PATENT DOCUMENT

Abstract:
The present invention provides a set of moieties specific for tumor markers, in particular of follicular thyroid carcinoma (FTC) and papillary thyroid carcinoma (PTC) as well as a method for identifying markers of any genetic disease.

Full Description:
CROSS-REFERENCE TO RELATED APPLICATIONS 
       [0001]    This application is a continuation of U.S. patent application Ser. No. 12/675,736, which is a national phase application under 35 U.S.C. §371 of International Application No. PCT/AT2008/000311 filed 29 Aug. 2008, which claims priority to Austrian Application No. A 1359/2007 filed 30 Aug. 2007. The entire text of each of the above-referenced disclosures is specifically incorporated herein by reference without disclaimer. 
     
    
     BACKGROUND OF THE INVENTION 
       [0002]    1. Field of the Invention 
         [0003]    The present invention relates to the field of cancer diagnosis and diagnostic means therefor. 
         [0004]    2. Description of Related Art 
         [0005]    Thyroid nodules are endemic in iodine deficient areas, like Europe&#39;s alpine regions, where they have a prevalence of 10-20%. They are classified by their histology into the 2 benign types Struma nodosa (SN) and Follicular Thyroid Adenoma (FTA) and the malignant entities Follicular Thyroid Carcinoma (FTC), Papillary Thyroid Carcinoma (PTC), Medullary Thyroid Carcinoma (MTC) and Anaplastic Thyroid Carcinoma (ATC). Conventionally, discrimination between benign and malignant thyroid nodules is done by scintigraphy and fine needle aspiration followed by histology. Despite many advances in the diagnosis and therapy of thyroid nodules and thyroid cancer, these methods have a well-known lack of specificity, particularly for the discrimination between FTA and FTC, which leads to a number of patients unnecessarily treated for malignant disease. 
         [0006]    Given the diagnostic limitations of previous methods, in particular fine needle aspiration followed by cytology, multiple investigators have carried out expression profiling studies with hopes of identifying new diagnostic tools. Such analyses attempt to identify differentially expressed genes with an important role in disease development or progression using large-scale transcript-level expression profiling technologies such as cDNA microarrays, oligonucleotide arrays and Serial Analysis of Gene Expression (SAGE). Typically, dozens or hundreds of genes are identified, many of which are expected to be false positives, and only a small fraction useful as diagnostic/prognostic markers or therapeutic targets (Griffith et al., J Clin Oncol 24(31):5043-5051 (2006)). 
         [0007]    In other types of cancer it has been shown that gene expression profiling can add substantial value to the discrimination of the different clinically relevant tumour-entities. The US 2006/183141 A e.g. describes classification of tumor markers from a core serum response signature. Different studies have tried to classify the different entities of thyroid carcinoma on the basis of their gene expression profiles each of them discriminates between 2 of the 5 entities. However, the studies have no or very few genes in common and applying a classier from one study to the data from another study generally yields poor classification results. 
       SUMMARY OF THE INVENTION 
       [0008]    It is a goal of the present invention to provide reliable distinctive markers for the diagnosis of cancer, in particular to distinguish benign thyroid nodules from malignant follicular thyroid carcinoma (FTC) and papillary thyroid carcinoma (PTC). 
         [0009]    Therefore the present invention provides a set of moieties specific for at least 3 tumor markers selected from the tumor markers PI-1 to PI-33, PII-1 to PII-64, PIII-1 to PIII-70, fi-1 to fi-147, PIV-1 to PIV-9, preferably PIV-4 or PIV-5, and PV-1 to PV-11, preferably PV-1, PV-2 and PV-4 to PV-11. These tumor markers are related to different genes aberrantly expressed in tumors and are given in tables 1 to 6 and can be identified by their gene identification sign, their descriptive gene name, but most unambiguously by their UniGeneID or their Accession number referring to specific sequences in common sequence databases such as NCBI GenBank, EMBL-EBI Database, EnsEMBL or the DNA Data Bank of Japan. These markers have been identified in form of preferred sets (PI to PV, FI) but can be combined in any form as targets for the inventive set. 
         [0000]    
       
         
               
             
               
               
               
               
               
             
               
               
               
               
               
             
           
               
                 TABLE 1 
               
             
             
               
                   
               
               
                 PTC marker set PI-1 to PI-33 
               
             
          
           
               
                 Number 
                 marker 
                   
                   
                   
               
               
                 P I- 
                 gene 
                 description of gene 
                 Accession Nr. 
                 UniGeneID 
               
               
                   
               
             
          
           
               
                 1 
                 BBS9 
                 Bardet-Biedl 
                 NM_198428 
                 Hs.372360 
               
               
                   
                   
                 syndrome 9 
                 NM_001033605 
               
               
                   
                   
                   
                 NM_001033604 
               
               
                   
                   
                   
                 NM_014451 
               
               
                 2 
                 C13orf1 
                 Chromosome 
                 NM_020456 
                 Hs.44235 
               
               
                   
                   
                 13 open 
               
               
                   
                   
                 reading frame 1 
               
               
                 3 
                 CBFA2T3 
                 Core-binding 
                 NM_005187 NM_175931 
                 Hs.513811 
               
               
                   
                   
                 factor, runt domain, alpha subunit 2 
               
               
                 4 
                 CDT1 
                 Chromatin licensing and DANN 
                 NM_030928 
                 Hs.122908 
               
               
                   
                   
                 replication factor 1 
               
               
                 5 
                 CRK 
                 V-crk sarcoma virus CT10 oncogene 
                 NM_016823 NM_005206 
                 Hs.638121 
               
               
                   
                   
                 homolog (avian) 
               
               
                 6 
                 CTPS 
                 CTP synthase 
                 NM_001905 
                 Hs.473087 
               
               
                 7 
                 DAPK2 
                 Death-associated protein kinase 2 
                 NM_014326 
                 Hs.237886 
               
               
                 8 
                 EIF5 
                 Eukaryotic translation initiation factor 5 
                 NM_001969 NM_183004 
                 Hs.433702 
               
               
                 9 
                 EREG 
                 Epiregulin 
                 NM_001432 
                 Hs.115263 
               
               
                 10 
                 GK 
                 Glycerol kinase 
                 NM_203391 NM_000167 
                 Hs.1466 
               
               
                 11 
                 GPATCH8 
                 G patch domain containing 8 
                 NM_001002909 
                 Hs.463129 
               
               
                 12 
                 HDGF 
                 Hepatoma-derived growth factor 
                 NM_004494 
                 Hs.506748 
               
               
                   
                   
                 (high-mobility group protein 1-like) 
               
               
                 13 
                 IRF2BP1 
                 Interferon regulatory factor 2 binding protein 1 
                 NM_015649 
                 Hs.515477 
               
               
                 14 
                 KRT83 
                 Keratin 83 
                 NM_002282 
                 Hs.661428 
               
               
                 15 
                 MYOD1 
                 Myogenic differentiation 1 
                 NM_002478 
                 Hs.181768 
               
               
                 16 
                 NME6 
                 Non-metastatic cells 6, protein expressed in 
                 NM_005793 
                 Hs.465558 
               
               
                   
                   
                 (nucleoside-diphosphate kinase) 
               
               
                 17 
                 POLE3 
                 Polymerase (DNA directed), epsilon 3 
                 NM_017443 
                 Hs.108112 
               
               
                   
                   
                 (p17 subunit) 
               
               
                 18 
                 PPP1R13B 
                 Protein phosphatase 1, regulatory (inhibitor) 
                 NM_015316 
                 Hs.436113 
               
               
                   
                   
                 subunit 13B 
               
               
                 19 
                 PRPH2 
                 Peripherin 2 (retinal degeneration, slow) 
                 NM_000322 
                 Hs.654489 
               
               
                 20 
                 RASSF7 
                 Ras association (RalGDS/AF-6) domain 
                 NM_003475 
                 Hs.72925 
               
               
                   
                   
                 family 7 
               
               
                 21 
                 ROCK2 
                 Rho-associated, coiled-coil containing 
                 NM_004850 
                 Hs.591600 
               
               
                   
                   
                 protein kinase 2 
               
               
                 22 
                 RTN1 
                 Reticulon 1 
                 NM_021136 NM_206857 
                 Hs.368626 
               
               
                   
                   
                   
                 NM_206852 
               
               
                 23 
                 S100B 
                 S100 calcium binding protein B 
                 NM_006272 
                 Hs.422181 
               
               
                 24 
                 SLIT2 
                 Slit homolog 2 ( Drosophila ) 
                 NM_004787 
                 Hs.29802 
               
               
                 25 
                 SNRPB2 
                 Small nuclear ribonucleoprotein polypeptide B″ 
                 NM_003092 NM_198220 
                 Hs.280378 
               
               
                 26 
                 SPAG7 
                 Sperm associated antigen 7 
                 NM_004890 
                 Hs.90436 
               
               
                 27 
                 STAU1 
                 Staufen, RNA binding protein, homolog 1 
                 NM_017453 
                 Hs.596704 
               
               
                   
                   
                 ( Drosophila ) 
                 NM_001037328 
               
               
                   
                   
                   
                 NM_004602 NM_017452 
               
               
                   
                   
                   
                 NM_017454 
               
               
                 28 
                 SUPT5H 
                 Suppressor of Ty 5 homolog ( S. cerevisiae ) 
                 NM_003169 
                 Hs.631604 
               
               
                 29 
                 TBX10 
                 T-box 10 
                 NM_005995 
                 Hs.454480 
               
               
                 30 
                 TLK1 
                 Tousled-like kinase 1 
                 NM_012290 
                 Hs.655640 
               
               
                 31 
                 TM4SF4 
                 Transmembrane 4 L six family member 4 
                 NM_004617 
                 Hs.133527 
               
               
                 32 
                 TXN 
                 Thioredoxin 
                 NM_003329 
                 Hs.435136 
               
               
                 33 
                 UFD1L 
                 Ubiquitin fusion degradation 1 like (yeast) 
                 NM_005659 
                 Hs.474213 
               
               
                   
                   
                   
                 NM_001035247 
               
               
                   
               
             
          
         
       
     
         [0000]    
       
         
               
             
               
               
               
               
               
             
               
               
               
               
               
             
           
               
                 TABLE 2 
               
             
             
               
                   
               
               
                 PTC marker set PII-1 to PII-64 
               
             
          
           
               
                 Number 
                 marker 
                   
                   
                   
               
               
                 P II- 
                 gene 
                 description of gene 
                 Accession Nr. 
                 UniGeneID 
               
               
                   
               
             
          
           
               
                 1 
                 ADH1B 
                 Alcohol dehydrogenase IB (class I), beta 
                 NM_000668 
                 Hs.4 
               
               
                   
                   
                 polypeptide 
               
               
                 2 
                 AGR2 
                 Anterior gradient homolog 2 
                 NM_006408 
                 Hs.530009 
               
               
                   
                   
                 ( Xenopus laevis ) 
               
               
                 3 
                 AGTR1 
                 Angiotensin II receptor, type 1 
                 NM_031850 NM_004835 
                 Hs.477887 
               
               
                   
                   
                   
                 NM_009585 NM_032049 
               
               
                 4 
                 AGTR1 
                 Angiotensin II receptor, type 1 
                 NM_000685 
                 Hs.654382 
               
               
                 5 
                 ALDH1A1 
                 Aldehyde dehydrogenase 
                 NM_000689 
                 Hs.76392 
               
               
                   
                   
                 1 family, member A1 
               
               
                 6 
                 ALDH1A3 
                 Aldehyde dehydrogenase 
                 NM_000693 
                 Hs.459538 
               
               
                   
                   
                 1 family, member A3 
               
               
                 7 
                 AMIGO2 
                 Adhesion molecule with Ig-like 
                 NM_181847 
                 Hs.121520 
               
               
                   
                   
                 domain 2 
               
               
                 8 
                 ATP2C2 
                 ATPase, Ca++ transporting, 
                 NM_014861 
                 Hs.6168 
               
               
                   
                   
                 type 2C, member 2 
               
               
                 9 
                 BID 
                 BH3 interacting domain death 
                 NM_197966 NM_001196 
                 Hs.591054 
               
               
                   
                   
                 agonist 
                 NM_197967 
               
               
                 10 
                 C7orf24 
                 Chromosome 7 open reading 
                 NM_024051 
                 Hs.530024 
               
               
                   
                   
                 frame 24 
               
               
                 11 
                 CA4 
                 Carbonic anhydrase IV 
                 NM_000717 
                 Hs.89485 
               
               
                 12 
                 CCL21 
                 Chemokine (C-C motif) ligand 21 
                 NM_002989 
                 Hs.57907 
               
               
                 13 
                 CD55 
                 CD55 molecule, decay 
                 NM_000574 
                 Hs.527653 
               
               
                   
                   
                 accelerating factor for 
               
               
                   
                   
                 complement (Cromer blood 
               
               
                   
                   
                 group) 
               
               
                 14 
                 CDH16 
                 Cadherin 16, KSP-cadherin 
                 NM_004062 
                 Hs.513660 
               
               
                 15 
                 CDH3 
                 Cadherin 3, type 1, P-cadherin 
                 NM_133458 NM_001793 
                 Hs.461074 
               
               
                   
                   
                 (placental) 
               
               
                 16 
                 CFI 
                 Complement factor I 
                 NM_000204 
                 Hs.312485 
               
               
                 17 
                 CHI3L1 
                 Chitinase 3-like 1 (cartilage 
                 NM_001276 
                 Hs.382202 
               
               
                   
                   
                 glycoprotein-39) 
               
               
                 18 
                 CHST2 
                 Carbohydrate 
                 NM_004267 
                 Hs.8786 
               
               
                   
                   
                 (N-acetylglucosamine-6-O) 
               
               
                   
                   
                 sulfotransferase 2 
               
               
                 19 
                 CITED2 
                 Cbp/p300-interacting 
                 NM_006079 
                 Hs.82071 
               
               
                   
                   
                 transactivator, with Glu/Asp-rich 
               
               
                   
                   
                 carboxy-terminal domain, 2 
               
               
                 20 
                 CLCNKB 
                 Chloride channel Kb 
                 NM_000085 
                 Hs.352243 
               
               
                 21 
                 COMP 
                 Cartilage oligomeric matrix 
                 NM_000095 
                 Hs.1584 
               
               
                   
                   
                 protein 
               
               
                 22 
                 CTSH 
                 Cathepsin H 
                 NM_004390 NM_148979 
                 Hs.148641 
               
               
                 23 
                 DIO2 
                 Deiodinase, iodothyronine, 
                 NM_013989 NM_000793 
                 Hs.202354 
               
               
                   
                   
                 type II 
                 NM_001007023 
               
               
                 24 
                 DIRAS3 
                 DIRAS family, GTP-binding 
                 NM_004675 
                 Hs.194695 
               
               
                   
                   
                 RAS-like 3 
               
               
                 25 
                 DUSP4 
                 Dual specificity phosphatase 4 
                 NM_057158 NM_001394 
                 Hs.417962 
               
               
                 26 
                 DUSP5 
                 Dual specificity phosphatase 5 
                 NM_004419 
                 Hs.2128 
               
               
                 27 
                 EDN3 
                 Endothelin 3 
                 NM_207032 NM_207034 
                 Hs.1408 
               
               
                   
                   
                   
                 NM_207033 NM_000114 
               
               
                 28 
                 ENTPD1 
                 Ectonucleoside triphosphate 
                 NM_001776 
                 Hs.576612 
               
               
                   
                   
                 diphosphohydrolase 1 
                 NM_001098175 
               
               
                 29 
                 FHL1 
                 Four and a half LIM domains 1 
                 NM_001449 
                 Hs.435369 
               
               
                 30 
                 GDF15 
                 Growth differentiation factor 15 
                 NM_004864 
                 Hs.616962 
               
               
                 31 
                 GPM6A 
                 Glycoprotein M6A 
                 NM_201591 NM_005277 
                 Hs.75819 
               
               
                   
                   
                   
                 NM_201592 
               
               
                 32 
                 HBA1 
                 Hemoglobin, alpha 1 
                 NM_000558 
                 Hs.449630 
               
               
                 33 
                 IRS1 
                 Insulin receptor substrate 1 
                 NM_005544 
                 Hs.471508 
               
               
                 34 
                 KCNJ2 
                 Potassium inwardly-rectifying 
                 NM_000891 
                 Hs.1547 
               
               
                   
                   
                 channel, subfamily J, member 2 
               
               
                 35 
                 KCNN4 
                 Potassium intermediate/small 
                 NM_002250 
                 Hs.10082 
               
               
                   
                   
                 conductance calcium-activated 
               
               
                   
                   
                 channel, subfamily N, member 4 
               
               
                 36 
                 KLK10 
                 Kallikrein-related peptidase 10 
                 NM_002776 
                 Hs.275464 
               
               
                   
                   
                   
                 NM_001077500 
               
               
                   
                   
                   
                 NM_145888 
               
               
                 37 
                 LAMB3 
                 Laminin, beta 3 
                 NM_001017402 
                 Hs.497636 
               
               
                   
                   
                   
                 NM_000228 
               
               
                 38 
                 LCN2 
                 Lipocalin 2 (oncogene 24p3) 
                 NM_005564 
                 Hs.204238 
               
               
                 39 
                 LMOD1 
                 Leiomodin 1 (smooth muscle) 
                 NM_012134 
                 Hs.519075 
               
               
                 40 
                 MATN2 
                 Matrilin 2 
                 NM_002380 NM_030583 
                 Hs.189445 
               
               
                 41 
                 MPPED2 
                 Metallophosphoesterase 
                 NM_001584 
                 Hs.289795 
               
               
                   
                   
                 domain containing 2 
               
               
                 42 
                 MVP 
                 Major vault protein 
                 NM_017458 NM_005115 
                 Hs.632177 
               
               
                 43 
                 NELL2 
                 NEL-like 2 (chicken) 
                 NM_006159 
                 Hs.505326 
               
               
                 44 
                 NFE2L3 
                 Nuclear factor (erythroid-derived 
                 NM_004289 
                 Hs.404741 
               
               
                   
                   
                 2)-like 3 
               
               
                 45 
                 NPC2 
                 Niemann-Pick disease, type C2 
                 NM_006432 
                 Hs.433222 
               
               
                 46 
                 NRCAM 
                 Neuronal cell adhesion molecule 
                 NM_001037132 
                 Hs.21422 
               
               
                   
                   
                   
                 NM_005010 
               
               
                   
                   
                   
                 NM_001037133 
               
               
                 47 
                 NRIP1 
                 Nuclear receptor interacting 
                 NM_003489 
                 Hs.155017 
               
               
                   
                   
                 protein 1 
               
               
                 48 
                 PAPSS2 
                 3′-phosphoadenosine 
                 NM_001015880 
                 Hs.524491 
               
               
                   
                   
                 5′-phosphosulfate synthase 2 
                 NM_004670 
               
               
                 49 
                 PDLIM4 
                 PDZ and LIM domain 4 
                 NM_003687 
                 Hs.424312 
               
               
                 50 
                 PDZK1IP1 
                 PDZK1 interacting protein 1 
                 NM_005764 
                 Hs.431099 
               
               
                 51 
                 PIP3-E 
                 Phosphoinositide-binding protein 
                 NM_015553 
                 Hs.146100 
               
               
                   
                   
                 PIP3-E 
               
               
                 52 
                 PLAU 
                 Plasminogen activator, urokinase 
                 NM_002658 
                 Hs.77274 
               
               
                 53 
                 PRSS2 
                 Protease, serine, 2 (trypsin 2) 
                 NM_002770 
                 Hs.622865 
               
               
                 54 
                 PRSS23 
                 Protease, serine, 23 
                 NM_007173 
                 Hs.25338 
               
               
                 55 
                 RAP1GAP 
                 RAP1 GTPase activating protein 
                 NM_002885 
                 Hs.148178 
               
               
                 56 
                 S100A11 
                 S100 calcium binding protein A11 
                 NM_005620 
                 Hs.417004 
               
               
                 57 
                 SFTPB 
                 Surfactant, pulmonary-associated 
                 NM_198843 NM_000542 
                 Hs.512690 
               
               
                   
                   
                 protein B 
               
               
                 58 
                 SLPI 
                 Secretory leukocyte peptidase 
                 NM_003064 
                 Hs.517070 
               
               
                   
                   
                 inhibitor 
               
               
                 59 
                 SOD3 
                 Superoxide dismutase 3, 
                 NM_003102 
                 Hs.2420 
               
               
                   
                   
                 extracellular 
               
               
                 60 
                 SPINT1 
                 Serine peptidase inhibitor, Kunitz type 1 
                 NM_181642 NM_003710 
                 Hs.233950 
               
               
                   
                   
                   
                 NM 
               
               
                   
                   
                   
                 001032367 
               
               
                 61 
                 SYNE1 
                 Spectrin repeat containing, 
                 NM_182961 NM_033071 
                 Hs.12967 
               
               
                   
                   
                 nuclear envelope 1 
                 NM_015293 NM_133650 
               
               
                 62 
                 TACSTD2 
                 Tumor-associated calcium signal transducer 2 
                 NM_002353 
                 Hs.23582 
               
               
                 63 
                 UPP1 
                 Uridine phosphorylase 1 
                 NM_181597 NM_003364 
                 Hs.488240 
               
               
                 64 
                 WASF3 
                 WAS protein family, member 3 
                 NM_006646 
                 Hs.635221 
               
               
                   
               
             
          
         
       
     
         [0000]    
       
         
               
             
               
               
               
               
               
             
               
               
               
               
               
             
           
               
                 TABLE 3 
               
             
             
               
                   
               
               
                 PTC marker set PIII-1 to PIII-70 
               
             
          
           
               
                 Number 
                 marker 
                   
                   
                   
               
               
                 P III- 
                 gene 
                 description of gene 
                 Accession Nr. 
                 UniGeneID 
               
               
                   
               
             
          
           
               
                 1 
                 APOE 
                 Apolipoprotein E 
                 NM_000041 
                 Hs.654439 
               
               
                 2 
                 ATIC 
                 5-aminoimidazole-4-carboxamide 
                 NM_004044 
                 Hs.90280 
               
               
                   
                   
                 ribonucleotide formyltransferase/IMP 
               
               
                   
                   
                 cyclohydrolase 
               
               
                 3 
                 BASP1 
                 Brain abundant, membrane attached 
                 NM_006317 
                 Hs.201641 
               
               
                   
                   
                 signal protein 1 
               
               
                 4 
                 C9orf61 
                 Chromosome 9 open reading frame 61 
                 NM_004816 
                 Hs.118003 
               
               
                 5 
                 CCL13 
                 Chemokine (C-C motif) ligand 13 
                 NM_005408 
                 Hs.414629 
               
               
                 6 
                 CD36 
                 CD36 molecule (thrombospondin receptor) 
                 NM_001001548 
                 Hs.120949 
               
               
                   
                   
                   
                 NM_001001547 
               
               
                   
                   
                   
                 NM_000072 
               
               
                 7 
                 CDH6 
                 Cadherin 6, type 2, K-cadherin (fetal 
                 NM_004932 
                 Hs.171054 
               
               
                   
                   
                 kidney) 
               
               
                 8 
                 CFB 
                 Complement factor B 
                 NM_001710 
                 Hs.69771 
               
               
                 9 
                 CFD 
                 Complement factor D (adipsin) 
                 NM_001928 
                 Hs.155597 
               
               
                 10 
                 CLDN10 
                 Claudin 10 
                 NM_182848 NM_006984 
                 Hs.534377 
               
               
                 11 
                 COL11A1 
                 Collagen, type XI, alpha 1 
                 NM_080629 NM_001854 
                 Hs.523446 
               
               
                   
                   
                   
                 NM_080630 
               
               
                 12 
                 COL13A1 
                 Collagen, type XIII, alpha 1 
                 NM_005203 NM_080804 
                 Hs.211933 
               
               
                   
                   
                   
                 NM_080798 NM_080803 
               
               
                   
                   
                   
                 NM_080802 NM_080799 
               
               
                   
                   
                   
                 NM_080800 
               
               
                   
                   
                   
                 NM_080801 NM_080808 
               
               
                   
                   
                   
                 NM_080809 NM_080805 
               
               
                   
                   
                   
                 NM_080807 NM_080806 
               
               
                   
                   
                   
                 NM_080811 
               
               
                   
                   
                   
                 NM_080810 NM_080812 
               
               
                   
                   
                   
                 NM_080813 NM_080814 
               
               
                   
                   
                   
                 NM_080815 
               
               
                 13 
                 CORO2B 
                 Coronin, actin binding protein, 2B 
                 NM_006091 
                 Hs.551213 
               
               
                 14 
                 CRLF1 
                 Cytokine receptor-like factor 1 
                 NM_004750 
                 Hs.114948 
               
               
                 15 
                 CXorf6 
                 Chromosome X open reading frame 6 
                 NM_005491 
                 Hs.20136 
               
               
                 16 
                 DDB2 
                 Damage-specific DNA binding protein 2, 
                 NM_000107 
                 Hs.655280 
               
               
                   
                   
                 48 kDa 
               
               
                 17 
                 DPP6 
                 Dipeptidyl-peptidase 6 
                 NM_001039350 
                 Hs.490684 
               
               
                   
                   
                   
                 NM_130797 NM_001936 
               
               
                 18 
                 ECM1 
                 Extracellular matrix protein 1 
                 NM_004425 NM_022664 
                 Hs.81071 
               
               
                 19 
                 EFEMP1 
                 EGF-containing fibulin-like extracellular 
                 NM_004105 
                 Hs.76224 
               
               
                   
                   
                 matrix protein 1 
                 NM_001039348 
               
               
                   
                   
                   
                 NM_001039349 
               
               
                 20 
                 ESRRG 
                 Estrogen-related receptor gamma 
                 NM_206594 NM_001438 
                 Hs.444225 
               
               
                   
                   
                   
                 NM_206595 
               
               
                 21 
                 ETHE1 
                 Ethylmalonic encephalopathy 1 
                 NM_014297 
                 Hs.7486 
               
               
                 22 
                 FAS 
                 Fas (TNF receptor superfamily, member 6) 
                 NM_000043 NM_152872 
                 Hs.244139 
               
               
                   
                   
                   
                 NM_152871 NM_152873 
               
               
                   
                   
                   
                 NM_152875 NM_152874 
               
               
                   
                   
                   
                 NM_152877 NM_152876 
               
               
                 23 
                 FMOD 
                 Fibromodulin 
                 NM_002023 
                 Hs.519168 
               
               
                 24 
                 GABBR2 
                 Gamma-aminobutyric acid (GABA) B 
                 NM_005458 
                 Hs.198612 
               
               
                   
                   
                 receptor, 2 
               
               
                 25 
                 GALE 
                 UDP-galactose-4-epimerase 
                 NM_000403 
                 Hs.632380 
               
               
                   
                   
                   
                 NM_001008216 
               
               
                 26 
                 GATM 
                 Glycine amidinotransferase (L- 
                 NM_001482 
                 Hs.75335 
               
               
                   
                   
                 arginine: glycine amidinotransferase) 
               
               
                 27 
                 GDF10 
                 Growth differentiation factor 10 
                 NM_004962 
                 Hs.2171 
               
               
                 28 
                 GHR 
                 Growth hormone receptor 
                 NM_000163 
                 Hs.125180 
               
               
                 29 
                 GPC3 
                 Glypican 3 
                 NM_004484 
                 Hs.644108 
               
               
                 30 
                 ICAM1 
                 Intercellular adhesion molecule 1 (CD54), 
                 NM_000201 
                 Hs.643447 
               
               
                   
                   
                 human rhinovirus receptor 
               
               
                 31 
                 ID3 
                 Inhibitor of DNA binding 3, dominant 
                 NM_002167 
                 Hs.76884 
               
               
                   
                   
                 negative helix-loop-helix protein 
               
               
                 32 
                 IER2 
                 Immediate early response 2 
                 NM_004907 
                 Hs.501629 
               
               
                 33 
                 IGFBP6 
                 Insulin-like growth factor binding protein 6 
                 NM_002178 
                 Hs.274313 
               
               
                 34 
                 IQGAP2 
                 IQ motif containing GTPase activating 
                 NM_006633 
                 Hs.291030 
               
               
                   
                   
                 protein 2 
               
               
                 35 
                 ITGA2 
                 Integrin, alpha 2 (CD49B, alpha 2 subunit 
                 NM_002203 
                 Hs.482077 
               
               
                   
                   
                 of VLA-2 receptor) 
               
               
                 36 
                 ITGA3 
                 Integrin, alpha 3 (antigen CD49C, alpha 3 
                 NM_002204 NM_005501 
                 Hs.265829 
               
               
                   
                   
                 subunit of VLA-3 receptor) 
               
               
                 37 
                 ITM2A 
                 Integral membrane protein 2A 
                 NM_004867 
                 Hs.17109 
               
               
                 38 
                 KIAA0746 
                 KIAA0746 protein 
                 NM_015187 
                 Hs.479384 
               
               
                 39 
                 LRIG1 
                 Leucine-rich repeats and immunoglobulin- 
                 NM_015541 
                 Hs.518055 
               
               
                   
                   
                 like domains 1 
               
               
                 40 
                 LRP2 
                 Low density lipoprotein-related protein 2 
                 NM_004525 
                 Hs.470538 
               
               
                 41 
                 LY6E 
                 Lymphocyte antigen 6 complex, locus E 
                 NM_002346 
                 Hs.521903 
               
               
                 42 
                 MAPK13 
                 Mitogen-activated protein kinase 13 
                 NM_002754 
                 Hs.178695 
               
               
                 43 
                 MDK 
                 Midkine (neurite growth-promoting factor 
                 NM_001012334 
                 Hs.82045 
               
               
                   
                   
                 2) 
                 NM_001012333 
               
               
                   
                   
                   
                 NM_002391 
               
               
                 44 
                 MLLT11 
                 Myeloid/lymphoid or mixed-lineage leukemia 
                 NM_006818 
                 Hs.75823 
               
               
                   
                   
                 (trithorax homolog,  Drosophila ) 
               
               
                 45 
                 MMRN1 
                 Multimerin 1 
                 NM_007351 
                 Hs.268107 
               
               
                 46 
                 MTMR11 
                 Myotubularin related protein 11 
                 NM_181873 
                 Hs.425144 
               
               
                 47 
                 MXRA8 
                 Matrix-remodelling associated 8 
                 NM_032348 
                 Hs.558570 
               
               
                 48 
                 NAB2 
                 NGFI-A binding protein 2 (EGR1 binding 
                 NM_005967 
                 Hs.159223 
               
               
                   
                   
                 protein 2) 
               
               
                 49 
                 NMU 
                 Neuromedin U 
                 NM_006681 
                 Hs.418367 
               
               
                 50 
                 OCA2 
                 Oculocutaneous albinism II (pink-eye 
                 NM_000275 
                 Hs.654411 
               
               
                   
                   
                 dilution homolog, mouse) 
               
               
                 51 
                 PDE5A 
                 Phosphodiesterase 5A, cGMP-specific 
                 NM_001083 NM_033430 
                 Hs.647971 
               
               
                   
                   
                   
                 NM_033437 
               
               
                 52 
                 PLAG1 
                 Pleiomorphic adenoma gene 1 
                 NM_002655 
                 Hs.14968 
               
               
                 53 
                 PLP2 
                 Proteolipid protein 2 (colonic epithelium- 
                 NM_002668 
                 Hs.77422 
               
               
                   
                   
                 enriched) 
               
               
                 54 
                 PLXNC1 
                 Plexin C1 
                 NM_005761 
                 Hs.584845 
               
               
                 55 
                 PRKCQ 
                 Protein kinase C, theta 
                 NM_006257 
                 Hs.498570 
               
               
                 56 
                 PRUNE 
                 Prune homolog ( Drosophila ) 
                 NM_021222 
                 Hs.78524 
               
               
                 57 
                 RAB27A 
                 RAB27A, member RAS oncogene family 
                 NM_004580 NM_183234 
                 Hs.654978 
               
               
                   
                   
                   
                 NM_183235 NM_183236 
               
               
                 58 
                 RYR2 
                 Ryanodine receptor 2 (cardiac) 
                 NM_001035 
                 Hs.109514 
               
               
                 59 
                 SCEL 
                 Sciellin 
                 NM_144777 NM_003843 
                 Hs.534699 
               
               
                 60 
                 SELENBP1 
                 Selenium binding protein 1 
                 NM_003944 
                 Hs.632460 
               
               
                 61 
                 SORBS2 
                 Sorbin and SH3 domain containing 2 
                 NM_021069 NM_003603 
                 Hs.655143 
               
               
                 62 
                 STMN2 
                 Stathmin-like 2 
                 NM_007029 
                 Hs.521651 
               
               
                 63 
                 TBC1D4 
                 TBC1 domain family, member 4 
                 NM_014832 
                 Hs.210891 
               
               
                 64 
                 TM4SF4 
                 Transmembrane 4 L six family member 4 
                 NM_004617 
                 Hs.133527 
               
               
                 65 
                 TNC 
                 Tenascin C (hexabrachion) 
                 NM_002160 
                 Hs.143250 
               
               
                 66 
                 TPD52L1 
                 Tumor protein D52-like 1 
                 NM_001003395 
                 Hs.591347 
               
               
                   
                   
                   
                 NM_003287 
               
               
                   
                   
                   
                 NM_001003396 
               
               
                   
                   
                   
                 NM_001003397 
               
               
                 67 
                 TSC22D1 
                 TSC22 domain family, member 1 
                 NM_183422 NM_006022 
                 Hs.507916 
               
               
                 68 
                 TTC30A 
                 Tetratricopeptide repeat domain 30A 
                 NM_152275 
                 Hs.128384 
               
               
                 69 
                 VLDLR 
                 Very low density lipoprotein receptor 
                 NM_003383 
                 Hs.370422 
               
               
                   
                   
                   
                 NM_001018056 
               
               
                 70 
                 WFS1 
                 Wolfram syndrome 1 (wolframin) 
                 NM_006005 
                 Hs.518602 
               
               
                   
               
             
          
         
       
     
         [0000]    
       
         
               
             
               
               
               
               
               
             
               
               
               
               
               
             
           
               
                 TABLE 4 
               
             
             
               
                   
               
               
                 FTC marker set FI-1 to FI-147 
               
             
          
           
               
                 Number 
                   
                   
                   
                   
               
               
                 FI- 
                 marker gene 
                 description of gene 
                 Accession Nr. 
                 UniGeneID 
               
               
                   
               
             
          
           
               
                 1 
                 AATF 
                 Apoptosis antagonizing transcription 
                 NM_012138 
                 Hs.195740 
               
               
                   
                   
                 factor 
               
               
                 2 
                 ACOX3 
                 Acyl-Coenzyme A oxidase 3, 
                 NM_003501 
                 Hs.479122 
               
               
                   
                   
                 pristanoyl 
               
               
                 3 
                 AHDC1 
                 AT hook, DNA binding motif, 
                 NM_001029882 
                 Hs.469280 
               
               
                   
                   
                 containing 1 
               
               
                 4 
                 ALAS2 
                 Aminolevulinate, delta-, synthase 2 
                 NM_000032 
                 Hs.522666 
               
               
                   
                   
                 (sideroblastic/hypochromic anemia) 
                 NM_001037968 
               
               
                   
                   
                   
                 NM_001037967 
               
               
                   
                   
                   
                 NM_001037969 
               
               
                 5 
                 ALKBH1 
                 AlkB, alkylation repair homolog 1 
                 NM_006020 
                 Hs.94542 
               
               
                   
                   
                 ( E. coli ) 
               
               
                 6 
                 ANGPTL2 
                 Angiopoietin-like 2 
                 NM_012098 
                 Hs.653262 
               
               
                 7 
                 AP2A2 
                 Adaptor-related protein complex 2, 
                 NM_012305 
                 Hs.19121 
               
               
                   
                   
                 alpha 2 subunit 
               
               
                 8 
                 APOBEC3G 
                 Apolipoprotein B mRNA editing 
                 NM_021822 
                 Hs.660143 
               
               
                   
                   
                 enzyme, catalytic polypeptide-like 3G 
               
               
                 9 
                 APRIN 
                 Androgen-induced proliferation 
                 NM_015032 
                 Hs.693663 
               
               
                   
                   
                 inhibitor 
               
               
                 10 
                 ARNT 
                 Aryl hydrocarbon receptor nuclear 
                 NM_001668 
                 Hs.632446 
               
               
                   
                   
                 translocator 
                 NM_178427 
               
               
                   
                   
                   
                 NM_178426 
               
               
                 11 
                 AZGP1 
                 Alpha-2-glycoprotein 1, zinc-binding 
                 NM_001185 
                 Hs.546239 
               
               
                 12 
                 BAT2D1 
                 BAT2 domain containing 1 
                 NM_015172 
                 Hs.494614 
               
               
                 13 
                 BATF 
                 Basic leucine zipper transcription fac- 
                 NM_006399 
                 Hs.509964 
               
               
                   
                   
                 tor, ATF-like 
               
               
                 14 
                 BPHL 
                 Biphenyl hydrolase-like (serine hydro- 
                 NM_004332 
                 Hs.10136 
               
               
                   
                   
                 lase 
               
               
                 15 
                 C13orf1 
                 Chromosome 13 open reading frame 1 
                 NM_020456 
                 Hs.44235 
               
               
                 16 
                 C14orf1 
                 Chromosome 14 open reading frame 1 
                 NM_007176 
                 Hs.15106 
               
               
                 17 
                 C2orf3 
                 Chromosome 2 open reading frame 3 
                 NM_003203 
                 Hs.303808 
               
               
                 18 
                 CBFB 
                 Core-binding factor, beta subunit 
                 NM_001755 
                 Hs.460988 
               
               
                   
                   
                   
                 NM_022845 
               
               
                 19 
                 CBR3 
                 Carbonyl reductase 3 
                 NM_001236 
                 Hs.154510 
               
               
                 20 
                 CBX5 
                 Chromobox homolog 5 (HP1 alpha 
                 NM_012117 
                 Hs.632724 
               
               
                   
                   
                 homolog,  Drosophila ) 
               
               
                 21 
                 CCNE2 
                 Cyclin E2 
                 NM_057749 
                 Hs.567387 
               
               
                   
                   
                   
                 NM_057735 
               
               
                 22 
                 CD46 
                 CD46 molecule, complement 
                 NM_002389 
                 Hs.510402 
               
               
                   
                   
                 regulatory protein 
                 NM_172354 
               
               
                   
                   
                   
                 NM_172351 
               
               
                   
                   
                   
                 NM_172355 
               
               
                   
                   
                   
                 NM_172352 
               
               
                   
                   
                   
                 NM_172359 
               
               
                   
                   
                   
                 NM_172357 
               
               
                   
                   
                   
                 NM_172360 
               
               
                   
                   
                   
                 NM_153826 
               
               
                   
                   
                   
                 NM_172358 
               
               
                   
                   
                   
                 NM_172356 
               
               
                   
                   
                   
                 NM_172353 
               
               
                   
                   
                   
                 NM_172361 
               
               
                   
                   
                   
                 NM_172350 
               
               
                 23 
                 CHPF 
                 Chondroitin polymerizing factor 
                 NM_024536 
                 Hs.516711 
               
               
                 24 
                 CHST3 
                 Carbohydrate (chondroitin 6) 
                 NM_004273 
                 Hs.158304 
               
               
                   
                   
                 sulfotransferase 3 
               
               
                 25 
                 CLCN2 
                 Chloride channel 2 
                 NM_004366 
                 Hs.436847 
               
               
                 26 
                 CLCN4 
                 Chloride channel 4 
                 NM_001830 
                 Hs.495674 
               
               
                 27 
                 CLIC5 
                 Chloride intracellular channel 5 
                 NM_016929 
                 Hs.485489 
               
               
                 28 
                 CNOT2 
                 CCR4-NOT transcription complex, 
                 NM_014515 
                 Hs.133350 
               
               
                   
                   
                 subunit 2 
               
               
                 29 
                 COPS6 
                 COP9 constitutive photomorphogenic 
                 NM_006833 
                 Hs.15591 
               
               
                   
                   
                 homolog subunit 6 ( Arabidopsis ) 
               
               
                 30 
                 CPZ 
                 Carboxypeptidase Z 
                 NM_001014448 
                 Hs.78068 
               
               
                   
                   
                   
                 NM_001014447 
               
               
                   
                   
                   
                 NM_003652 
               
               
                 31 
                 CSK 
                 C-src tyrosine kinase 
                 NM_004383 
                 Hs.77793 
               
               
                 32 
                 CTDP1 
                 CTD (carboxy-terminal domain, RNA 
                 NM_004715 
                 Hs.465490 
               
               
                   
                   
                 polymerase II, polypeptide A) 
                 NM_048368 
               
               
                   
                   
                 phosphatase, subunit 1 
               
               
                 33 
                 DDEF2 
                 Development and differentiation en- 
                 NM_003887 
                 Hs.555902 
               
               
                   
                   
                 hancing factor 2 
               
               
                 34 
                 DKFZP586H2123 
                 Regeneration associated muscle 
                 NM_015430 
                 Hs.55044 
               
               
                   
                   
                 protease 
                 NM_001001991 
               
               
                 35 
                 DLG2 
                 Discs, large homolog 2, chapsyn-110 
                 NM_001364 
                 Hs.654862 
               
               
                   
                   
                 ( Drosophila ) 
               
               
                 36 
                 DPAGT1 
                 Dolichyl-phosphate (UDP-N- 
                 NM_001382 
                 Hs.524081 
               
               
                   
                   
                 acetylglucosamine) N- 
                 NM_203316 
               
               
                   
                   
                 acetylglucosaminephosphotransferase 
               
               
                   
                   
                 1 (GlcNAc-1-P transferase) 
               
               
                 37 
                 DSCR1 
                 Down syndrome critical region gene 1 
                 NM_004414 
                 Hs.282326 
               
               
                   
                   
                   
                 NM_203418 
               
               
                   
                   
                   
                 NM_203417 
               
               
                 38 
                 DUSP8 
                 Dual specificity phosphatase 8 
                 NM_004420 
                 Hs.41688 
               
               
                 39 
                 EI24 
                 Etoposide induced 2.4 mRNA 
                 NM_004879 
                 Hs.643514 
               
               
                   
                   
                   
                 NM_001007277 
               
               
                 40 
                 ENOSF1 
                 Enolase superfamily member 1 
                 NM_017512 
                 Hs.369762 
               
               
                 41 
                 ERCC1 
                 Excision repair cross-complementing 
                 NM_202001 
                 Hs.435981 
               
               
                   
                   
                 rodent repair deficiency, complementa- 
                 NM_001983 
               
               
                   
                   
                 tion group 1 (includes overlapping 
               
               
                   
                   
                 antisense sequence) 
               
               
                 42 
                 ERCC3 
                 Excision repair cross-complementing 
                 NM_000122 
                 Hs.469872 
               
               
                   
                   
                 rodent repair deficiency, complementa- 
               
               
                   
                   
                 tion group 3 (xeroderma pigmentosum 
               
               
                   
                   
                 group B complementing) 
               
               
                 43 
                 ERH 
                 Enhancer of rudimentary homolog 
                 NM_004450 
                 Hs.509791 
               
               
                   
                   
                 ( Drosophila ) 
               
               
                 44 
                 F13A1 
                 Coagulation factor XIII, A1 polypeptide 
                 NM_000129 
                 Hs.335513 
               
               
                 45 
                 FAM20B 
                 Family with sequence similarity 20, 
                 NM_014864 
                 Hs.5737 
               
               
                   
                   
                 member B 
               
               
                 46 
                 FBP1 
                 Fructose-1,6-bisphosphatase 1 
                 NM_000507 
                 Hs.494496 
               
               
                 47 
                 FCGR2A 
                 Fc fragment of IgG, low affinity IIa, 
                 NM_021642 
                 Hs.352642 
               
               
                   
                   
                 receptor (CD32) 
               
               
                 48 
                 FGF13 
                 Fibroblast growth factor 13 
                 NM_004114 
                 Hs.6540 
               
               
                   
                   
                   
                 NM_033642 
               
               
                 49 
                 FGFR1OP 
                 FGFR1 oncogene partner 
                 NM_007045 
                 Hs.487175 
               
               
                   
                   
                   
                 NM_194429 
               
               
                 50 
                 FLNC 
                 Filamin C, gamma (actin binding 
                 NM_001458 
                 Hs.58414 
               
               
                   
                   
                 protein 280) 
               
               
                 51 
                 FMO5 
                 Flavin containing monooxygenase 5 
                 NM_001461 
                 Hs.642706 
               
               
                 52 
                 FRY 
                 Furry homolog ( Drosophila ) 
                 NM_023037 
                 Hs.591225 
               
               
                 53 
                 GADD45G 
                 Growth arrest and DNA-damage- 
                 NM_006705 
                 Hs.9701 
               
               
                   
                   
                 inducible, gamma 
               
               
                 54 
                 GCH1 
                 GTP cyclohydrolase 1 (dopa- 
                 NM_000161 
                 Hs.86724 
               
               
                   
                   
                 responsive dystonia) 
                 NM_001024024 
               
               
                   
                   
                   
                 NM_001024070 
               
               
                   
                   
                   
                 NM_001024071 
               
               
                 55 
                 GFRA1 
                 GDNF family receptor alpha 1 
                 NM_005264 
                 Hs.591913 
               
               
                   
                   
                   
                 NM_145793 
               
               
                 56 
                 GLB1 
                 Galactosidase, beta 1 
                 NM_001039770 
                 Hs.443031 
               
               
                   
                   
                   
                 NM_000404 
               
               
                   
                   
                   
                 NM_001079811 
               
               
                 57 
                 GOLGA8A 
                 Golgi autoantigen, golgin subfamily a, 
                 NM_181077 
                 Hs.182982 
               
               
                   
                   
                 8A 
                 NM_001023567 
               
               
                 58 
                 HCLS1 
                 Hematopoietic cell-specific Lyn 
                 NM_005335 
                 Hs.14601 
               
               
                   
                   
                 substrate 1 
               
               
                 59 
                 HDGF 
                 Hepatoma-derived growth factor 
                 NM_004494 
                 Hs.506748 
               
               
                   
                   
                 (high-mobility group protein 1-like) 
               
               
                 60 
                 HRC 
                 Histidine rich calcium binding protein 
                 NM_002152 
                 Hs.436885 
               
               
                 61 
                 ICMT 
                 Isoprenylcysteine carboxyl 
                 NM_012405 
                 Hs.562083 
               
               
                   
                   
                 methyltransferase 
               
               
                 62 
                 IFNA5 
                 Interferon, alpha 5 
                 NM_002169 
                 Hs.37113 
               
               
                 63 
                 IGF2BP3 
                 Insulin-like growth factor 2 mRNA 
                 NM_006547 
                 Hs.648088 
               
               
                   
                   
                 binding protein 3 
               
               
                 64 
                 IL12A 
                 Interleukin 12A (natural killer cell 
                 NM_000882 
                 Hs.673 
               
               
                   
                   
                 stimulatory factor 1, cytotoxic 
               
               
                   
                   
                 lymphocyte maturation factor 1, p35) 
               
               
                 65 
                 ITIH2 
                 Inter-alpha (globulin) inhibitor H2 
                 NM_002216 
                 Hs.75285 
               
               
                 66 
                 ITPKC 
                 Inositol 1,4,5-trisphosphate 3-kinase C 
                 NM_025194 
                 Hs.515415 
               
               
                 67 
                 JMJD2A 
                 Jumonji domain containing 2A 
                 NM_014663 
                 Hs.155983 
               
               
                 68 
                 KCNJ15 
                 Potassium inwardly-rectifying channel, 
                 NM_170736 
                 Hs.411299 
               
               
                   
                   
                 subfamily J, member 15 
                 NM_002243 
               
               
                   
                   
                   
                 NM_170737 
               
               
                 69 
                 KCTD12 
                 Potassium channel tetramerisation 
                 NM_138444 
                 Hs.693617 
               
               
                   
                   
                 domain containing 12 
               
               
                 70 
                 KIAA0652 
                 KIAA0652 
                 NM_014741 
                 Hs.410092 
               
               
                 71 
                 KIAA0913 
                 KIAA0913 
                 NM_015037 
                 Hs.65135 
               
               
                 72 
                 KLKB1 
                 Kallikrein B, plasma (Fletcher factor) 1 
                 NM_000892 
                 Hs.646885 
               
               
                 73 
                 KRT37 
                 Keratin 37 
                 NM_003770 
                 Hs.673852 
               
               
                 74 
                 LAMB3 
                 Laminin, beta 3 
                 NM_001017402 
                 Hs.497636 
               
               
                   
                   
                   
                 NM_000228 
               
               
                 75 
                 LPHN3 
                 Latrophilin 3 
                 NM_015236 
                 Hs.694758 
               
               
                   
                   
                   
                   
                 Hs.649524 
               
               
                 76 
                 LRIG1 
                 Leucine-rich repeats and immuno- 
                 NM_015541 
                 Hs.518055 
               
               
                   
                   
                 globulin-like domains 1 
               
               
                 77 
                 LSR 
                 Lipolysis stimulated lipoprotein 
                 NM_205834 
                 Hs.466507 
               
               
                   
                   
                 receptor 
                 NM_015925 
               
               
                   
                   
                   
                 NM_205835 
               
               
                 78 
                 MANBA 
                 Mannosidase, beta A, lysosomal 
                 NM_005908 
                 Hs.480415 
               
               
                 79 
                 MAP7 
                 Microtubule-associated protein 7 
                 NM_003980 
                 Hs.486548 
               
               
                 80 
                 MAPKAPK5 
                 Mitogen-activated protein kinase- 
                 NM_139078 
                 Hs.413901 
               
               
                   
                   
                 activated protein kinase 5 
                 NM_003668 
               
               
                 81 
                 MET 
                 Met proto-oncogene (hepatocyte 
                 NM_000245 
                 Hs.132966 
               
               
                   
                   
                 growth factor receptor) 
               
               
                 82 
                 MMP14 
                 Matrix metallopeptidase 14 
                 NM_004995 
                 Hs.2399 
               
               
                   
                   
                 (membrane-inserted) 
               
               
                 83 
                 MX1 
                 Myxovirus (influenza virus) resistance 
                 NM_002462 
                 Hs.517307 
               
               
                   
                   
                 1, interferon-inducible protein p78 
               
               
                   
                   
                 (mouse) 
               
               
                 84 
                 MYL9 
                 Myosin, light chain 9, regulatory 
                 NM_006097 
                 Hs.504687 
               
               
                   
                   
                   
                 NM_181526 
               
               
                 85 
                 MYO9B 
                 Myosin IXB 
                 NM_004145 
                 Hs.123198 
               
               
                 86 
                 NCOR1 
                 Nuclear receptor co-repressor 1 
                 NM_006311 
                 Hs.462323 
               
               
                 87 
                 NDRG4 
                 NDRG family member 4 
                 NM_020465 
                 Hs.322430 
               
               
                   
                   
                   
                 NM_022910 
               
               
                 88 
                 NDUFA5 
                 NADH dehydrogenase (ubiquinone) 1 
                 NM_005000 
                 Hs.651219 
               
               
                   
                   
                 alpha subcomplex, 5, 13 kDa 
               
               
                 89 
                 NEUROD2 
                 Neurogenic differentiation 2 
                 NM_006160 
                 Hs.322431 
               
               
                 90 
                 NFKB2 
                 Nuclear factor of kappa light polypep- 
                 NM_001077494 
                 Hs.73090 
               
               
                   
                   
                 tide gene enhancer in B-cells 2 
                 NM_001077493 
               
               
                   
                   
                 (p49/p100) 
                 NM_002502 
               
               
                 91 
                 NME6 
                 Non-metastatic cells 6, protein 
                 NM_005793 
                 Hs.465558 
               
               
                   
                   
                 expressed in (nucleoside-diphosphate 
               
               
                   
                   
                 kinase) 
               
               
                 92 
                 NPY1R 
                 Neuropeptide Y receptor Y1 
                 NM_000909 
                 Hs.519057 
               
               
                 93 
                 NUP50 
                 Nucleoporin 50 kDa 
                 NM_007172 
                 Hs.475103 
               
               
                   
                   
                   
                 NM_153645 
               
               
                 94 
                 PDGFRA 
                 Platelet-derived growth factor receptor, 
                 NM_006206 
                 Hs.74615 
               
               
                   
                   
                 alpha polypeptide 
               
               
                 95 
                 PDHX 
                 Pyruvate dehydrogenase complex, 
                 NM_003477 
                 Hs.502315 
               
               
                   
                   
                 component X 
               
               
                 96 
                 PDLIM1 
                 PDZ and LIM domain 1 (elfin) 
                 NM_020992 
                 Hs.368525 
               
               
                 97 
                 PEX1 
                 Peroxisome biogenesis factor 1 
                 NM_000466 
                 Hs.164682 
               
               
                 98 
                 PEX13 
                 Peroxisome biogenesis factor 13 
                 NM_002618 
                 Hs.567316 
               
               
                 99 
                 PIB5PA 
                 Phosphatidylinositol (4, 5) 
                 NM_014422 
                 Hs.517549 
               
               
                   
                   
                 bisphosphate 5-phosphatase, A 
                 NM_001002837 
               
               
                 100 
                 PICK1 
                 Protein interacting with PRKCA 1 
                 NM_012407 
                 Hs.180871 
               
               
                   
                   
                   
                 NM_001039583 
               
               
                   
                   
                   
                 NM_001039584 
               
               
                 101 
                 PLEC1 
                 Plectin 1, intermediate filament 
                 NM_201380 
                 Hs.434248 
               
               
                   
                   
                 binding protein 500 kDa 
                 NM_201384 
               
               
                   
                   
                   
                 NM_000445 
               
               
                   
                   
                   
                 NM_201379 
               
               
                   
                   
                   
                 NM_201383 
               
               
                   
                   
                   
                 NM_201382 
               
               
                   
                   
                   
                 NM_201381 
               
               
                   
                   
                   
                 NM_201378 
               
               
                 102 
                 POLE2 
                 Polymerase (DNA directed), epsilon 2 
                 NM_002692 
                 Hs.162777 
               
               
                   
                   
                 (p59 subunit) 
               
               
                 103 
                 POLE3 
                 Polymerase (DNA directed), epsilon 3 
                 NM_017443 
                 Hs.108112 
               
               
                   
                   
                 (p17 subunit) 
               
               
                 104 
                 PPIF 
                 Peptidylprolyl isomerase F (cyclophilin F) 
                 NM_005729 
                 Hs.381072 
               
               
                 105 
                 PPP2R5A 
                 Protein phosphatase 2, regulatory 
                 NM_006243 
                 Hs.497684 
               
               
                   
                   
                 subunit B′, alpha isoform 
               
               
                 106 
                 PSCD2 
                 Pleckstrin homology, Sec7 and coiled- 
                 NM_017457 
                 Hs.144011 
               
               
                   
                   
                 coil domains 2 (cytohesin-2) 
                 NM_004228 
               
               
                 107 
                 PSMA5 
                 Proteasome (prosome, macropain) 
                 NM_002790 
                 Hs.485246 
               
               
                   
                   
                 subunit, alpha type, 5 
               
               
                 108 
                 PTPN12 
                 Protein tyrosine phosphatase, non- 
                 NM_002835 
                 Hs.61812 
               
               
                   
                   
                 receptor type 12 
               
               
                 109 
                 PTPN3 
                 Protein tyrosine phosphatase, non- 
                 NM_002829 
                 Hs.436429 
               
               
                   
                   
                 receptor type 3 
               
               
                 110 
                 PTPRCAP 
                 Protein tyrosine phosphatase, recep- 
                 NM_005608 
                 Hs.155975 
               
               
                   
                   
                 tor type, C-associated protein 
               
               
                 111 
                 QKI 
                 Quaking homolog, KH domain RNA 
                 NM_206855 
                 Hs.510324 
               
               
                   
                   
                 binding (mouse) 
                 NM_206854 
               
               
                   
                   
                   
                 NM_206853 
               
               
                   
                   
                   
                 NM_006775 
               
               
                 112 
                 RASAL2 
                 RAS protein activator like 2 
                 NM_170692 
                 Hs.656823 
               
               
                   
                   
                   
                 NM_004841 
               
               
                 113 
                 RASSF7 
                 Ras association (RalGDS/AF-6) 
                 NM_003475 
                 Hs.72925 
               
               
                   
                   
                 domain family 7 
               
               
                 114 
                 RBM10 
                 RNA binding motif protein 10 
                 NM_005676 
                 Hs.401509 
               
               
                   
                   
                   
                 NM_152856 
               
               
                 115 
                 RBM38 
                 RNA binding motif protein 38 
                 NM_017495 
                 Hs.236361 
               
               
                   
                   
                   
                 NM_183425 
               
               
                 116 
                 RER1 
                 RER1 retention in endoplasmic reticu- 
                 NM_007033 
                 Hs.525527 
               
               
                   
                   
                 lum 1 homolog ( S. cerevisiae ) 
               
               
                 117 
                 RGL2 
                 Ral guanine nucleotide dissociation 
                 NM_004761 
                 Hs.509622 
               
               
                   
                   
                 stimulator-like 2 
               
               
                 118 
                 RHOG 
                 Ras homolog gene family, member G 
                 NM_001665 
                 Hs.501728 
               
               
                   
                   
                 (rho G) 
               
               
                 119 
                 RNASE1 
                 Ribonuclease, RNase A family, 1 
                 NM_198235 
                 Hs.78224 
               
               
                   
                   
                 (pancreatic) 
                 NM_198234 
               
               
                   
                   
                   
                 NM_198232 
               
               
                   
                   
                   
                 NM_002933 
               
               
                 120 
                 RTN4 
                 Reticulon 4 
                 NM_020532 
                 Hs.645283 
               
               
                   
                   
                   
                 NM_207521 
               
               
                   
                   
                   
                 NM_207520 
               
               
                   
                   
                   
                 NM_153828 
               
               
                   
                   
                   
                 NM_007008 
               
               
                 121 
                 RYR2 
                 Ryanodine receptor 2 (cardiac) 
                 NM_001035 
                 Hs.109514 
               
               
                 122 
                 SCC-112 
                 SCC-112 protein 
                 NM_015200 
                 Hs.331431 
               
               
                 123 
                 SDS 
                 Serine dehydratase 
                 NM_006843 
                 Hs.654416 
               
               
                 124 
                 SF3B2 
                 Splicing factor 3b, subunit 2, 145 kDa 
                 NM_006842 
                 Hs.406423 
               
               
                 125 
                 SH3PXD2A 
                 SH3 and PX domains 2A 
                 NM_014631 
                 Hs.594708 
               
               
                 126 
                 SIX6 
                 Sine oculis homeobox homolog 6 
                 NM_007374 
                 Hs.194756 
               
               
                   
                   
                 ( Drosophila ) 
               
               
                 127 
                 SLC10A1 
                 Solute carrier family 10 (sodium/bile 
                 NM_003049 
                 Hs.952 
               
               
                   
                   
                 acid cotransporter family), member 1 
               
               
                 128 
                 SLC6A8 
                 Solute carrier family 6 (neurotransmitter 
                 NM_005629 
                 Hs.540696 
               
               
                   
                   
                 transporter, creatine), member 8 
               
               
                 129 
                 SMG6 
                 Smg-6 homolog, nonsense mediated 
                 NM_017575 
                 Hs.448342 
               
               
                   
                   
                 mRNA decay factor ( C. elegans ) 
               
               
                 130 
                 SNRPB2 
                 Small nuclear ribonucleoprotein poly- 
                 NM_003092 
                 Hs.280378 
               
               
                   
                   
                 peptide B″ 
                 NM_198220 
               
               
                 131 
                 SOX11 
                 SRY (sex determining region Y)-box 11 
                 NM_003108 
                 Hs.432638 
               
               
                 132 
                 SPI1 
                 Spleen focus forming virus (SFFV) 
                 NM_001080547 
                 Hs.502511 
               
               
                   
                   
                 proviral integration oncogene spi1 
                 NM_003120 
               
               
                 133 
                 SRGAP3 
                 SLIT-ROBO Rho GTPase activating 
                 NM_014850 
                 Hs.654743 
               
               
                   
                   
                 protein 3 
                 NM_001033117 
               
               
                 134 
                 STX12 
                 Syntaxin 12 
                 NM_177424 
                 Hs.523855 
               
               
                 135 
                 SYK 
                 Spleen tyrosine kinase 
                 NM_003177 
                 Hs.371720 
               
               
                 136 
                 TAF4 
                 TAF4 RNA polymerase II, TATA box 
                 NM_003185 
                 Hs.18857 
               
               
                   
                   
                 binding protein (TBP)-associated factor, 
               
               
                   
                   
                 135 kDa 
               
               
                 137 
                 TCN2 
                 Transcobalamin II 
                 NM_000355 
                 Hs.417948 
               
               
                 138 
                 TGOLN2 
                 Trans-golgi network protein 2 
                 NM_006464 
                 Hs.593382 
               
               
                 139 
                 TIA1 
                 TIA1 cytotoxic granule-associated 
                 NM_022173 
                 Hs.516075 
               
               
                   
                   
                 RNA binding protein 
                 NM_022037 
               
               
                 140 
                 TOMM40 
                 Translocase of outer mitochondrial 
                 NM_006114 
                 Hs.655909 
               
               
                   
                   
                 membrane 40 homolog (yeast) 
               
               
                 141 
                 TXN2 
                 Thioredoxin 2 
                 NM_012473 
                 Hs.211929 
               
               
                 142 
                 UGCG 
                 UDP-glucose ceramide 
                 NM_003358 
                 Hs.304249 
               
               
                   
                   
                 glucosyltransferase 
               
               
                 143 
                 USP11 
                 Ubiquitin specific peptidase 11 
                 NM_004651 
                 Hs.171501 
               
               
                 144 
                 VDR 
                 Vitamin D (1,25-dihydroxyvitamin D3) 
                 NM_001017535 
                 Hs.524368 
               
               
                   
                   
                 receptor 
                 NM_000376 
               
               
                 145 
                 VEGFC 
                 Vascular endothelial growth factor C 
                 NM_005429 
                 Hs.435215 
               
               
                 146 
                 YWHAQ 
                 Tyrosine 3- 
                 NM_006826 
                 Hs.74405 
               
               
                   
                   
                 monooxygenase/tryptophan 5- 
               
               
                   
                   
                 monooxygenase activation protein, 
               
               
                   
                   
                 theta polypeptide 
               
               
                 147 
                 ZNF140 
                 Zinc finger protein 140 
                 NM_003440 
                 Hs.181552 
               
               
                   
               
             
          
         
       
     
         [0000]    
       
         
               
             
               
               
               
               
               
             
           
               
                 TABLE 5 
               
             
             
               
                   
               
               
                 PTC marker set PIV-1 to PIV-9 
               
             
          
           
               
                 Number 
                   
                   
                   
                   
               
               
                 PIV- 
                 marker gene 
                 description of gene 
                 Accession Nr. 
                 UniGeneID 
               
               
                   
               
               
                 1 
                 WAS 
                 Wiskott-Aldrich syndrome (eczema- 
                 BC012738 
                 Hs.2157 
               
               
                   
                   
                 thrombocytopenia) 
               
               
                 2 
                 LRP4 
                 Low density lipoprotein receptor- 
                 BM802977 
                 Hs.4930 
               
               
                   
                   
                 related protein 4 
               
               
                 3 
                 TFF3 
                 Trefoil factor 3 (intestinal) 
                 BC017859 
                 Hs.82961 
               
               
                 4 
                 ST3GAL6 
                 ST3 beta-galactoside alpha-2,3- 
                 BC023312 
                 Hs.148716 
               
               
                   
                   
                 sialyltransferase 6 
               
               
                 5 
                 STK39 
                 Serine threonine kinase 39 
                 BM455533 
                 Hs.276271 
               
               
                   
                   
                 (STE20/SPS1 homolog, yeast) 
               
               
                 6 
                 DPP4 
                 Dipeptidyl-peptidase 4 (CD26, 
                 BC065265 
                 Hs.368912 
               
               
                   
                   
                 adenosine deaminase complexing 
               
               
                   
                   
                 protein 2) 
               
               
                 7 
                 CHI3L1 
                 Chitinase 3-like 1 (cartilage 
                 BC038354 
                 Hs.382202 
               
               
                   
                   
                 glycoprotein-39) 
               
               
                 8 
                 FABP4 
                 Fatty acid binding protein 4, adipocyte 
                 BC003672 
                 Hs.391561 
               
               
                 9 
                 LAMB3 
                 Laminin, beta 3 
                 BC075838 
                 Hs.497636 
               
               
                   
               
             
          
         
       
     
         [0000]    
       
         
               
             
               
               
               
               
               
             
               
               
               
               
               
             
           
               
                 TABLE 6 
               
             
             
               
                   
               
               
                 PTC marker set PV-1 to PV-11 
               
             
          
           
               
                 Number 
                   
                   
                   
                   
               
               
                 PV- 
                 marker gene 
                 description of gene 
                 Accession Nr. 
                 UniGeneID 
               
               
                   
               
             
          
           
               
                 1 
                 GPR4 
                 G protein-coupled receptor 4 
                 BC067535 
                 Hs.17170 
               
               
                 2 
                 STAM2 
                 Signal transducing adaptor molecule 
                 BC028740 
                 Hs.17200 
               
               
                   
                   
                 (SH3 domain and ITAM motif) 2 
               
               
                 3 
                 QPCT 
                 Glutaminyl-peptide cyclotransferase 
                 BC047756 
                 Hs.79033 
               
               
                   
                   
                 (glutaminyl cyclase) 
               
               
                 4 
                 CDK7 
                 Cyclin-dependent kinase 7 (MO15 
                 BC000834 
                 Hs.184298 
               
               
                   
                   
                 homolog,  Xenopus laevis , cdk- 
               
               
                   
                   
                 activating kinase) 
               
               
                 5 
                 SFTPD 
                 Surfactant, pulmonary-associated 
                 BC022318 
                 Hs.253495 
               
               
                   
                   
                 protein D 
               
               
                 6 
                 CYB5R1 
                 Cytochrome b5 reductase 1 
                 BC018732 
                 Hs.334832 
               
               
                 7 
                 VWF 
                 Von Willebrand factor 
                 BI490763 
                 Hs.440848 
               
               
                 8 
                 VWF 
                 Von Willebrand factor 
                 BQ888783 
                 Hs.440848 
               
               
                 9 
                 PDHX 
                 Pyruvate dehydrogenase complex, 
                 BC010389 
                 Hs.502315 
               
               
                   
                   
                 component X 
               
               
                 10 
                 HOXA4 
                 Homeobox A4 
                 BM996071 
                 Hs.654466 
               
               
                 11 
                 HOXA4 
                 Homeobox A4 
                 BI521357 
                 Hs.654466 
               
               
                   
               
             
          
         
       
     
         [0010]    The inventive set can be used to detect cancer or tumor cells, in particular thyroid cancer, and even to distinguish benign thyroid nodules from malignant follicular thyroid carcinoma (FTC) and papillary thyroid carcinoma (PTC). In preferred embodiments the set comprises moieties specific for at least 3 tumor markers selected from the tumor markers PI-1 to PI-33, PII-1 to PII-64, PIII-1 to PIII-70 and PIV-1 to PIV-9, preferably PIV-4 or PIV-5, and PV-1 to PV-11, preferably PV-1, PV-2 and PV-4 to PV-11, in particular from the tumor markers PI-1 to PI-33. These markers are specific for papillary thyroid carcinoma (PTC) and the diagnosed thyroid cancer can be characterized as PTC. 
         [0011]    In a similar preferred embodiment the set comprises moieties specific for at least 3 tumor markers selected from the tumor markers FI-1 to FI-147. These markers are specific for follicular thyroid carcinoma (FTC) and the diagnosed thyroid cancer can be characterized as FTC. 
         [0012]    Particularly preferred the set comprises a moiety specific for the tumor marker SERPINA1 (Serine (or cysteine) protease inhibitor, Glade A (alpha-1 antiproteinase, antitrypsin), member 1; NM — 000295, NM — 001002236, NM — 001002235), which is a very potent marker for PTC. This marker as single member of the set can distinguish PTC form benign conditions. 
         [0013]    Preferably the set comprises at least 5 or at least 10, preferably at least 15, more preferred at least 20, particular preferred at least 25, most preferred at least 30, moieties specific for the tumor markers of table 1 to 6 above. The set may be selected from moieties specific for any at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 33, 35, 40, 45, 50, 55, 60, 64, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 145, 147, 150, 160, 170, 180, 190 or 200 of the above tumor markers, e.g. selected from PI-1 to PI-33, PII-1 to PII-64, PIII-1 to PIII-70, FI-1 to FI-147, PIV-1 to PIV-9, preferably PIV-4 or PIV-5, and PV-1 to PV-11, preferably PV-1, PV-2 and PV-4 to PV-11, in particular from any one of PI-1, PI-2, PI-3, PI-4, PI-5, PI-6, PI-7, PI-8, PI-9, PI-10, PI-11, PI-12, PI-13, PI-14, PI-15, PI-16, PI-17, PI-18, PI-19, PI-20, PI-21, PI-22, PI-23, PI-24, PI-25, PI-26, PI-27, PI-28, PI-29, PI-30, PI-31, PI-32, PI-33, PII-1, PII-2, PII-3, PII-4, PII-5, PII-6, PII-7, PII-8, PII-9, PII-10, PII-11, PII-12, PII-13, PII-14, PII-15, PII-16, PII-17, PII-18, PII-19, PII-20, PII-21, PII-22, PII-23, PII-24, PII-25, PII-26, PII-27, PII-28, PII-29, PII-30, PII-31, PII-32, PII-33, PII-34, PII-35, PII-36, PII-37, PII-38, PII-39, PII-40, PII-41, PII-42, PII-43, PII-44, PII-45, PII-46, PII-47, PII-48, PII-49, PII-50, PII-51, PII-52, PII-53, PII-54, PII-55, PII-56, PII-57, PII-58, PII-59, PII-60, PII-61, PII-62, PII-63, PII-64, PIII-1, PIII-2, PIII-3, PIII-4, PIII-5, PIII-6, PIII-7, PIII-8, PIII-9, PIII-10, PIII-11, PIII-12, PIII-13, PIII-14, PIII-15, PIII-16, PIII-17, PIII-18, PIII-19, PIII-20, PIII-21, PIII-22, PIII-23, PIII-24, PIII-25, PIII-26, PIII-27, PIII-28, PIII-29, PIII-30, PIII-31, PIII-32, PIII-33, PIII-34, PIII-35, PIII-36, PIII-37, PIII-38, PIII-39, PIII-40, PIII-41, PIII-42, PIII-43, PIII-44, PIII-45, PIII-46, PIII-47, PIII-48, PIII-49, PIII-50, PIII-51, PIII-52, PIII-53, PIII-54, PIII-55, PIII-56, PIII-57, PIII-58, PIII-59, PIII-60, PIII-61, PIII-62, PIII-63, PIII-64, PIII-65, PIII-66, PIII-67, PIII-68, PIII-69, PIII-70, FI-1, FI-2, FI-3, FI-4, FI-5, FI-6, FI-7, FI-8, FI-9, FI-10, FI-11, FI-12, FI-13, FI-14, FI-15, FI-16, FI-17, FI-18, FI-19, FI-20, FI-21, FI-22, FI-23, FI-24, FI-25, FI-26, FI-27, FI-28, FI-29, FI-30, FI-31, FI-32, FI-33, FI-34, FI-35, FI-36, FI-37, FI-38, FI-39, FI-40, FI-41, FI-42, FI-43, FI-44, FI-45, FI-46, FI-47, FI-48, FI-49, FI-50, FI-51, FI-52, FI-53, FI-54, FI-55, FI-56, FI-57, FI-58, FI-59, FI-60, FI-61, FI-62, FI-63, FI-64, FI-65, FI-66, FI-67, FI-68, FI-69, FI-70, FI-71, FI-72, FI-73, FI-74, FI-75, FI-76, FI-77, FI-78, FI-79, FI-80, FI-81, FI-82, FI-83, FI-84, FI-85, FI-86, FI-87, FI-88, FI-89, FI-90, FI-91, FI-92, FI-93, FI-94, FI-95, FI-96, FI-97, FI-98, FI-99, FI-100, FI-101, FI-102, FI-103, FI-104, FI-105, FI-106, FI-107, FI-108, FI-109, FI-110, FI-111, 112, FI-113, FI-114, FI-115, FI-116, FI-117, FI-118, FI-119, FI-120, FI-121, FI-122, FI-123, FI-124, FI-125, FI-126, FI-127, FI-128, FI-129, FI-130, FI-131, FI-132, FI-133, FI-134, FI-135, FI-136, FI-137, FI-138, FI-139, FI-140, FI-141, FI-142, FI-143, FI-144, FI-145, FI-146, FI-147, PIV-1, PIV-2, PIV-3, PIV-4, PIV-5, PIV-6, PIV-7, PIV-8, PIV-9, PV-1, PV-2, PV-3, PV-4, PV-5, PV-6, PV-7, PV-8, PV-9, PV-10, PV-11. Preferably the set is specific for any complete subset selected from PI, PII, PIII, PIV, PV or FI. However it is also possible to pick any small number from these subsets or combined set since a distinction between benign and malignant states or the diagnosis of cancer can also be performed with acceptable certainty. For example in a preferred embodiment the inventive set comprises at least 5 (or any of the above mentioned numbers) of moieties specific for the tumor markers selected from FI-1 to FI-147.  FIGS. 4 and 5  show such diagnostic classification probabilities for PTC and FTC. E.g. a set specific for any number of markers from table 2 (subset PII) specific for 5 markers has only an error margin of 4%, i.e. 96% of all cases would be classified correctly. An error value of 1% (99% certainty) is achieved with at least 20 members. In the case of the FTC specific markers a stable value of 8% errors is achieved with at least 11 different markers selected from the FI subset. 
         [0014]    The moieties according to the invention are molecules suitable for specific recognition of the inventive markers. Such molecular recognition can be on the nucleotide, peptide or protein level. Preferably, the moieties are nucleic acids, especially oligonucleotides or primers specific for tumor marker nucleic acids. In another embodiment the moieties are antibodies (monoclonal or polyclonal) or antibody fragments, preferably selected from Fab, Fab′ Fab 2 , F(ab′) 2  or scFv (single-chain variable fragments), specific for tumor marker proteins. According to the invention it is not of essence which sequence portion of the nucleic acids or which epitopes of the proteins are recognized by the moieties as long as molecular recognition is facilitated. Moieties already known in the art, especially disclosed in the references cited herein, which are all incorporated by reference, are suitable. 
         [0015]    In a preferred embodiment the moieties of the set are immobilized on a solid support, preferably in the form of a microarray or nanoarray. The term “microarray”, likewise “nanoarray”, is used to describe a array of an microscopic arrangement (nanoarray for an array in nanometer scale) or refers to a carrier comprising such an array. Both definitions do not contradict each other and are applicable in the sense of the present invention. Preferably the set is provided on a chip whereon the moieties can be immobilized. Chips may be of any material suitable for the immobilization of biomolecules such as the moieties, including glass, modified glass (aldehyde modified) or metal chips. 
         [0016]    According to the present invention a set for the specific use for tumor diagnosis is provided. However, it is also possible to provide larger sets including additional moieties for other purposes, in particular in a microarray set-up, where it is possible to immobilize a multitude of oligonucleotides. However, it is preferred to provide a cost-efficient set including a limited amount of moieties for a single purpose. 
         [0017]    Therefore, in a preferred embodiment the set comprises at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, especially preferred at least 100%, of the total analyte binding moieties of the set are moieties, which are specific for the tumor markers selected from the group of PI-1 to PI-33, PII-1 to PII-64, PIII-1 to PIII-70, FI-1 to FI-147, PIV-1 to PIV-9, and PV-1 to PV-11 (all markers disclosed in tables 1 to 6, above) or from at least one of the groups of any one of PI-1 to PI-33, PII-1 to PII-64, PIII-1 to PIII-70, FI-1 to FI-147, PIV-1 to PIV-9, PV-1 to PV-11 or any combination thereof. Such preferred combinations are e.g. all markers of the groups PI-1 to PI-33, PII-1 to PII-64, PIII-1 to PIII-70, PIV-1 to PIV-9, and PV-1 to PV-11, being especially suitable for PTC diagnosis. As used herein “analyte binding moieties” refers to all moieties which can be used to specifically detect a marker, in particular a marker gene or gene product, including mRNA or expressed proteins. The genes are preferably genes of a mammal, in particular a human. The moieties are included in this generic term of any “analyte binding moieties” which can have multiple diagnostic targets. E.g., in the embodiment of a microarray the array comprises at least 10% oligonucleotides specific for the inventive markers. Since according to current technology detection means for genes on a chip (nucleic acid molecules, such as DNA-ESTs or complementary DNA-ESTs, respectively) allow easier and more robust array design, gene chips using DNA molecules (for detection of expressed mRNA in the sample) is a preferred embodiment of the present invention. Such gene chips also allow detection of a large number of gene products, whereas detection of a large number of proteins using protein chips (e.g. antibody chips) is more difficult. Detection of proteins is usually performed using ELISA techniques (i.e. a microtiter plate-, bead-, or chip-based ELISA) as an embodiment of a protein chip. A protein chip may comprise suitable means for specifically binding the gene products of the gene from the list according to tables 1 to 6, e.g. affinity molecules such as monoclonal or polyclonal antibodies or lectins. 
         [0018]    In a further embodiment the set comprises up to 50000 analyte binding moieties, preferably up to 40000, up to 35000, up to 30000, up to 25000, up to 20000, up to 15000, up to 10000, up to 7500, up to 5000, up to 3000, up to 2000, up to 1000, up to 750, up to 500, up to 400, up to 300, or even more preferred up to 200 analyte binding moieties of any kind, such as oligonucleotides specific for any gene or gene product. 
         [0019]    In a further aspect the present invention relates to a method for the detection of one or more thyroid cancer markers in a sample comprising using the inventive set and detecting the presence or measuring amount of the occurrence of tumor markers in the sample. The incidence or pattern of the detected markers can specifically identify the presence of these markers which can be relevant for cancer diagnosis or as a reference of healthy samples, or simply a genetic investigation of subjects. 
         [0020]    Preferably the sample comprises cells preferably, mammal cells, particular preferred human cells, which can be provided from a biopsy or body fluid. In particular the presence or amount of the tumor markers is detected or measured in these cells after e.g. cell disintegration. 
         [0021]    The method may comprise a detection or measurement by RNA-expression analysis, preferably by microarray or quantitative PCR, or protein analysis, preferably by tissue microarray detection, protein microarray detection, mRNA microarray detection, ELISA, multiplex assays, immunohistochemistry, or DNA analysis, comparative genomic hybridization (CGH)-arrays or single nucleotide polymorphism (SNP)-analysis. These methods are known in the art and can be readily used for the method of the present invention, as examples of the vast field of genetic marker analysis. 
         [0022]    In another aspect the present invention provides a method for the diagnosis of cancer in a patient, comprising providing a sample, preferably a sample of cells, of the patient, detecting one or more tumor markers by measuring tumor marker signals with the set according to the present invention, comparing the measured signal values of the tumor markers with values of the tumor markers in healthy samples and diagnosing cancer if more than 50%, preferably more than 60%, more preferred more than 70%, most preferred more than 80%, of the values differ compared to the values of the healthy samples by at least the standard deviation, preferably two times the standard deviation, even more preferred three times the standard deviation, of the method of measurement. The differences in genetic expression between samples of diseased subjects and healthy subjects can be of any kind and includes upregulation (e.g. of oncogenes) or downregulation (e.g. of tumor suppressor genes). It is possible that in healthy samples a gene is not expressed whereas expression occurs in diseased samples. The other way around it is also possible that in diseased samples a gene is not expressed whereas expression occurs in healthy samples. 
         [0023]    Cancer can also be diagnosed if more than 50%, preferably more than 60%, more preferred more than 70%, most preferred more than 80%, of the values of the sample differ compared to the values of the healthy samples by at least a factor 1.5, at least a factor 2, at least a factor 3 or at least a factor 4. Usually the tumor marker expression products ar up or down regulated by a factor of 2 to 6, but also differences by a factor 60 are possible. 
         [0024]    In yet another aspect the invention relates to a method for the identification of disease specific markers, as e.g. given in tables 1 to 6, preferably genes or gene expression patterns, comprising:
       providing gene expression data on multiple potential disease specific genes of at least two different expression datasets,   determining common genes of the datasets,   normalising each gene expression dataset, preferably by lowess or quantile normalisation,   combining the gene expression datasets to a combined dataset, and preferably normalising the combined dataset, and integrating the combined dataset,   determination of genes of the combined data set by determining its nearest shrunken centroid, which includes the determination of a cross-validated error value of assigning the genes to the disease and minimizing the error value by reducing the number of members of the combined, preferably normalized, data set,
 
wherein the genes of the reduced data set are the markers specific for the disease. The cross-validation can e.g. the leave-one-out method. Preferably the determination step (the classification step) comprises the determination of a maximized threshold of the difference of the normalized expression value for each gene to the centroid value through the cross-validation. Then the genes with normalized expression values lower than the threshold are removed from the reduced (or shrunken) set and genes with values greater than the threshold to the centroid are specific for the disease. Classification by the shrunken centrois methods are e.g. disclosed by Tibshirani et al. (PNAS USA 99(10):105-114 (2004)), Shen et al. (Bioinformatics 22(22) (2006): 2635-42) and Wang et al. (Bioinformatics 23(8) (2007): 972-9), which disclosures are incorporated herein by reference.
       
 
         [0030]    The determination step can be repeated multiple times by leaving out the resulting markers of each previous step. The nearest shrunken centroid method will yield a new result set of further markers which are specific for the disease. Preferably the determination step is repeated 2, 3, 4, 5, 6, 7, 8, 9, 10 or more times. Depending on the size of the combined data set it will give further specific markers. Preferably a cross-validation is performed on each result. The determination can be repeated until the cross-validation indicates an error value of e.g. below 50%, 60%, 70% or 80%. At lower values it can be expected that all markers have been identified. 
         [0031]    The initial gene expression data sets are raw expression profiles, e.g. each obtained from a multi genetic microarray analysis. Most of the measured genes are expected not to be involved with the disease and the inventive method is capable to identify characteristic marker genes form at least two, preferably at least three, at least four, at least five, at least six, at least seven or at least eight expression data sets. Therefore the expression data of the initial data sets preferably comprises data of at least two different microarray datasets, in particular with study or platform specific biases. Such biases can occur by using only a specific set up during the measurement of the expression data, e.g. a microarray, which can significantly differ from set ups of other datasets. The present invention has the advantage that during the combination of such sets the problems of such measurement biases are overcome. Furthermore the obtained (initial) gene expression data is raw, unprocessed gene expression data, i.e. no refinement or data conversion was performed prior to the inventive method. 
         [0032]    Preferably the disease is a genetic disorder, preferably a disorder with altered gene expression, in particular preferred cancer. Other types of disorders with altered gene expression can be e.g. pathogen infections, in particular viral including retroviral infections, radiation damage and age related disorders. 
         [0033]    The step of combining and integrating the combined dataset removed study specific biases. In preferred embodiments this step is performed by stepwise combination of two gene expression datasets per step and integration of the combined dataset, preferably by DWD (Distance Weighted Discrimination). E.g. in the case of 3 data sets at first set 1 is combined with set 2 and the merged set 1+2 is combined with set 3. Integration may e.g. include calculating the normal vector of the combined dataset and subsequently a hyperplane which separates clusters (e.g. of the initial datasets) of data values of the dataset and subtracting the dataset means as in the DWD method. In principle any data integration method which removes biases can be used for the inventive method. 
         [0034]    Preferably the at least one, preferably two, three, four, five, six, seven or eight, obtained expression datasets comprise data of at least 10, preferably at least 20, more preferred at least 30, even more preferred at least 40, at least 50, at least 70, at least 100, at least 120, at least 140, at least 160 or at even at least 200 different genes. The inventive method is particularly suitable to filter through large data sets and identify the characteristic markers therein. The obtained set of these markers is also referred to as “classifier”. 
         [0035]    This method of identifying cancer specific markers and thus moieties, e.g. oligonucleotides or antibodies, specific for cancer can also be used in the above method of diagnosing cancer. I.e. the markers corresponding to the set of moieties used for the diagnostic method are identified (also called “classified”) according to the above method which includes the refinement and establishing of centroid values of the measured values of the initial data sets. This pattern can then be used to diagnose cancer if the values of the sample of the patient are closer to the clustered centroid value of the tumor markers. Accordingly a method for the diagnosis of cancer in a patient is provided, comprising providing a sample, preferably a sample of cells, from the patient, detecting one or more tumor markers by measuring tumor marker signals with the set according to the present invention, comparing the measured signal values of the tumor markers with values of the tumor markers in cancer samples by the identification method mentioned above and diagnosing cancer if the nearest shrunken centroid of values of the sample of the patient for at least 50%, preferably at least 60%, more preferred at least 70% or even at least 80%, most preferred 90%, markers of the set is within the standard deviation, preferably two times the standard deviation, even more preferred three times the standard deviation, of the method of measurement to the nearest shrunken centroid of the tumor markers identified with the cancer samples. 
         [0036]    The present invention is further illustrated by the following figures and examples without being specifically restricted thereto. All references cited herein are incorporated by reference. 
     
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
         [0037]      FIG. 1 : The first two principal components before and after DWD—integration. Datasets are coded by colour and tumor entities are coded by letters according to the legend. 
           [0038]      FIG. 2 : Dendrogram of the DWD integrated data on all genes. The colors of branches of the dendrogram indicate the dataset of the corresponding sample, the color of the leaf-label indicates the tumor entity. 
           [0039]      FIG. 3 : Discrimination between papillary carcinoma and benign nodules across four different datasets by only one gene (SERPINA1) 
           [0040]      FIG. 4  shows a graph of the average error probability during PTC classification of seduced sets (classifier) of markers from table 2. 
           [0041]      FIG. 5  shows a graph of the average error probability during FTC classification of seduced sets (classifier) of markers from table 4. 
       
    
    
     DETAILED DESCRIPTION 
     EXAMPLES 
     Example 1 
     Datasets 
       [0042]    Datasets were downloaded either from websites or from public repositories (GEO, ArrayExpress). Table 7 shows a summary of the datasets used in this study (He et al, PNAS USA 102(52): 19075-80 (2005); Huang et al. PNAS USA 98(26): 15044-49 (2001); Jarzab Cancer Res 65(4): 1587-97 (2005); Lacroix Am J Pathol 167(1): 223-231 (2005); J Clin Endocrinol Metab 90(5): 2512-21 (2005)). Here, three different categories of non-cancer tissues are used: contralateral (c.lat) for healthy surrounding tissue paired with a tumor sample, other disease (o.d.) for thyroid tissue operated for other disease and SN (Struma nodosa) for benign thyroid nodules. For all subsequent analysis these were combined as healthy. 
         [0000]    
       
         
               
             
               
               
               
               
               
               
               
               
               
             
               
               
               
               
               
               
               
               
               
             
           
               
                 TABLE 7 
               
             
             
               
                   
               
               
                 Microarray Data used for Meta Analysis 
               
             
          
           
               
                   
                 Published 
                 FTA 
                 FTC 
                 PTC 
                 SN 
                 o.d. 
                 c.lat  
                 Platform 
               
               
                   
               
             
          
           
               
                 He 
                 PNAS 2005 
                 0 
                 0 
                 9 
                 0 
                 0 
                 9 
                 Affy U133plus 
               
               
                 Huang 
                 PNAS 2001 
                 0 
                 0 
                 8 
                 8 
                 0 
                 0 
                 Affy U133A 
               
               
                 Jarzab 
                 Cancer Res 2005 
                 0 
                 0 
                 23 
                 0 
                 11 
                 17 
                 Affy U133A 
               
               
                 Lacroix 
                 Am J Path 2005 
                 4 
                 8 
                 0 
                 11 
                 0 
                 0 
                 Agilent Custom 
               
               
                 Reyes 
                 not published? 
                 0 
                 0 
                 7 
                 0 
                 0 
                 7 
                 Affy U133A 
               
               
                 Weber 
                 J Clin Endocr 
                 12 
                 12 
                 0 
                 0 
                 0 
                 0 
                 Affy U95A 
               
               
                   
                 Metabol 2005 
                   
                   
                   
                   
                   
                   
                   
               
               
                   
               
             
          
         
       
     
       Example 2 
     Finding the Gene Overlap 
       [0043]    The first step in any MetaAnalysis of microarray data is to find the set of genes which is shared by all microarray platforms used in the analysis. Traditionally, overlap is assessed by finding common UniGene identifiers. This, however, disregards all possible splice variations in the genes under investigation. For example, if a gene had 2 splice variants, one of which was differentially expressed in the experiment and the other not and if one platform would contain an oligo specific only to the differentially expressed variant and the other platform only an oligo to the other variant, then a matching based on UniGene would merge probes which measure different things. 
         [0044]    To overcome this problem, the approach adopted here merges only probes which annotate to the same set of RefSeq identifiers. To this end all matching RefSeqs were downloaded for each probe(set), either via the Bioconductor annotation packages (hgu133a, hgu95a and hgu133plus2; available at the web www.bioconductor.org) or by a BLAST search of the sequences at NCBI Database. Then, for each probe the RefSeqs were sorted and concatenated. This is the most accurate representation of the entity measured on the array. The median value was used, if one set of RefSeqs was represented by multiple probes on the array. 5707 different sets of RefSeqs were present on all arrays. 
       Example 3 
     Preprocessing and Data Integration 
       [0045]    First each dataset was background-corrected and normalised separately, as recommended for each platform (lowess for dual color and quantile normalisation for single color experiments) (Bolstad et al. Bioinformatics 19(2): 185-193(2003); Smyth et al. Methods 31(4): 265-273 (2003)), then they were merged and quantile normalised collectively. Despite all preprocessing, it has been shown that data generated on different microarray platforms or on different generations of the same platform may not be comparable due to platform specific biases (Eszlinger et al. Clin Endocrinol Metab 91(5): 1934-1942 (2006)). This is also evident from principal component analysis of the merged data as shown in  FIG. 1 . In order to correct for these biases, methods have been developed for integration of microarray data. One of these methods is Distance Weighted Discrimination (DWD) which is described in detail elsewhere (Benito et al. Bioinformatics 20(1): 105-114 (2004)). Briefly, DWD projects data points onto the normal vector of a class (dataset)—separating hyperplane as calculated by a modified Support Vector Machine (SVM) and subtracts the class (dataset) means. Therefore, for a multiclass problem (more than 2 datasets to merge), the datasets need to be merged sequentially. For 6 datasets this leads to 720 different possibilities for merging, not including tree structured approaches, e.g instead of (((1+2)+3)+4), consider ((1+2)+(3+4)). The merging orders applied here were chosen on the general idea that similar and larger datasets should be merged first and more disparate ones later. It is also worth noting, that adding a sample to a DWD merged dataset will change the whole dataset just like adding a new number to a vector of numbers will change its mean. 
         [0046]    Data Integration by DWD is illustrated in  FIG. 1  which shows the effect of the data integration method on the first two principal components. In this analysis, DWD was able to remove the separation between the datasets as indicated by the PC-plots and by the mixing of the branches in the dendrogram (see  FIG. 2 ). However, even in the DWD-integrated dataset the Lacroix data still partly separates from the other data. Most likely this is due to the platform; the lacroix-data is the only data from a non-Affymetrix platform.  FIG. 2  shows dendrograms of the respective integrated datasets. Also, DWD integration does not seem to hamper the discrimination between the tumor entities (see table 8 below). 
       Example 4 
     Classification 
       [0047]    For probe selection, classification and cross-validation a nearest shrunken centroid method was chosen (Tibshirani et al. PNAS USA 99(10):105-114 (2004)) (implemented in the Bioconductor package pamr). It was chosen for several reasons: it allows multiclass classification and it runs features selection, classification and cross-validation in one go. Briefly, it calculates several different possible classifiers using different shrinkage thresholds (i.e. different number of genes) and finds the best threshold from crossvalidation. The classifier was picked with the smallest number of genes (largest threshold), if more than one threshold yielded the same crossvalidation results. 
       Example 5 
     Papillary Thyroid Carcinoma (PTC) 
       [0048]    First, and as a quality measure for each study, each dataset was taken separately (before DWD-integration) and a pamr classification and leave-one-out cross-validation (loocv) was performed. The results of the cross-validation are near perfect with single samples classifying wrongly. However, with the exception of the classifier from the He dataset, none of these classifiers can be applied to any of the other dataset. Classification results are rarely ever higher than expected by chance. If, however, one uses the DWD-integrated data (below), the classifiers already fit much better (see table 8). 
         [0000]    
       
         
               
             
               
               
               
               
               
               
               
               
               
               
             
           
               
                 TABLE 8 
               
             
             
               
                   
               
               
                 Classification results when applying classifiers from one study on another  
               
               
                 study. Before data integration (left) and after DWD integration (right) 
               
             
          
           
               
                 test 
                   
                   
                   
                   
                 test 
                   
                   
                   
                   
               
               
                 train 
                 he 
                 huang 
                 jarzab 
                 reyes 
                 train 
                 he 
                 huang  
                 jarzab 
                 reyes 
               
               
                   
               
               
                 he 
                 1.00 
                 1.00 
                 0.98 
                 1.00 
                 he 
                 1.00 
                 1.00 
                 0.96 
                 1.00 
               
               
                 huang 
                 0.50 
                 1.00 
                 0.55 
                 0.50 
                 huang 
                 0.50 
                 1.00 
                 0.90 
                 0.71 
               
               
                 jarzab 
                 0.50 
                 0.81 
                 1.00 
                 0.57 
                 jarzab 
                 0.89 
                 1.00 
                 1.00 
                 1.00 
               
               
                 reyes 
                 0.78 
                 0.50 
                 0.92 
                 1.00 
                 reyes 
                 0.89 
                 0.88 
                 0.90 
                 1.00 
               
               
                   
               
             
          
         
       
     
         [0049]    Then a pamr-classifier was built for the complete DWD-integrated dataset and validated in a leave-one-out cross validation. This identified a one (!) gene classifier, which classifies 99% of samples correctly in loocv. The discriminative gene is SERPINA1.  FIG. 3  shows the discrimination of PTC vs SN before and after DWD. One could add up to 422 genes to the classifier and still yield 99% accuracy (from loocv). If one removes the SERPINA1-probe from the analysis, one can build again a classifier (subsequently denominated classifier) with 99% accuracy in loocv, this time using a 9-gene signature (see Table 3). Removing these 9 genes yields another 9-gene classifier with a similar performance (99% accuracy), and further an 11-gene classifier with 99% accuracy. Such further classifiers are e.g. given in tables 1 to 3, 5 and 6 (above) for PTC. 
         [0050]    However, similar results are obtained doing the same analysis on the non-integrated data. Taking into account the results of PCA ( FIG. 1 ), where it was obvious that the variance explained by the different datasets is much larger than the variance explained by tumor entity, one could imagine that the bias introduced by the datasets may help (or hamper) classification. Therefore a study-crossvalidation was performed, whereby sequentially one study was taken out from the dataset, a was classifier built from the remaining samples and tested on the eliminated dataset. On the DWD-integrated data, the accuracy of prediction was 100, 100, 98 and 100% leaving out He, Huang, Jarzab and Reyes from the classifier, respectively. For the non-integrated data, the results were similar (100, 100, 94 and 100%). 
         [0000]    
       
         
               
             
               
               
               
               
             
           
               
                 TABLE 9 
               
             
             
               
                   
               
               
                 Genes in classifier2 (after leaving out SERPINA1) 
               
             
          
           
               
                 Symbol 
                 Title 
                 Cluster 
                 Accession 
               
               
                   
               
               
                 WAS 
                 Wiskott-Aldrich syndrome 
                 Hs.2157 
                 BC012738 
               
               
                   
                 (eczema-thrombocytopenia) 
               
               
                 LRP4 
                 Low density lipoprotein receptor- 
                 Hs.4930 
                 BM802977 
               
               
                   
                 related protein 4 
               
               
                 TFF3 
                 Trefoil factor 3 (intestinal) 
                 Hs.82961 
                 BC017859 
               
               
                 ST3GAL6 
                 ST3 beta-galactoside alpha-2,3- 
                 Hs.148716 
                 BC023312 
               
               
                   
                 sialyltransferase 6 
               
               
                 STK39 
                 Serine threonine kinase 39 
                 Hs.276271 
                 BM455533 
               
               
                   
                 (STE20/SPS1 homolog, yeast) 
               
               
                 DPP4 
                 Dipeptidyl-peptidase 4 (CD26, 
                 Hs.368912 
                 BC065265 
               
               
                   
                 adenosine deaminase completing 
               
               
                   
                 protein 2) 
               
               
                 CHI3L1 
                 Chitinase 3-like 1 (cartilage 
                 Hs.382202 
                 BC038354 
               
               
                   
                 glycoprotein-39) 
               
               
                 FABP4 
                 Fatty acid binding protein 4, 
                 Hs.391561 
                 BC003672 
               
               
                   
                 adipocyte 
               
               
                 LAMB3 
                 Laminin, beta 3 
                 Hs.497636 
                 BC075838 
               
               
                   
               
             
          
         
       
     
       Example 6 
     Follicular Carcinoma 
       [0051]    A similar analysis was also performed for the FTC data, but cross-validation was hampered, due to the very limited availability of data. Again, a classifier was built for each dataset (Lacroix and Weber). They achieved a loocv-accuracy of 96% (Weber) and 100% (Lacroix) on 25 and 3997 genes. The number of genes in the Lacroix-data already suggests overfitting, which was confirmed by cross-classification with the other dataset (25 and 35% accuracy, respectively). Also, the gene-overlap between the two classifiers is low (between 0 and 10% depending on the threshold). If, however the 2 datasets are combined using DWD, a 147-gene classifier (table 4 above) could be built which was able to correctly identify samples (with a 92% accuracy). 
       Example 7 
     Discussion 
       [0052]    The present invention represents the largest cohort of thyroid carcinoma microarray data analysed to date. It makes use of the novel combinatory method using the latest algorithms for microarray data integration and classification. Nevertheless, meta-analysis of microarray data still poses a challenge, mainly because single microrarray investigations are aimed at at least partly different questions and hence use different experimental designs. Moreover, the number of thyroid tumor microarray data available to date is still comparably low (compared to breast cancer, e.g.). Therefore, when doing meta-analysis, one is forced to use all data available, even if the patient cohorts represent a rather heterogeneous and potentially biased population. More specifically, it is difficult to obtain a homogenous collection of control material (from healthy patients). These are usually taken from patients who were operated for other thyroid disease which is in turn very likely to cause a change in gene expression as measured on microarrays. The generation of homogeneous patient cohorts is further hampered by limited availability of patient data like age, gender, genetic background, etc. 
         [0053]    When doing meta-analysis of microarray data, many researchers have based their approach on comparing gene lists from published studies (Griffith et al, cited above). This is very useful, as one can include all studies in the analysis and is not limited to the studies where raw data is available. However, the studies generally follow very different analysis strategies, some more rigorous than others. It is not under the control of the meta-analyst how the authors arrived at the gene lists. Therefore these analyses may be biased. 
         [0054]    Regarding data integration, according to the original DWD paper, DWD performs best when at least 25-30 samples per dataset are present. In the present study, 4 out of 6 datasets contained less than 20 samples. Still DWD performed comparably well for removing platform biases (see Table 8). 
         [0055]    DWD greatly improved the results of PCA ( FIG. 1 ), hierarchical clustering ( FIG. 2 ) and the classification accuracy when applying a classifier from one study to another study (Table 8). In this light it was surprising to see that the non-integrated data performed equally well in the study cross-validation compared to the DWD-integrated data. One explanation for this is that any study-specific bias will become less important the more studies are being evaluated. Given that the study bias affects some genes more than others, the more affected genes will be less likely to survive the pamr-thresholding due to the variance introduced by the study-bias. However, as shown above, there is a large abundance of genes discriminating PTC and benign nodules. As long as one (or a few) of those genes is not affected by the study bias, it (they) will survive thresholding and discrimination between tumor entities will still be possible. 
         [0056]    There is an apparent discrepancy when one looks at  FIG. 3 : Before DWD, the PTC samples have a higher SERPINA1 expression while after DWD it is the other way round. However, as noted in the Materials and Methods section, DWD subtracts the class means from each sample. This simply means that before DWD the study bias for SERPINA1 is higher than the difference in expression between the tumor classes. This also explains, why in the not-integrated data SERPINA1 is not a well working classifier. 
         [0057]    A recent Meta-Analysis and Meta-Review by Griffith et. al. (cited above) has summarised genes with a diagnostic potential in the context of thyroid disease. They published lists of genes which appeared in more than one high-throughput study (Microarray, SAGE) analysing thyroid disease and applied a ranking system. In their analysis SERPINA1 scored the third highest, and TFF3, which is part of classifier2 (when leaving out SERPINA1), scored second. Four out of nine genes from classifier2 appeared in the list from Griffith et. al. (LRP4, TFF3, DPP4 and FABP4). 
         [0058]    Most of these lists were generated from microarray analysis. However, even when comparing the genes in the classifiers to gene lists generated with independent technologies, like cDNA library generation, there is substantial overlap. SERPINA1 appears in their lists as well as four out of the nine genes from classifier2 (TFF3, DPP4, CHI3L1 and LAMB3). 
         [0059]    For the case of follicular thyroid disease, building a robust classifier is much more difficult. This is mainly down to the limited availability of data. Also, the two datasets were very different in terms of the platforms used; while all other datasets were generated on Affymetrix GeneChips arrays of different generations, the Lacroix data was generated on a custom Agilent platform. Nevertheless the classifier (set) of table 4 was able to identify most samples correctly in loocv. 
         [0060]    The power of the meta analysis approach adopted here is demonstrated by a 99% loocv-accuracy (97.9% weighted average accuracy in the study cross-validation) for the distinction between papillary thyroid carcinoma and benign nodules. This has been achieved on the largest and most diverse dataset so far (99 samples from 4 different studies). 
         [0061]    One sample was classified wrongly, and although it is not possible to correctly map the samples from this analysis to the original analysis, the misclassified sample is from the same group (PTC, validation group) as the sample which was wrongly classified in the original analysis. According to Jarzab et. al. the sample was an outlier because it contained only ≈20% tumor cells.