_x_at 
                   224428_s_at 
                 
                     
                   212531_at 
                   202954_at 
                   224646_x_at 
                 
                     
                   212942_s_at 
                   202998_s_at 
                   224915_x_at 
                 
                     
                   213880_at 
                   203083_at 
                   225295_at 
                 
                     
                   213975_s_at 
                   203213_at 
                   225520_at 
                 
                     
                   214235_at 
                   203878_s_at 
                   225664_at 
                 
                     
                   214651_s_at 
                   204051_s_at 
                   225681_at 
                 
                     
                   217523_at 
                   204127_at 
                   225767_at 
                 
                     
                   217867_x_at 
                   204170_s_at 
                   225799_at 
                 
                     
                   218086_at 
                   204320_at 
                   225806_at 
                 
                     
                   218211_s_at 
                   204470_at 
                   226227_x_at 
                 
                     
                   218704_at 
                   204475_at 
                   226237_at 
                 
                     
                   218796_at 
                   204580_at 
                   226311_at 
                 
                     
                   218872_at 
                   204620_s_at 
                   226777_at 
                 
                     
                   219630_at 
                   205361_s_at 
                   226835_s_at 
                 
                     
                   219682_s_at 
                   205476_at 
                   227140_at 
                 
                     
                   219727_at 
                   205479_s_at 
                   229802_at 
                 
                     
                   219955_at 
                   205713_s_at 
                   231766_s_at 
                 
                     
                   219956_at 
                   205815_at 
                   232151_at; and/or 
                 
                     
                   200665_s_at 
                 
                 
                 
                 
                 
                 
               
                   (ii) 
                   SORD 
                   NFE2L3 
                   CDCA7 
                   LOXL2 
                 
                     
                   KIAA1199 
                   RNF43 
                   TDGF1 
                   AZGP1 
                 
                     
                   FOXQ1 
                   CCL20 
                   MTHFD1L 
                   MYC 
                 
                     
                   MMP1 
                   CTSE 
                   ANLN 
                   COMP 
                 
                     
                   TCN1 
                   MSLN 
                   H19 
                   AURKA 
                 
                     
                   MMP7 
                   TIMP1 
                   FAP 
                   PAICS 
                 
                     
                   WDR72 
                   PCSK1 
                   DACH1 
                   PUS7 
                 
                     
                   INHBA 
                   CST1 
                   VCAN 
                   ZNRF3 
                 
                     
                   COL11A1 
                   BGN 
                   SQLE 
                   CCND1 
                 
                     
                   GDF15 
                   AXIN2 
                   REG3A 
                   CSE1L 
                 
                     
                   CTHRC1 
                   MET 
                   TESC 
                   PFDN4 
                 
                     
                   COL1A1 
                   SOX9 
                   UBE2C 
                   C20orf42 
                 
                     
                   LGR5 
                   TMEPAI 
                   TMEM97 
                   SLC11A2 
                 
                     
                   DUSP27 
                   CDH11 
                   TRIM29 
                   CEL 
                 
                     
                   SERPINB5 
                   MMP11 
                   KLK11 
                   NLF1 
                 
                     
                   ASCL2 
                   CXCL1 
                   LY6G6D 
                   NPDC1 
                 
                     
                   SULF1 
                   QPCT 
                   SLC7A5 
                   ENC1 
                 
                     
                   SLC6A6 
                   PDZK1IP1 
                   FABP6 
                   SERPINE2 
                 
                     
                   TACSTD2 
                   CD55 
                   SLITRK6 
                   UBE2S 
                 
                     
                   NEBL 
                   ECT2 
                   MLPH 
                   TOP2A 
                 
                     
                   PCCA 
                   COL12A1 
                   HOXA9 
                   CDC2 
                 
                     
                   FLJ37644 
                   L1TD1 
                   TBX3 
                   RFC3 
                 
                     
                   KRT23 
                   WDR51B 
                   BACE2 
                   LILRB1 
                 
                     
                   CXCL3 
                   HOXB6 
                   GPX2 
                   NPM1 
                 
                     
                   MMP3 
                   FAM84A 
                   TPX2 
                   RDHE2 
                 
                     
                   SFRP4 
                   COL5A2 
                   KCNN4 
                   PLAU 
                 
                     
                   UBD 
                   MMP12 
                   LOC541471 
                   HSPH1 
                 
                     
                   SCD 
                   PSAT1 
                   CYP3A5 
                   GTF3A 
                 
                     
                   DPEP1 
                   CXCL5 
                   ANXA3 
                   KLK10 
                 
                     
                   LCN2 
                   IGFBP2 
                   CYP3A5P2 
                   GPSM2 
                 
                     
                   PLCB4 
                   TGIF1 
                   C14orf94 
                   NME1 
                 
                     
                   SPINK1 
                   CXCL2 
                   RP5-875H10.1 
                   MUC20 
                 
                     
                   DUOX2 
                   SLCO4A1 
                   RPL22L1 
                   RPESP 
                 
                     
                   SOX4 
                   CKS2 
                   APOBEC1 
                   RRM2 
                 
                     
                   THBS2 
                   PHLDA1 
                   HIG2 
                   DKC1 
                 
                     
                   CLDN1 
                   SERPINA1 
                   COL10A1 
                   CD44 
                 
                     
                   REG1B 
                   COL1A2 
                   AHCY 
                 
                     
                   CDH3 
                     
                   IL8 
                 
                     
                   SPARC 
                 
                     
                 
             
                
               
               
                
               
            
             
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
               
            
             
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
               
            
           
         
       
       in a biological sample from said individual wherein a higher level of expression of the genes or transcripts of group (i) and/or group (ii) relative to control levels is indicative of a neoplastic large intestine cell or a cell predisposed to the onset of a neoplastic state. 
     
     
         32 . The method according to  claim 31  wherein said one or more genes or transcripts are selected from:
 (i) 201563_at, 204702_s_at; and/or   (ii) SORD, NFE2L3.   
     
     
         33 . The method according to  claim 31  wherein said one or more genes or transcripts are selected from:
 (i) the gene, genes or transcripts detected by Affymetrix probeset IDs:
 225681_at; 227140_at; and/or 
   (ii) CTHRC1;   (ii) the gene, genes or transcripts detected by Affymetrix probeset IDs:
 227475_at, 204475_at, 202859_x_at, 202404_s_at; and/or 
 FOXQ1, MMP1, IL8, COL1A2; 
   (iii) the gene, genes or transcripts detected by Affymetrix probeset IDs:
 205513_at, 204259_at, 227174_at, 210511_s_at, 37892_at; and/or 
 TCN1, MMP7, WDR72, INHBA, COL11A1; 
   
       
         
           
                 
                 
               
                     
                 
                   (i) 
                   the gene, genes or transcripts detected by Affymetrix probeset IDs: 
                 
                 
                 
                 
                 
               
                     
                   221577_x_at 
                   212942_s_at 
                   202310_s_at 
                 
                     
                   213880_at 
                   232252_at 
                   204855_at 
                 
                     
                   229215_at 
                   212354_at 
                   228754_at 
                 
                     
                   202286_s_at 
                   203962_s_at 
                   203860_at 
                 
                     
                   202935_s_at 
                   218963_s_at 
                   207850_at 
                 
                     
                   205828_at 
                   204051_s_at 
                   205890_s_at 
                 
                     
                   200832_s_at 
                   205983_at 
                   212531_at; and/or 
                 
                     
                   KIAA1199 
                   GDF15 
                   COL1A1 
                 
                     
                   LGR5 
                   DUSP27 
                   SERPINB5 
                 
                     
                   ASCL2 
                   SULF1 
                   SLC6A6 
                 
                     
                   TACSTD2 
                   NEBL 
                   PCCA 
                 
                     
                   FLJ37644 
                   KRT23 
                   CXCL3 
                 
                     
                   MMP3 
                   SFRP4 
                   UBD 
                 
                     
                   SCD 
                   DPEP1 
                   LCN2; 
                 
                     
                     
                 
             
                
               
               
                
               
            
             
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
               
            
           
         
       
     
     
         34 . The method according to any one of  claims 31 - 33  wherein said control level is a non-neoplastic level. 
     
     
         35 . The method according to  claim 31  wherein said neoplastic cell is an adenoma or an adenocarcinoma. 
     
     
         36 . The method according to  claim 31  wherein said neoplasm is an adenoma and said one or more genes or transcripts are selected from: 
       
         
           
                 
                 
               
                     
                 
                   (i) 
                   the gene, genes or transcripts detected by Affymetrix probeset IDs: 
                 
                 
                 
                 
                 
               
                     
                   201328_at 
                   205825_at 
                   219956_at 
                 
                     
                   201468_s_at 
                   205927_s_at 
                   221922_at 
                 
                     
                   201656_at 
                   206239_s_at 
                   223447_at 
                 
                     
                   201925_s_at 
                   207158_at 
                   223970_at 
                 
                     
                   201926_s_at 
                   210445_at 
                   225835_at 
                 
                     
                   202718_at 
                   210519_s_at 
                   226360_at 
                 
                     
                   202831_at 
                   211429_s_at 
                   228303_at 
                 
                     
                   202833_s_at 
                   212063_at 
                   228653_at 
                 
                     
                   203124_s_at 
                   213975_s_at 
                   228915_at 
                 
                     
                   203313_s_at 
                   214235_at 
                   231832_at 
                 
                     
                   203860_at 
                   214651_s_at 
                   231941_s_at 
                 
                     
                   203895_at 
                   217523_at 
                   232176_at 
                 
                     
                   203896_s_at 
                   217867_x_at 
                   232481_s_at 
                 
                     
                   204401_at 
                   218086_at 
                   234331_s_at 
                 
                     
                   204885_s_at 
                   218211_s_at 
                   235210_s_at 
                 
                     
                   205174_s_at 
                   218796_at 
                   235976_at 
                 
                     
                   205366_s_at 
                   219630_at 
                   236894_at 
                 
                     
                   205470_s_at 
                   219682_s_at 
                   238017_at 
                 
                     
                   205513_at 
                   219727_at 
                   238984_at 
                 
                     
                   205765_at 
                   219955_at; 
                   241031_at; and/or 
                 
                   (ii) 
                   APOBEC1 
                   HOXB6 
                   QPCT 
                 
                     
                   BACE2 
                   IGFBP2 
                   RDHE2 
                 
                     
                   C20orf42 
                   ITGA6 
                   REG4 
                 
                     
                   CD44 
                   KCNN4 
                   RETNLB 
                 
                     
                   CD55 
                   KLK11 
                   RP5-875H10.1 
                 
                     
                   CTSE 
                   L1TD1 
                   RPESP 
                 
                     
                   CYP3A5 
                   LILRB1 
                   SERPINA1 
                 
                     
                   CYP3A5P2 
                   MLPH 
                   SLC11A2 
                 
                     
                   DACH1 
                   MSLN 
                   SLC12A2 
                 
                     
                   DUOX2 
                   MUC20 
                   SLITRK6 
                 
                     
                   ETS2 
                   NLF1 
                   SPINK1 
                 
                     
                   FABP6 
                   NPDC1 
                   TBX3 
                 
                     
                   FAM84A 
                   NQO1 
                   TCN1 
                 
                     
                   GALNT6 
                   PCCA 
                   TGIF1 
                 
                     
                   GPSM2 
                   PCSK1 
                   WDR51B 
                 
                     
                   GPX2 
                   PDZK1IP1 
                   ZNRF3 
                 
                     
                   HOXA9 
                   PLCB4. 
                 
                     
                 
             
                
               
               
                
               
            
             
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
               
            
           
         
       
     
     
         37 . The method according to  claim 31  wherein said neoplasm is a cancer and said one or more genes or transcripts are selected from: 
       
         
           
                 
                 
               
                     
                 
                   (i) 
                   the gene, genes or transcripts detected by Affymetrix probeset IDs: 
                 
                 
                 
                 
                 
               
                     
                   204702_s_at 
                   205476_at 
                   217430_x_at 
                 
                     
                   200660_at 
                   205479_s_at 
                   217996_at 
                 
                     
                   200665_s_at 
                   205713_s_at 
                   218507_at 
                 
                     
                   200832_s_at 
                   205815_at 
                   218963_s_at 
                 
                     
                   200903_s_at 
                   205828_at 
                   218984_at 
                 
                     
                   201014_s_at 
                   205886_at 
                   219787_s_at 
                 
                     
                   201112_s_at 
                   205890_s_at 
                   219911_s_at 
                 
                     
                   201195_s_at 
                   205910_s_at 
                   221729_at 
                 
                     
                   201261_x_at 
                   205941_s_at 
                   221730_at 
                 
                     
                   201292_at 
                   206224_at 
                   221731_x_at 
                 
                     
                   201338_x_at 
                   206976_s_at 
                   221923_s_at 
                 
                     
                   201479_at 
                   207173_x_at 
                   37892_at 
                 
                     
                   201577_at 
                   207457_s_at 
                   222449_at 
                 
                     
                   201601_x_at 
                   208079_s_at 
                   222450_at 
                 
                     
                   201666_at 
                   208712_at 
                   222549_at 
                 
                     
                   202310_s_at 
                   209218_at 
                   222608_s_at 
                 
                     
                   202311_s_at 
                   209309_at 
                   223062_s_at 
                 
                     
                   202403_s_at 
                   209752_at 
                   224428_s_at 
                 
                     
                   202404_s_at 
                   209773_s_at 
                   224646_x_at 
                 
                     
                   202431_s_at 
                   209774_x_at 
                   224915_x_at 
                 
                     
                   202504_at 
                   209792_s_at 
                   225295_at 
                 
                     
                   202779_s_at 
                   209875_s_at 
                   225520_at 
                 
                     
                   202859_x_at 
                   209955_s_at 
                   225664_at 
                 
                     
                   202954_at 
                   210052_s_at 
                   225681_at 
                 
                     
                   202998_s_at 
                   210511_s_at 
                   225767_at 
                 
                     
                   203083_at 
                   210559_s_at 
                   225799_at 
                 
                     
                   203213_at 
                   210766_s_at 
                   225806_at 
                 
                     
                   203878_s_at 
                   211506_s_at 
                   226227_x_at 
                 
                     
                   204051_s_at 
                   212281_s_at 
                   226237_at 
                 
                     
                   204127_at 
                   212344_at 
                   226311_at 
                 
                     
                   204170_s_at 
                   212353_at 
                   226777_at 
                 
                     
                   204320_at 
                   212354_at 
                   226835_s_at 
                 
                     
                   204470_at 
                   213905_x_at 
                   227140_at 
                 
                     
                   204475_at 
                   214022_s_at 
                   229802_at 
                 
                     
                   204580_at 
                   214974_x_at 
                   231766_s_at 
                 
                     
                   204620_s_at 
                   215091_s_at; 
                   232151_at; and/or 
                 
                     
                   205361_s_at 
                 
                   (ii) 
                   NFE2L3 
                   DKC1 
                   PSAT1 
                 
                     
                   AHCY 
                   ECT2 
                   PUS7 
                 
                     
                   ANLN 
                   FAP 
                   REG1A 
                 
                     
                   AURKA 
                   GTF3A 
                   REG1B 
                 
                     
                   AZGP1 
                   H19 
                   REG3A 
                 
                     
                   BGN 
                   HIG2 
                   RFC3 
                 
                     
                   C14orf94 
                   HSPH1 
                   RRM2 
                 
                     
                   C20orf199 
                   IFITM1 
                   S100A11 
                 
                     
                   CCL20 
                   IL8 
                   SCD 
                 
                     
                   CCND1 
                   INHBA 
                   SFRP4 
                 
                     
                   CDC2 
                   KLK10 
                   SLC39A10 
                 
                     
                   CDCA7 
                   KRT23 
                   SLC7A5 
                 
                     
                   CDH11 
                   LOC541471 
                   SLCO4A1 
                 
                     
                   CEL 
                   LOXL2 
                   SPARC 
                 
                     
                   CKS2 
                   LY6G6D 
                   SPP1 
                 
                     
                   CLDN1 
                   MMP1 
                   SQLE 
                 
                     
                   COL10A1 
                   MMP11 
                   SULF1 
                 
                     
                   COL11A1 
                   MMP12 
                   THBS2 
                 
                     
                   COL12A1 
                   MMP3 
                   TIMP1 
                 
                     
                   COL1A1 
                   MTHFD1L 
                   TMEM97 
                 
                     
                   COL1A2 
                   MYC 
                   TMEPAI 
                 
                     
                   COL5A2 
                   NME1 
                   TOP2A 
                 
                     
                   COL8A1 
                   NPM1 
                   TPX2 
                 
                     
                   COMP 
                   PAICS 
                   TRIM29 
                 
                     
                   CSE1L 
                   PFDN4 
                   UBD 
                 
                     
                   CST1 
                   PHLDA1 
                   UBE2C 
                 
                     
                   CTHRC1 
                   PLAU 
                   UBE2S 
                 
                     
                   CXCL1 
                     
                   VCAN 
                 
                     
                   CXCL2 
                 
                     
                   CXCL5. 
                 
                     
                 
             
                
               
               
                
               
            
             
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
               
            
           
         
       
     
     
         38 . A method of screening for the onset of a large intestine neoplasm in an individual, said method comprising measuring the level of expression of one or more genes or transcripts selected from: 
       
         
           
                 
                 
               
                     
                 
                   (i) 
                   the gene, genes or transcripts detected by Affymetrix probeset IDs: 
                 
                 
                 
                 
                 
               
                     
                   204702_s_at 
                   235976_at 
                   209309_at 
                 
                     
                   202286_s_at 
                   236894_at 
                   211506_s_at 
                 
                     
                   204259_at 
                     
                   214974_x_at 
                 
                     
                   204885_s_at 
                   238984_at 
                   219787_s_at 
                 
                     
                   205174_s_at 
                   241031_at 
                   37892_at 
                 
                     
                   205825_at 
                   202311_s_at 
                   222608_s_at 
                 
                     
                   207850_at 
                   204320_at 
                   223062_s_at 
                 
                     
                   213880_at 
                   204475_at 
                   225806_at 
                 
                     
                   217523_at 
                   205910_s_at 
                   226237_at 
                 
                     
                   227174_at 
                   206224_at 
                   227140_at 
                 
                     
                   228915_at 
                     
                   229802_at; and/or 
                 
                     
                   232252_at 
                 
                   (ii) 
                   NFE2L3 
                   PCSK1 
                   ANLN 
                 
                     
                   MMP1 
                   CST1 
                   DACH1 
                 
                     
                   MMP7 
                   QPCT 
                   COL11A1 
                 
                     
                   LGR5 
                   ECT2 
                   C14orf94 
                 
                     
                   WDR72 
                   SLITRK6 
                   AZGP1 
                 
                     
                   COL11A1 
                   L1TD1 
                   REG4 
                 
                     
                   COL1A1 
                   KIAA1199 
                   CEL 
                 
                     
                   DUSP27 
                   PSAT1 
                   CD44 
                 
                     
                   NLF1 
                   CXCL5 
                   COL8A1 
                 
                     
                   IL8 
                   CXCL3 
                 
                     
                   TACSTD2 
                 
                     
                   MSLN 
                 
                     
                 
             
                
               
               
                
               
            
             
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
               
            
           
         
       
       in a biological sample from said individual wherein a higher level of expression of the genes or transcripts of group (i) and/or group (ii) relative to background levels is indicative of a neoplastic cell or a cell predisposed to the onset of a neoplastic state. 
     
     
         39 . The method according to  claim 38  wherein said neoplastic cell is an adenoma or adenocarcinoma. 
     
     
         40 . The method according to  claim 38  wherein said neoplasm is an adenoma and said one or more genes or transcripts are selected from:
 (i) the gene, genes or transcripts detected by Affymetrix probeset IDs:
 204885_s_at, 217523_at, 236894_at, 205174_s_at, 228915_at, 238984_at, 205825_at, 235976_at, 241031_at; and/or 
   (ii) CD44, MSLN, QPCT, DACH1, NLF1, REG4, L1TD1, PCSK1, SLITRK6.   
     
     
         41 . The method according to  claim 38  wherein said neoplasm is a cancer and said one or more genes or transcripts are selected from: 
       
         
           
                 
                 
               
                     
                 
                   (i) 
                   the gene or genes detected by Affymetrix probeset IDs: 
                 
                 
                 
                 
                 
               
                     
                   204702_s_at 
                   209309_at 
                   223062_s_at 
                 
                     
                   202311_s_at 
                   211506_s_at 
                   225806_at 
                 
                     
                   204320_at 
                   214974_x_at 
                   226237_at 
                 
                     
                   204475_at 
                   219787_s_at 
                   227140_at 
                 
                     
                   205910_s_at 
                   37892_at 
                   229802_at; and/or 
                 
                     
                   206224_at 
                   222608_s_at 
                 
                   (ii) 
                   NFE2L3 
                   COL1A1 
                   IL8 
                 
                     
                   ANLN 
                   COL8A1 
                   MMP1 
                 
                     
                   AZGP1 
                   CST1 
                 
                     
                   C14orf94 
                   CXCL5 
                 
                     
                   CEL 
                   ECT2. 
                   PSAT1 
                 
                     
                   COL11A1 
                 
                     
                 
             
                
               
               
                
               
            
             
                
                
                
                
                
                
                
                
                
                
                
                
                
               
            
           
         
       
     
     
         42 . The method according to any one of  claims 38 - 41  wherein said background level is the background of the testing methodology. 
     
     
         43 . A method of characterising a neoplastic cell or cellular population, which cell or cellular population is derived from the large intestine of an individual, said method comprising measuring the level of expression of one or more genes or transcripts selected from: 
       
         
           
                 
                 
               
                     
                 
                   (i) 
                   the gene, genes or transcripts detected by Affymetrix probeset IDs: 
                 
                 
                 
                 
                 
               
                     
                   200884_at 
                   214234_s_at 
                   226248_s_at 
                 
                     
                   203240_at 
                   214235_at 
                   226302_at 
                 
                     
                   203963_at 
                   214433_s_at 
                   227676_at 
                 
                     
                   204508_s_at 
                   215125_s_at 
                   227719_at 
                 
                     
                   204607_at 
                   215867_x_at 
                   227725_at 
                 
                     
                   204811_s_at 
                   217109_at 
                   228232_s_at 
                 
                     
                   204895_x_at 
                   217110_s_at 
                   229070_at 
                 
                     
                   204897_at 
                   218211_s_at 
                   231832_at 
                 
                     
                   205259_at 
                   219543_at 
                   232176_at 
                 
                     
                   205765_at 
                   219955_at 
                   232481_s_at 
                 
                     
                   205927_s_at 
                   221841_s_at 
                   235976_at 
                 
                     
                   208063_s_at 
                   221874_at 
                   236894_at 
                 
                     
                   208937_s_at 
                   223969_s_at 
                   237521_x_at 
                 
                     
                   210107_at 
                   223970_at 
                   242601_at 
                 
                     
                   213106_at; and/or 
                 
                   (ii) 
                   CLCA1 
                   CTSE 
                   ATP8B1 
                 
                     
                   FCGBP 
                   C6orf105 
                   CACNA2D2 
                 
                     
                   HMGCS2 
                   CKB 
                   KLF4 
                 
                     
                   RETNLB 
                   ATP8A1 
                   CYP3A5P2 
                 
                     
                   L1TD1 
                   MUC4 
                   CAPN9 
                 
                     
                   SLITRK6 
                   UGT1A1 
                   NR3C2 
                 
                     
                   VSIG2 
                   SELENBP1 
                   PBLD 
                 
                     
                   LOC253012 
                   PTGER4 
                   CA12 
                 
                     
                   ST6GALNAC1 
                   MLPH 
                   WDR51B 
                 
                     
                   ID1 
                   KIAA1324 
                   FAM3D 
                 
                     
                   CYP3A5 
                 
                     
                 
             
                
               
               
                
               
            
             
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
               
            
           
         
       
       in said cell or cellular population wherein a higher level of expression of the genes or transcripts of group (i) and/or group (ii) relative to a gastrointestinal cancer cell level is indicative of an adenoma cell or a cell predisposed to the onset of an adenoma state. 
     
     
         44 . A method of characterising a neoplastic cell or cellular population, which cell or cellular population is derived from the large intestine of an individual, said method comprising measuring the level of expression of one or more genes or transcripts selected from: 
       
         
           
                 
                 
               
                     
                 
                   (i) 
                   the gene, genes or transcripts detected by Affymetrix probeset IDs: 
                 
                 
                 
                 
                 
               
                     
                   200600_at 
                   204006_s_at 
                   213428_s_at 
                 
                     
                   200665_s_at 
                   204051_s_at 
                   213524_s_at 
                 
                     
                   200832_s_at 
                   204122_at 
                   213869_x_at 
                 
                     
                   200974_at 
                   204320_at 
                   213905_x_at 
                 
                     
                   200986_at 
                   204475_at 
                   214247_s_at 
                 
                     
                   201058_s_at 
                   204620_s_at 
                   215049_x_at 
                 
                     
                   201069_at 
                   205479_s_at 
                   215076_s_at 
                 
                     
                   201105_at 
                   205547_s_at 
                   215646_s_at 
                 
                     
                   201141_at 
                   205828_at 
                   216442_x_at 
                 
                     
                   201147_s_at 
                   207173_x_at 
                   217430_x_at 
                 
                     
                   201150_s_at 
                   207191_s_at 
                   217762_s_at 
                 
                     
                   201162_at 
                   208747_s_at 
                   217763_s_at 
                 
                     
                   201163_s_at 
                   208782_at 
                   217764_s_at 
                 
                     
                   201185_at 
                   208788_at 
                   218468_s_at 
                 
                     
                   201261_x_at 
                   208850_s_at 
                   218469_at 
                 
                     
                   201289_at 
                   208851_s_at 
                   218559_s_at 
                 
                     
                   201426_s_at 
                   209101_at 
                   218638_s_at 
                 
                     
                   201438_at 
                   209156_s_at 
                   219087_at 
                 
                     
                   201616_s_at 
                   209218_at 
                   221011_s_at 
                 
                     
                   201645_at 
                   209395_at 
                   221729_at 
                 
                     
                   201667_at 
                   209396_s_at 
                   221730_at 
                 
                     
                   201744_s_at 
                   209596_at 
                   221731_x_at 
                 
                     
                   201792_at 
                   209875_s_at 
                   37892_at 
                 
                     
                   201842_s_at 
                   209955_s_at 
                   223122_s_at 
                 
                     
                   201852_x_at 
                   210095_s_at 
                   223235_s_at 
                 
                     
                   201859_at 
                   210495_x_at 
                   224560_at 
                 
                     
                   201893_x_at 
                   210511_s_at 
                   224694_at 
                 
                     
                   202237_at 
                   210764_s_at 
                   224724_at 
                 
                     
                   202238_s_at 
                   210809_s_at 
                   225664_at 
                 
                     
                   202283_at 
                   211161_s_at 
                   225681_at 
                 
                     
                   202291_s_at 
                   211571_s_at 
                   225710_at 
                 
                     
                   202310_s_at 
                   211719_x_at 
                   225799_at 
                 
                     
                   202311_s_at 
                   211813_x_at 
                   226237_at 
                 
                     
                   202403_s_at 
                   211896_s_at 
                   226311_at 
                 
                     
                   202404_s_at 
                   211959_at 
                   226694_at 
                 
                     
                   202450_s_at 
                   211964_at 
                   226777_at 
                 
                     
                   202620_s_at 
                   211966_at 
                   226930_at 
                 
                     
                   202766_s_at 
                   211980_at 
                   227099_s_at 
                 
                     
                   202859_x_at 
                   211981_at 
                   227140_at 
                 
                     
                   202878_s_at 
                   212077_at 
                   227566_at 
                 
                     
                   202917_s_at 
                   212344_at 
                   229218_at 
                 
                     
                   202998_s_at 
                   212353_at 
                   229802_at 
                 
                     
                   203083_at 
                   212354_at 
                   231579_s_at 
                 
                     
                   203325_s_at 
                   212464_s_at 
                   231766_s_at 
                 
                     
                   203382_s_at 
                   212488_at 
                   231879_at 
                 
                     
                   203477_at 
                   212489_at 
                   232458_at 
                 
                     
                   203570_at 
                   212667_at 
                   233555_s_at 
                 
                     
                   203645_s_at 
                   213125_at 
                   234994_at 
                 
                     
                   203878_s_at; and/or 
                 
                   (ii) 
                   COL1A2 
                   LGALS1 
                   SRGN 
                 
                     
                   CTHRC1 
                   ELOVL5 
                   LBH 
                 
                     
                   FN1 
                   MGP 
                   CTGF 
                 
                     
                   POSTN 
                   MMP2 
                   TNC 
                 
                     
                   SPP1 
                   LOXL2 
                   G0S2 
                 
                     
                   MMP1 
                   MYL9 
                   SQLE 
                 
                     
                   SPARC 
                   DCN 
                   EFEMP1 
                 
                     
                   LUM 
                   CALD1 
                   APOE 
                 
                     
                   GREM1 
                   FBN1 
                   MSN 
                 
                     
                   IL8 
                   MMP3 
                   IGFBP3 
                 
                     
                   IGFBP5 
                   IGFBP7 
                   SERPINF1 
                 
                     
                   SFRP2 
                   FSTL1 
                   ISLR 
                 
                     
                   SULF1 
                   COL4A2 
                   HNT 
                 
                     
                   ASPN 
                   VCAN 
                   COL5A1 
                 
                     
                   COL6A3 
                   SMOC2 
                   OLFML2B 
                 
                     
                   COL8A1 
                   HTRA1 
                   KIAA1913 
                 
                     
                   COL12A1 
                   CYR61 
                   PALM2-AKAP2 
                 
                     
                   COL5A2 
                   FAP 
                   SERPING1 
                 
                     
                   CDH11 
                   VIM 
                   TYROBP 
                 
                     
                   THBS2 
                   TIMP2 
                   ACTA2 
                 
                     
                   COL15A1 
                   SCD 
                   COL3A1 
                 
                     
                   COL11A1 
                   TIMP3 
                   PLOD2 
                 
                     
                   S100A8 
                   AEBP1 
                   MMP11 
                 
                     
                   FNDC1 
                   GJA1 
                   CD163 
                 
                     
                   SFRP4 
                   NNMT 
                   FCGR3B 
                 
                     
                   INHBA 
                   COL1A1 
                   PLAU 
                 
                     
                   COL6A2 
                   SULF2 
                   MAFB 
                 
                     
                   ANTXR1 
                   COL6A1 
                   LOC541471 
                 
                     
                   GPNMB 
                   SPON2 
                   LOC387763 
                 
                     
                   BGN 
                   CTSK 
                   CHI3L1 
                 
                     
                   TAGLN 
                   MXRA5 
                   THY1 
                 
                     
                   COL4A1 
                   C1S 
                   LOXL1 
                 
                     
                   RAB31 
                   DKK3 
                   CD93 
                 
                     
                 
             
                
               
               
                
               
            
             
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
               
            
           
         
       
       in a biological sample from said individual wherein a higher level of expression of the genes or transcripts of group (i) and/or group (ii) relative to a gastrointestinal adenoma cell level is indicative of a cancer or a cell predisposed to the onset of a cancerous state. 
     
     
         45 . The method according to  claim 43  wherein said one or more genes or transcripts are selected from:
 (i) the gene or genes detected by Affymetrix probeset IDs:
 210107_at; and/or 
 CLCA1; 
   (ii) the gene, genes or transcripts detected by Affymetrix probeset IDs:
 203240_at, 219955_at, 242601_at, 204607_at, 232481_s_at, 227725_at, 223969_s_at, 228232_s_at; and/or 
 FCGBP, LITD1, LOC253012, HMGCS2, SLITRK6, ST6GALNAC1, RETNLB, VSIG2; 
   (iii) said control level is the background level of neoplastic tissue and said one or more genes or transcripts are selected from:   
       
         
           
                 
               
                     
                 
                   the gene, genes or transcripts detected by Affymetrix probeset IDs: 
                 
                     
                 
                     
                 
                 
                 
                 
               
                     
                   235976_at 
                   236894_at; and/or 
                 
                     
                   SLITRK6 
                   L1TD1. 
                 
                     
                     
                 
             
                
                
                
               
               
                
               
            
             
                
                
                
               
            
           
         
         (iv) said control level is the background level of neoplastic tissue and said one or more genes or transcripts selected from:
 the gene, genes or transcripts detected by Affymetrix probeset IDs: 
 202311_s_at, 209396_s_at, 226237_at, 204320_at, 215646_s_at, 227140_at, 204475_at, 37892_at, 229802_at, 209395_at; and/or, 
 COL1A1, VCAN, CHI3L1, MMP1, COL8A1, COL11A1. 
 
       
     
     
         46 . The method according to  claim 44  wherein said one or more genes or transcripts are selected from:
 (i) the gene, genes or transcripts detected by Affymetrix probeset IDs:
 202404_s_at, 210809_s_at, 227140_at, 225681_at, 209875_s_at, 204475_at, 212464_s_at; and/or 
 COL1A2, FN1, SPP1, CTHRC1, POSTN, MMP1; 
   (ii) the gene, genes or transcripts detected by Affymetrix probeset IDs:
 200665_s_at, 218468_s_at, 211959_at, 201744_s_at, 202859_x_at; and/or 
 SPARC, GREM1, IGFBP5, LUM, IL8; 
   
       
         
           
                 
                 
               
                     
                 
                   (iii) 
                   the gene, genes or transcripts detected by Affymetrix probeset IDs: 
                 
                 
                 
                 
                 
               
                     
                   223122_s_at 
                   207173_x_at 
                   210511_s_at 
                 
                     
                   212353_at 
                   203083_at 
                   209156_s_at 
                 
                     
                   219087_at 
                   203477_at 
                   224694_at 
                 
                     
                   201438_at 
                   37892_at 
                   201141_at 
                 
                     
                   226237_at 
                   202917_s_at 
                   213905_x_at 
                 
                     
                   225664_at 
                   226930_at 
                   205547_s_at 
                 
                     
                   221730_at 
                   204051_s_at; 
                   and/or 
                 
                     
                   SFRP2 
                   CDH11 
                   INHBA 
                 
                     
                   SULF1 
                   THBS2 
                   COL6A2 
                 
                     
                   ASPN 
                   COL15A1 
                   ANTXR1 
                 
                     
                   COL6A3 
                   COL11A1 
                   GPNMB 
                 
                     
                   COL8A1 
                   S100A8 
                   BGN 
                 
                     
                   COL12A1 
                   FNDC1 
                   TAGLN 
                 
                     
                   COL5A2 
                   SFRP4. 
                 
                     
                     
                 
             
                
               
               
                
               
            
             
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
               
            
           
         
       
     
     
         47 . The method according to any one of  claim 31 ,  38 ,  43  or  44  wherein said cell is a colorectal cell. 
     
     
         48 . The method according to any one of  claim 31 ,  38 ,  43  or  44  wherein said biological sample is a faecal sample, enema wash, surgical resection, tissue biopsy or blood sample. 
     
     
         49 . The method according to any one of  claim 31 ,  38 ,  43  or  44  wherein said level of expression is mRNA expression or protein expression. 
     
     
         50 . The method according to any one of  claim 31 ,  38 ,  43  or  44  wherein said individual is a human. 
     
     
         51 . A molecular array, which array comprises a plurality of:
 nucleic acid molecules comprising a nucleotide sequence corresponding to any one or more of the neoplastic marker genes listed in  claim 31  or a sequence exhibiting at least 80% identity thereto or a functional derivative, fragment, variant or homologue of said nucleic acid molecule; or   (ii) nucleic acid molecules comprising a nucleotide sequence capable of hybridising to any one or more of the sequences of (i) under medium stringency conditions or a functional derivative, fragment, variant or homologue of said nucleic acid molecule; or   (iii) nucleic acid probes or oligonucleotides comprising a nucleotide sequence capable of hybridising to any one or more of the sequences of (i) under medium stringency conditions or a functional derivative, fragment, variant or homologue of said nucleic acid molecule; or   (iv) probes capable of binding to any one or more of the proteins encoded by the nucleic acid molecules of (i) or a derivative, fragment or, homologue thereof   wherein the level of expression of said marker genes of (i) or proteins of (iv) is indicative of the neoplastic state of a cell or cellular subpopulation derived from the large intestine.   
     
     
         52 . The method according to any one of  claim 31 ,  38 ,  43  or  44  wherein said control level is a non-neoplastic level.

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