Colorectal cancer subtype recognizer

Abstract

The present invention relates to a colorectal cancer subtype identifier based on a percentage splice value (PSI) of a variable splice event. The invention also relates to a method for predicting the outcome of a subject suffering from colorectal cancer by using the PSI value. The invention also relates to a kit for predicting the outcome of a subject suffering from colorectal cancer by means of the PSI value. The invention also relates to the use of PSI values as outcome markers for subjects suffering from colorectal cancer. The invention also relates to a method of treating a subject suffering from colorectal cancer by obtaining a CMS likelihood related to the outcome of disease using PSI values.

Description

TECHNICAL FIELD

[0001] The present invention relates to a colorectal cancer subtype identifier based on the percent spliced-in (PSI) value of alternative splicing events. The present invention also relates to a method of predicting outcome of a subject having colorectal cancer using the PSI value. The present invention also relates to a kit for predicting outcome of a subject having colorectal cancer by the PSI value. The present invention also relates to the use of the PSI value as a marker of outcome of a subject having colorectal cancer. The present invention also relates to a method of treating a subject having colorectal cancer by using the PSI value to obtain the CMS likelihood of disease outcome. BACKGROUND

[0002] Colorectal cancer (CRC), also known as colon cancer or bowel cancer, is the third most common cancer worldwide. In 2020, there were over 1.9 million new cases of colorectal cancer, with over 500,000 patients ultimately dying from the disease each year (‘Colorectal Cancer Facts & Figures 2020-2022’, American Cancer Society, Atlanta, Georgia). Early stage patients are typically treated with a colon resection surgery followed by radiation therapy or systemic chemotherapy, which is based on macroscopic features of the tumor and tumor staging. In some patients who receive chemotherapy after colon resection surgery, 5-year recurrence-free survival rates are improved, while in others this statistic is not improved.

[0003] Clinical experience and colon cancer research have led to the recognition that colon cancer is not a single disease, but rather appears in several different subtypes. These subtypes are distinguished by unique gene expression patterns that influence or dictate tumor biology. Numerous papers have been published describing methods to classify colon tumors into molecularly distinct subtypes, for example, M. Pratap Singh et al., Genes & Diseases, 2021, 8, 133-145, G. Valenzuela et al., World J. Clin. Oncol., 2021, 12(11), 1000-1008, D. G. Menter et al., Curr. Gastroenterol. Rep., 2019, 21(5) 1-12, G. Martini et al., Ther. Adv. Med. Oncol., 2020, 12(1), 1-18, E. Fontana et al., Annals of oncology, 2019, 30, 520-527. Recognizing similarities that exist in many of these subtype classification systems, a consortium of experts has been established with the goal of deriving a subtype classification system that inherits the best features of each system.

[0004] The consensus molecular subtype (CMS) classification system divides colon cancer into four distinct groups, called subtypes, each with unique biological and molecular features: CMS1, CMS2, CMS3, and CMS4. Gene expression profiles from tumors have been used to establish these subgroups. CMS1 (MSI-immune) tumors have microsatellite instability and are heavily infiltrated by immune cells. CMS2 (classical) is an epithelial subtype with significant upregulation of downstream targets of WNT and MYC, and chromosomal instability (CIN) is a distinguishing feature of this subtype. CMS3 (metabolic) is similar to CMS2 with epithelial features but exhibits less CIN. In addition, the CMS3 subtype is enriched for KRAS mutations and exhibits dysregulation of genes involved in metabolism. CMS4 (mesenchymal) is a mesenchymal subtype that exhibits activation of pathways that regulate epithelial-mesenchymal transition (EMT) and stemness. The CMS subtype system is likely to play an important role in the treatment selection for colon cancer.

[0005] Identification of molecular subtypes of colorectal cancer (CRC) has prognostic and potential diagnostic value for patients, but reliable subtyping is still not available. The current consensus molecular subtype (CMS) classification of colorectal cancer is based on complex RNA expression patterns quantified at the gene level.

[0006] The following documents form the technical background of the present invention: WO 2021 / 101452, Jianyi et al., Molecular Carcinogenesis, 60 (4), 2021, p. 279-293, Haifeng et al., BMC Gastroenterology, 20 (1), 2020 and Guinney et al., Nature Medicine, 21 (11), 2015, p. 1350-1356.

[0007] Zhiyuan et al., Genomic Academic Press, 2020, 112 (6), p. 4032-4040, relates to a study on colorectal cancer (CRC) recurrence and alternative splicing (AS). A prognostic signature based on alternative splicing for predicting recurrence of stage I-III CRS was also constructed. It is to be noted that stages I-III of CRC are not equivalent to the colorectal cancer subtypes CM1 to CM4.

[0008] Haitao et al., BMC Cancer, 20 (1), 2020 relates to a study based on survival- associated alternative splicing events, identifying and validating alternative splicing signatures.

[0009] Yongfu et al., Ebiomedicine, 36, 2018, p. 183-195 relates to a study aiming at analyzing the genome-wide range of alternative splicing in a CRC cohort, identifying alternative splicing events associated with CRC and further analyzing their association with clinical outcome. Four clusters C1, C2, C3 and C4 were determined (this is not equivalent to CMS1-CMS4). In addition, the article states that overall, the distribution of different CMS, TNM stage, KRASm and survival status in CRC samples was not random between clusters.

[0010] Eilertsen et al., Int. J. of Cancer, 144 (4), 2018, 841-847 relates to a study of the prognostic impact of KRAS alternative splicing associated with mutational status.

[0011] Tong et al., Department of Pathology, Erasmus University Medical Cancer, 11 (7), 2022 relates to a study on alternative splicing in driving colon cancer epithelial malignancy phenotypic plasticity. The study focuses on the alternative splicing of the CD44 and NUMB genes.

[0012] WO2019173647 discloses a kit and method for predicting or determining a consensus molecular subtype (CMS) of colorectal cancer in a human patient. The kit comprises a plurality of oligonucleotide primers configured to complementarily bind to respective portions of cDNA from at least twelve RNA transcripts of a colorectal cancer tissue sample, and to initiate polymerase chain reaction of the cDNA, the at least twelve RNA transcripts comprising at least three RNA transcripts from each of four groups of genetic elements, wherein each of the four groups of genetic elements defines a CMS gene expression profile specific to a different one of CMS1, CMS2, CMS3, and CMS4.

[0013] WO2020206136 relates to a method of classifying a cancer status of a colorectal cancer patient by:

[0014] (a) obtaining a tumor sample from the subject;

[0015] (b) measuring expression levels of a plurality of genes in the tumor sample;

[0016] (c) generating an expression profile based on a comparison between the expression levels of the plurality of genes in the sample of the subject and corresponding expression levels obtained from reference samples, wherein the reference samples are from different subjects having known cancer status;

[0017] (d) classifying the cancer status of the subject based on the expression profile.

[0018] WO2021061990 discloses a method of determining whether a subject has a Cl subtype of colorectal cancer (CRC), wherein the expression level of at least one Cl subtype-related gene in a test sample is determined.

[0019] To date, the features of CMS and current CMS classification methods rely on expression patterns of hundreds of genes. The obstacles in clinical application of these techniques include: the uncertainty that exists when evaluating samples one by one for individual patients, which is common in a clinical setting, the batch effect susceptibility of expression quantification at the gene level, and the high cost associated with evaluating the expression levels of hundreds of genes.

[0020] Therefore, there are some drawbacks of the traditional consensus molecular subtype (CMS) determination method for colorectal cancer tumors that can be addressed. Therefore, in order to determine the consensus molecular subtype of colorectal tumors and its related prognosis, there is an urgent need for a time and cost effective clinical detection method.

[0021] Therefore, it is an object of the present application to provide a method for molecular subtype classification (CMS) of patients with colorectal cancer. It is another object of the present application to provide a method for predicting the outcome of a subject with colorectal cancer.

[0022] Surprisingly, it has been found that a colorectal cancer subtype identifier using percent splicing index (PSI) from alternative splicing events enables the classification of consensus molecular subtypes (CMS). SUMMARY

[0023] The present application relates to a colorectal cancer subtype identifier that classifies tumors by PSI values based on the occurrence of at least one alternative splicing event.

[0024] The present application also relates to a method of predicting the outcome of a subject with colorectal cancer using PSI values based on the occurrence of at least one alternative splicing event, wherein the method comprises the following steps:

[0025] a) collecting a sample from a tumor of a subject with cancer;

[0026] b) determining PSI values, in particular at least three, especially at least five PSI values;

[0027] c) transforming the PSI values to determine an indication of disease outcome.

[0028] The present application also relates to a kit for predicting the outcome of a subject suffering from colorectal cancer based on the occurrence of at least one alternative splicing event using PSI values, in particular at least three, especially at least five PSI values.

[0029] The present application also relates to the use of PSI values, in particular at least three, especially at least five PSI values, based on the occurrence of alternative splicing as an outcome marker for a subject suffering from colorectal cancer.

[0030] The present application also relates to a method for treating a subject suffering from colorectal cancer based on the occurrence of alternative splicing using PSI values, comprising the steps of:

[0031] d) collecting a sample from a tumor of a subject suffering from cancer;

[0032] e) determining PSI values, in particular at least three, especially at least five PSI values;

[0033] f) transforming the PSI values to determine an indication of disease outcome. DETAILED DESCRIPTION

[0034] The colorectal cancer subtype identifier and the method according to the present application have the following advantages:

[0035] - Facilitates the classification of patients into CMS1, CMS2, CMS3 and CMS4 subtypes and decides on further treatment measures and / or monitoring as an alternative to no intervention.

[0036] - Allows the identification of consensus molecular subtypes of colorectal cancer by transforming PSI values from a small number of alternative splicing events per CMS that can be measured using RT-PCR, multiplexed assay, or targeted sequencing.

[0037] - PSI values provide the ratio of a specific splice variant. The built-in normalization process for calculating PSI values makes this method more resistant to batch effects that would adversely affect the quantification of gene-level expression.

[0038] - Individual samples can be evaluated by providing four probabilities, each representing the likelihood that the sample belongs to a specific subtype.

[0039] - Outperforms gene expression-based classifiers.

[0040] CMS1 (MSI-immune) tumors have microsatellite instability and are heavily infiltrated by immune cells. The carcinogenic pathway is characterized by: 1) proximal colon location; 2) high BRAF V600E mutation rate; 3) high CpG island methylation leading to loss of function of tumor suppressor genes (CpG island methylation phenotype [CIMP]); 4) association with impaired DNA mismatch repair (MMR) system; and 5) immunogenic lymphocyte infiltrated tumor microenvironment. CMS1 tumor patients have a better prognosis compared to CMS2, CMS3 or CMS4 tumor patients.

[0041] CMS2 (classical) is an epithelial subtype with activated WNT-beta catenin and MYC signaling pathways, with chromosomal instability (CIN) being the distinguishing feature of this subtype. Tumors classified as CMS2 originate from the classical adenoma-carcinoma sequence. CMS2 tumors are usually treated with standard adjuvant chemotherapy. Five-year overall survival rates for CMS2 at each stage are the highest among all subtypes.

[0042] CMS3 (metabolic) has epithelial cell characteristics but exhibits less CIN. In addition, the CMS3 subtype is enriched for KRAS mutations and shows dysregulation of genes involved in metabolism. MSI is also higher in CMS3 than in CMS2 and CMS4. At the level of gene expression, CMS3 looks most similar to normal colon tissue. Pathway analysis indicates that CMS3 mRNA is enriched in 9 of the 10 metabolic pathways studied, including glutamine, fatty acid, and lysophospholipid metabolism.

[0043] CMS4 (mesenchymal) is a mesenchymal subtype that exhibits epithelial-mesenchymal transition (EMT) and activation of stemness regulatory pathways. CMS4 tumors exhibit very low levels of hypermutation. CMS4 CRCs exhibit a mesenchymal phenotype with a gene signature consistent with activated stroma: angiogenesis, integrin binding to matrix proteins, TGF signaling characteristic of cancer-associated fibroblasts (CAFs), and an inflammatory microenvironment with prominent innate immune cells. In contrast to the antitumor immune environment of CMS1 cancers, the CMS4 tumor microenvironment is proinflammatory, with Treg cells, T helper 17 cells, myeloid-derived suppressor cells, and tumor-promoting macrophages. CMS4 cancers are often diagnosed at a late stage and have a poor prognosis, with the lowest five-year overall survival rate.

[0044] In the present invention, the term "subject" refers to any human or animal. (Non-human) animals include all vertebrates, e.g., mammals and non-mammals, including cows, sheep, pigs, goats, horses, poultry, dogs, cats, non-human primates, rodents, and the like. In one embodiment, the subject is a human subject.

[0045] The term "marker" as used herein refers to a value of PSI used to determine the CMS1, CMS2, CMS3 and / or CMS4 group.

[0046] In the present application, "outcome" refers to the result of a treatment or a series of treatments for a certain disease.

[0047] The outcome is determined at a certain point in time during or after treatment based on one criterion or a set of criteria. Considering the outcome helps to determine the effectiveness and appropriateness of a medical intervention and to evaluate it in relation to alternative options, in particular no intervention.

[0048] There are various disease outcome definitions, for example, by using different endpoints. One way of determining the outcome is "long-term" survival, which refers to surviving a certain period of time (e.g. at least 3 years) after diagnosis and / or initial treatment. Another way is "relapse-free survival" (RFS), which refers to the time of survival from diagnosis and / or initial treatment to relapse of cancer or death from relapse of cancer (usually in years). Another way of determining is "overall survival" (OS), which refers to the time from diagnosis and / or initial treatment to death from any cause (in years). Yet another way is "disease-free survival" (DFS), which refers to the period of survival from diagnosis and / or initial treatment to first relapse of cancer or death from any cause (usually in years).

[0049] Outcome analysis often focuses on changes in quality of life; thus, it assesses the way of corresponding preventive or therapeutic measures in a more meaningful way for future subjects compared to so-called surrogate markers, parameters or endpoints, which are measurable variables that have no direct relationship to the individual involved, such as measurement values and laboratory values, tumor diameter.

[0050] The overall situation should be defined as precisely as possible instead of using surrogate parameters or intuitive case descriptions ("cured" / "not cured" or similar descriptions).

[0051] In a first embodiment of the present application, the present application relates to a colorectal cancer subtype identifier which classifies a tumor based on PSI values associated with at least one alternative splicing event.

[0052] The reference genome is designated as GRCh38, annotated as Gencode v28 (primary assembly).

[0053] The term "PSI" is an abbreviation for "percent spliced in" and refers to the exon-inclusion rate. It is a known statistical value used to measure alternative splicing events. Alternative splicing allows a gene to be transcribed into multiple spliced isoforms (or mRNA transcripts). PSI is defined as the ratio of the relative abundance of all spliced isoforms that include a particular exon to the relative abundance of all spliced isoforms of the gene that include that exon. In other words, the PSI value defines the frequency of the exon in all spliced isoforms of the gene that include the exon. The PSI value of an alternative splicing event reflects the strength / frequency of such event and has been widely used to detect differentially spliced exons.

[0054] Alternative splicing (AS) events increase the complexity of gene expression patterns and can be classified into five different types: (1) exon skipping (ES), (2) intron retention (IR), (3) alternative 5' splice site (A5SS), (4) alternative 3' splice site (A3SS), and (5) mutually exclusive exon usage (MXE) events. These events are regulated in a tissue and cell type-specific manner and introduce qualitative changes into the existing pool of RNAs, adding an additional layer of biological information.

[0055] Preferably, the PSI values are based on at least 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 141 alternative splicing events or a combination thereof.

[0056] The alternative splicing events are preferably at least one exon skipping event.

[0057] Advantageously, the colorectal cancer subtype identifier classifies the tumor as CMS1, CMS2, CMS3, or CMS4.

[0058] There are two types of alternative splicing patterns that can be used to discriminate colorectal cancer subtypes. The first one is subtype-specific alternative splicing events.

[0059] Preferably, for the identification of CMS1, there are at least 1 (preferably at least 5, more preferably at least 10, even more preferably at least 20, in particular at least 25) exon skipping events selected from the group consisting of: in exon with genomic coordinates chr17:3723287-3723383 of ITGAE (ENSG00000083457.11); in exon with genomic coordinates chr15:43194080-43194137 of CCNDBP1 (ENSG00000166946.13); in exon with genomic coordinates chr22:50573807-50573921 of CPT1B (ENSG00000205560.12); in exon with genomic coordinates chr13:114236644-114236699 of CDC16 (ENSG00000130177.14); in exon with genomic coordinates chr12:6951458-6951520 of PTPN6 (ENSG00000111679.16); in exon with genomic coordinates chr12:6951463-6951520 of PTPN6 (ENSG00000111679.16); in exon with genomic coordinates chr11:44073446-44073517 of ACCS (ENSG00000110455.13); in exon with genomic coordinates chr4:121816143-121816194 of EXOSC9 (ENSG00000123737.12); in exon with genomic coordinates chr4:121816368-121816447 of EXOSC9 (ENSG00000123737.12); in exon with genomic coordinates chr19:52707468-52707542 of ZNF611 (ENSG00000213020.9); in exon with genomic coordinates chr9:122285779-122285946 of MRRF (ENSG00000148187.17); in exon with genomic coordinates chr6:17668974-17669028 of NUP153 (ENSG00000124789.11); in exon with genomic coordinates chr14:100375282-100375350 of WARS (ENSG00000140105.17); in exon with genomic coordinates chr14:100375282-100375403 of WARS (ENSG00000140105.17), in exons with genomic coordinates chr14: 100375282-100375406; D2HGDH (ENSG00000180902.17), in exons with genomic coordinates chr2: 241748864-241749929; LUC7L (ENSG00000007392.16), in exons with genomic coordinates chr16: 228332-228402; EPB41 (ENSG00000159023.20), in exons with genomic coordinates chr1: 29058588-29058645; DGUOK (ENSG00000114956.19), in exons with genomic coordinates chr2: 73938909-73939022; MDM4 (ENSG00000198625.12), in exons with genomic coordinates chr1: 204537429-204537497; MDM4 (ENSG00000198625.12), in exons with genomic coordinates chr1: 204537458-204537497; PTP4A2 (ENSG00000184007.19), in exons with genomic coordinates chr1: 31915894-31915987; MKNK2 (ENSG00000099875.14), in exons with genomic coordinates chr19: 2039630-2039856; CCDC112 (ENSG00000164221.12), in exons with genomic coordinates chr5: 115269702-115269798; FRYL (ENSG00000075539.14), in exons with genomic coordinates chr4: 48593929-48594016; CEP78 (ENSG00000148019.13), in exons with genomic coordinates chr9: 78265858-78265906; FNBP1 (ENSG00000187239.16), in exons with genomic coordinates chr9: 129923843-129923996; FNBP1 (ENSG00000187239.16), in exons with genomic coordinates chr9: 129923843-129924026; ECT2 (ENSG00000114346.13), in exons with genomic coordinates chr3: 172752149-172752472; ECT2 (ENSG00000114346.13), in exons with genomic coordinates chr3: 172755482-172755575; ANKRD26 (ENSG00000107890.16), in exons with genomic coordinates chr10: 27044156-27044190; ZMIZ2 (ENSG00000122515.14), in exons with genomic coordinates chr7: 44760150-44760228; C6orf48 (ENSG00000204387.12), in exons with genomic coordinates chr6: 31836423-31836517; or USPL1 (ENSG00000132952.11), in exons with genomic coordinates chr13: 30621072-30621239.

[0060] In particular, for identifying CMS1, there are 1, 2, 3, 4, 5, 6, 7, 8, 9 exon skipping events selected from: ITGAE (ENSG00000083457.11), in exons with genomic coordinates chr17: 3723287-3723383; MRRF (ENSG00000148187.17), in exons with genomic coordinates chr9: 122285779-122285946; LUC7L (ENSG00000007392.16), in exons with genomic coordinates chr16: 228332-228402; MDM4 (ENSG00000198625.12), in exons with genomic coordinates chr1: 204537458-204537497; CCDC112 (ENSG00000164221.12), in exons with genomic coordinates chr5: 115269702-115269798; FRYL (ENSG00000075539.14), in exons with genomic coordinates chr4: 48593929-48594016; CEP78 (ENSG00000148019.13), in exons with genomic coordinates chr9: 78265858-78265906; FNBP1 (ENSG00000187239.16), in exons with genomic coordinates chr9: 129923843-129923996; ANKRD26 (ENSG00000107890.16), in exons with genomic coordinates chr10: 27044156-27044190.

[0061] Preferably, for identifying CMS2, there are at least 1 (preferably at least 5, more preferably at least 10, and particularly preferably at least 15) exon skipping events selected from: ZMIZ2 (ENSG00000122515.14) in exons with genomic coordinates chr7:44760150-44760228; C6orf48 (ENSG00000204387.12) in exons with genomic coordinates chr6:31836423-31836517; USPL1 (ENSG00000132952.11) in exons with genomic coordinates chr13:30621072-30621239; RBM39 (ENSG00000131051.22) in exons with genomic coordinates chr20:35740524-35740597; MIS12 (ENSG00000167842.15) in exons with genomic coordinates chr17:5488195-5488589; AFMID (ENSG00000183077.15) in exons with genomic coordinates chr17:78204655-78204741; MACROD1 (ENSG00000133315.10) in exons with genomic coordinates chr11:63998837-63998872; FN1 (ENSG00000115414.18) in exons with genomic coordinates chr2:215380810-215381080; WBP1 (ENSG00000239779.6) in exons with genomic coordinates chr2:74459477-74459562; XPO1 (ENSG00000082898.16) in exons with genomic coordinates chr2:61525269-61525333; PTPN18 (ENSG00000072135.12) in exons with genomic coordinates chr2:130359232-130359309; ARHGAP27 (ENSG00000159314.11) in exons with genomic coordinates chr17:45404268-45404334; C16orf13 (ENSG00000130731.15) in exons with genomic coordinates chr16:635280-635340; C16orf13 (ENSG00000130731.15) in exons with genomic coordinates chr16:635517-635774; C16orf13 (ENSG00000130731.15) in exons with genomic coordinates chr16:635611-635774.

[0062] In particular, to identify a CMS2, there is 1, 2, 3, 4, 5 exon skipping event selected from: USPL1 (ENSG00000132952.11 ) in exons with genomic coordinates of chr13:30621072-30621239; MACROD1 (ENSG00000133315.10) in exons with genomic coordinates of chr11 :63998837-63998872; ENAH (ENSG00000154380.17) in exons with genomic coordinates of chr1 :225504990-225505053; FNIP1 (ENSG00000217128.11 ) in exons with genomic coordinates of chr5:131710577-131710661 ; or SORBS1 (ENSG00000095637.21 ) in exons with genomic coordinates of chr10:95414493-95414862.

[0063] Preferably, for identifying CMS3, there are at least 1 (preferably at least 5, more preferably at least 15, even more preferably at least 30, in particular at least 41) exon skipping events selected from the group consisting of: in an exon of C16orf13 (ENSG00000130731.15), genomic coordinates chr 16:635280-635340; in an exon of C16orf13 (ENSG00000130731.15), genomic coordinates chr 16:635517-635774; in an exon of C16orf13 (ENSG00000130731.15), genomic coordinates chr 16:635611-635774; in an exon of AURKA (ENSG00000087586.17), genomic coordinates chr 20:56388686-56388784; in an exon of EPB41L3 (ENSG00000082397.17), genomic coordinates chr 18:5394676-5394793; in an exon of KALRN (ENSG00000160145.15), genomic coordinates chr 3:124637207-124637303; in an exon of ADAM15 (ENSG00000143537.13), genomic coordinates chr 1 :155061903-155061975; in an exon of KRAS (ENSG00000133703.11), genomic coordinates chr 12:25215436-25215560; in an exon of SLC39A14 (ENSG00000104635.13), genomic coordinates chr 8:22412036-22412206; in an exon of MYO9A (ENSG00000066933.15), genomic coordinates chr 15:71951776-71951896; in an exon of TPM1 (ENSG00000140416.20), genomic coordinates chr 15:63044026-63044152; in an exon of TPM1 (ENSG00000140416.20), genomic coordinates chr 15:63061197-63061273; in an exon of TPM1 (ENSG00000140416.20), genomic coordinates chr 15:63061712-63061788; in an exon of MYO6 (ENSG00000196586.13), genomic coordinates chr 6:75894813-75894840; in an exon of MYO6 (ENSG00000196586.13), in an exon with genomic coordinates chr6:75898372-75898411; KIAA1217 (ENSG00000120549.17), in an exon with genomic coordinates chr10:24494499-24494604; KIAA1217 (ENSG00000120549.17), in an exon with genomic coordinates chr10:24542692-24542770; KIAA1217 (ENSG00000120549.17), in an exon with genomic coordinates chr10:24542882-24544481; GIT2 (ENSG00000139436.20), in an exon with genomic coordinates chr12:109945259-109945349; MYL6 (ENSG00000092841.18), in an exon with genomic coordinates chr12:56160625-56160670; CTNND1 (ENSG00000198561.13), in an exon with genomic coordinates chr11 :57789036-57789155; CTNND1 (ENSG00000198561.13), in an exon with genomic coordinates chr11 :57791384-57791673; CTNND1 (ENSG00000198561.13), in an exon with genomic coordinates chr11 :57791491-57791673; CD44 (ENSG00000026508.18), in an exon with genomic coordinates chr11 :35208104-35208206; CD44 (ENSG00000026508.18), in an exon with genomic coordinates chr11 :35211245-35211449; APBB2 (ENSG00000163697.16), in an exon with genomic coordinates chr4:40935076-40935139; SEC31A (ENSG00000138674.16), in an exon with genomic coordinates chr4:82830936-82830975; SEC31A (ENSG00000138674.16), in an exon with genomic coordinates chr4:82830936-82830975; SEC31A (ENSG00000138674.16), in an exon with genomic coordinates chr4:82842139-82842481; SEC31A (ENSG00000138674.16), in an exon with genomic coordinates chr4:82842184-82842481; SYTL2 (ENSG00000137501.17), in an exon with genomic coordinates chrll:85717482-85717530; MYOF (ENSG00000138119.16), in an exon with genomic coordinates chr10:93392916-93392955; NAV2 (ENSG00000166833.19), in an exon with genomic coordinates chrll:20051288-20051333; GAB1 (ENSG00000109458.8), in an exon with genomic coordinates chr4:143434087-143434168; PLEKHM2 (ENSG00000116786.12), in an exon with genomic coordinates chr1:15721328-15721388; CLSTN1 (ENSG00000171603.16), in an exon with genomic coordinates chr1:9737497-9737554; CLSTN1 (ENSG00000171603.16), in an exon with genomic coordinates chr1:9756480-9756510; GOLGA4 (ENSG00000144674.16), in an exon with genomic coordinates chr3:37361242-37361305; PBX1 (ENSG00000185630.18), in an exon with genomic coordinates chr1:164820071-164820184; FKBP14 (ENSG00000106080.10), in an exon with genomic coordinates chr7:30020212-30020304; XPO1 (ENSG00000082898.16), in an exon with genomic coordinates chr2:61525269-61525333.

[0064] In particular, for identifying CMS3, there are 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 exon skipping events selected from: XPO1 (ENSG00000082898.16) in exons with genomic coordinates chr2:61525269-61525333; C16orf13 (ENSG00000130731.15) in exons with genomic coordinates chr16:635517-635774; PXN (ENSG00000089159.16) in exons with genomic coordinates chr12:120224642-120224727; ENAH (ENSG00000154380.17) in exons with genomic coordinates chr1:225504990-225505053; AURKA (ENSG00000087586.17) in exons with genomic coordinates chr20:56388686-56388784; EPB41L3 (ENSG00000082397.17) in exons with genomic coordinates chr18:5394676-5394793; KALRN (ENSG00000160145.15) in exons with genomic coordinates chr3:124637207-124637303; TPM1 (ENSG00000140416.20) in exons with genomic coordinates chr15:63061197-63061273; KIAA1217 (ENSG00000120549.17) in exons with genomic coordinates chr10:24542692-24542770; MYOF (ENSG00000138119.16) in exons with genomic coordinates chr10:93392916-93392955; PBX1 (ENSG00000185630.18) in exons with genomic coordinates chr1:164820071-164820184.

[0065] Preferably, in order to identify a CMS4, there are at least 1 (preferably at least 5, more preferably at least 15, even more preferably at least 30, in particular at least 55) exon skipping events selected from the group consisting of: in an exon with genomic coordinates chr 15: 71951776-71951896 of MYO9A (ENSG00000066933.15); in an exon with genomic coordinates chr 15: 63044026-63044152 of TPM1 (ENSG00000140416.20); in an exon with genomic coordinates chr 15: 63061197-63061273 of TPM1 (ENSG00000140416.20); in an exon with genomic coordinates chr 15: 63061712-63061788 of TPM1 (ENSG00000140416.20); in an exon with genomic coordinates chr 6: 75894813-75894840 of MYO6 (ENSG00000196586.13); in an exon with genomic coordinates chr 6: 75898372-75898411 of MYO6 (ENSG00000196586.13); in an exon with genomic coordinates chr 10: 24494499-24494604 of KIAA1217 (ENSG00000120549.17); in an exon with genomic coordinates chr 10: 24542692-24542770 of KIAA1217 (ENSG00000120549.17); in an exon with genomic coordinates chr 10: 24542882-24544481 of KIAA1217 (ENSG00000120549.17); in an exon with genomic coordinates chr 12: 109945259-109945349 of GIT2 (ENSG00000139436.20); in an exon with genomic coordinates chr 12: 56160625-56160670 of MYL6 (ENSG00000092841.18); in an exon with genomic coordinates chr 17: 67875555-67875744 of BPTF (ENSG00000171634.17); in an exon with genomic coordinates chr 16: 15708802-15708841 of MYH11 (ENSG00000133392.17); in an exon with genomic coordinates chr 14: 73279280-73279424 of NUMB (ENSG00000133961.20); in an exon with genomic coordinates chr 17: 67875555-67875744 of TEAD1 (ENSG00000187079.16), in an exon with genomic coordinates chrll:12878888-12878900; SPAG9 (ENSG00000008294.20), in an exon with genomic coordinates chr17:50975862-50975901; FAT1 (ENSG00000083857.13), in an exon with genomic coordinates chr4:186590367-186590403; TNS1 (ENSG00000079308.17), in an exon with genomic coordinates chr2:217830366-217830390; ESYT2 (ENSG00000117868.15), in an exon with genomic coordinates chr7:158752780-158752843; SLMAP (ENSG00000163681.14), in an exon with genomic coordinates chr3:57925844-57925934; AKAP9 (ENSG00000127914.16), in an exon with genomic coordinates chr7:91992157-91992211; RUBCN (ENSG00000145016.15), in an exon with genomic coordinates chr3:197691073-197691148; ATP2B4 (ENSG00000058668.14), in an exon with genomic coordinates chrll:203733222-203733400; LRRFIP2 (ENSG00000093167.17), in an exon with genomic coordinates chr3:37091466-37091538; TBC1D23 (ENSG00000036054.12), in an exon with genomic coordinates chr3:100311832-100311877; EHBP1 (ENSG00000115504.14), in an exon with genomic coordinates chr2:62987930-62988038; SLK (ENSG00000065613.13), in an exon with genomic coordinates chr10:104010815-104010908; WDFY3 (ENSG00000163625.15), in an exon with genomic coordinates chr4:84726860-84726911; SMARCC2 (ENSG00000139613.11), in an exon with genomic coordinates chr12:56164302-56164368; KIF13A (ENSG00000137177.19), in an exon with genomic coordinates chr6:17771113-17771218; MPRIP (ENSG00000133030.20), in exons with genomic coordinates chr17: 17180606-17180669; LRRFIP1 (ENSG00000124831.18), in exons with genomic coordinates chr2: 237769625- 237769818; NIN (ENSG00000100503.23), in exons with genomic coordinates chr14: 50756491-50758630; RPS24 (ENSG00000138326.19), in exons with genomic coordinates chr10: 78040203-78040225; ACTN1 (ENSG00000072110.13), in exons with genomic coordinates chr14: 68878988-68879069; CTNND1 (ENSG00000198561.13), in exons with genomic coordinates chr11: 57789036-57789155; CTNND1 (ENSG00000198561.13), in exons with genomic coordinates chr11: 57791384-57791673; CTNND1 (ENSG00000198561.13), in exons with genomic coordinates chr11: 57791491-57791673; CD44 (ENSG00000026508.18), in exons with genomic coordinates chr11: 35208104-35208206; CD44 (ENSG00000026508.18), in exons with genomic coordinates chr11: 35211245-35211449; APBB2 (ENSG00000163697.16), in exons with genomic coordinates chr4: 40935076-40935139; SEC31A (ENSG00000138674.16), in exons with genomic coordinates chr4: 82830936-82830975; SEC31A (ENSG00000138674.16), in exons with genomic coordinates chr4: 82830936-82830975; SEC31A (ENSG00000138674.16), in exons with genomic coordinates chr4: 82842139-82842481; SEC31A (ENSG00000138674.16), in exons with genomic coordinates chr4: 82842184-82842481; SYTL2 (ENSG00000137501.17), in exons with genomic coordinates chr11: 85717482-85717530; MYOF (ENSG00000138119.16), in an exon with genomic coordinates chr10:93392916-93392955; NAV2 (ENSG00000166833.19), in an exon with genomic coordinates chrll:20051288-20051333; GAB1 (ENSG00000109458.8), in an exon with genomic coordinates chr4:143434087-143434168; PLEKHM2 (ENSG00000116786.12), in an exon with genomic coordinates chr 1 : 15721328-15721388; CLSTN1 (ENSG00000171603.16), in an exon with genomic coordinates chr 1 :9737497-9737554; CLSTN1 (ENSG00000171603.16), in an exon with genomic coordinates chr 1 :9756480-9756510; GOLGA4 (ENSG00000144674.16), in an exon with genomic coordinates chr3:37361242-37361305; PBX1 (ENSG00000185630.18), in an exon with genomic coordinates chr 1 : 164820071-164820184; FKBP14 (ENSG00000106080.10), in an exon with genomic coordinates chr7:30020212-30020304.

[0066] In particular, for identifying CMS4, there are 1, 2, 3, 4, 5, 6, 7, 8 exon skipping events selected from: ENAH (ENSG00000154380.17) in exons with genomic coordinates chr1:225504990-225505053; TPM1 (ENSG00000140416.20) in exons with genomic coordinates chr15:63061197-63061273; MYO6 (ENSG00000196586.13) in exons with genomic coordinates chr6:75898372-75898411; SLMAP (ENSG00000163681.14) in exons with genomic coordinates chr3:57925844-57925934; KIF13A (ENSG00000137177.19) in exons with genomic coordinates chr6:17771113-17771218; MPRIP (ENSG00000133030.20) in exons with genomic coordinates chr17:17180606-17180669; SEC31A (ENSG00000138674.16) in exons with genomic coordinates chr4:82842184-82842481; MYOF (ENSG00000138119.16) in exons with genomic coordinates chr10:93392916-93392955.

[0067] The second class of exon skipping events has a complex PSI pattern that simultaneously distinguishes multiple types.

[0068] Preferably, in order to distinguish CMS2 and CMS3 from CMS1 and CMS4, there are at least 1 (preferably at least 5, more preferably at least 10, especially preferably at least 20, in particular at least 23) exon skipping events selected from the group consisting of: FCGRT (ENSG00000104870.12) in exon with genomic coordinates chr19:49521694-49521813; DOCK6 (ENSG00000130158.13) in exon with genomic coordinates chr19:11229297-11229390; EXOC7 (ENSG00000182473.21) in exon with genomic coordinates chr17:76090328-76090397; BPTF (ENSG00000171634.17) in exon with genomic coordinates chr17:67875555-67875744; PXN (ENSG00000089159.16) in exon with genomic coordinates chr12:120224642-120224727; EXOC1 (ENSG00000090989.17) in exon with genomic coordinates chr4:55888887-55888932; PLOD2 (ENSG00000152952.11) in exon with genomic coordinates chr3:146077861-146077924; CD47 (ENSG00000196776.15) in exon with genomic coordinates chr3:108049618-108049651; CD47 (ENSG00000196776.15) in exon with genomic coordinates chr3:108050577-108050602; ARHGEF11 (ENSG00000132694.18) in exon with genomic coordinates chr1:156938417-156938513; PBRM1 (ENSG00000163939.18) in exon with genomic coordinates chr3:52558248-52558413; MAGI1 (ENSG00000151276.23) in exon with genomic coordinates chr3:65448021-65448057; MBNL1 (ENSG00000152601.17) in exon with genomic coordinates chr3:152446703-152446757; TNC (ENSG00000041982.15) in exon with genomic coordinates chr9:115064646-115064919; ENAH (ENSG00000154380.17), in an exon with genomic coordinates chr1 :225504990-225505053; BAZ2B (ENSG00000123636.17), in an exon with genomic coordinates chr2: 159397073-159397100; RAI14 (ENSG00000039560.13), in an exon with genomic coordinates chr5:34813573-34813660; FNIP1 (ENSG00000217128.11), in an exon with genomic coordinates chr5:131710577-131710661; MAP3K7 (ENSG00000135341.17), in an exon with genomic coordinates chr6:90544551-90544632; ERBIN (ENSG00000112851.14), in an exon with genomic coordinates chr5:66068876-66069020; SULF2 (ENSG00000196562.14), in an exon with genomic coordinates chr20:47659398-47659452; SORBS1 (ENSG00000095637.21), in an exon with genomic coordinates chr10:95414493-95414655; SORBS1 (ENSG00000095637.21), in an exon with genomic coordinates chr10:95414493-95414862.

[0069] Preferably, in order to discriminate CMS2 and CMS4 from CMS1 and CMS3, there are at least 1 (preferably at least 5, more preferably at least 8, even more preferably at least 11) exon skipping events selected from: SRSF6 (ENSG00000124193.14) in exons with genomic coordinates chr20:43459152-43459420; WASH3P (ENSG00000185596.16) in exons with genomic coordinates chr15:101972595-101972694; OPA1 (ENSG00000198836.9) in exons with genomic coordinates chr3:193626091-193626202; GOLGB1 (ENSG00000173230.15) in exons with genomic coordinates chr3:121719645-121719753; GOLGB1 (ENSG00000173230.15) in exons with genomic coordinates chr3:121719645-121719768; APLP2 (ENSG00000084234.16) in exons with genomic coordinates chr11:130137255-130137291; CPNE1 (ENSG00000214078.12) in exons with genomic coordinates chr20:35658929-35659014; WIPF1 (ENSG00000115935.17) in exons with genomic coordinates chr2:174597600-174597858; ATG9A (ENSG00000198925.11) in exons with genomic coordinates chr2:219228433-219228482; NUBP2 (ENSG00000095906.16) in exons with genomic coordinates chr16:1786737-1786955; ANO1 (ENSG00000131620.17) in exons with genomic coordinates chr11:70111125-70111191.

[0070] A preferred embodiment is a colorectal cancer subtype identifier, wherein the alternative splicing events are based on at least one exon skipping event on at least one gene, particularly at least 50 genes, especially at least 116 genes, selected from the group consisting of ITGAE (ENSG00000083457.11), CCNDBP1 (ENSG00000166946.13), CPT1B (ENSG00000205560.12), CDC16 (ENSG00000130177.14), PTPN6 (ENSG00000111679.16), ACCS (ENSG00000110455.13), EXOSC9 (ENSG00000123737.12), ZNF611 (ENSG00000213020.9), MRRF (ENSG00000148187.17), NUP153 (ENSG00000124789.11), WARS (ENSG00000140105.17), D2HGDH (ENSG00000180902.17), LUC7L (ENSG00000007392.16), EPB41 (ENSG00000159023.20), DGUOK (ENSG00000114956.19), MDM4 (ENSG00000198625.12), PTP4A2 (ENSG00000184007.19), MKNK2 (ENSG00000099875.14), CCDC112 (ENSG00000164221.12), FRYL (ENSG00000075539.14), CEP78 (ENSG00000148019.13), FNBP1 (ENSG00000187239.16), ECT2 (ENSG00000114346.13), ANKRD26 (ENSG00000107890.16), ZMIZ2 (ENSG00000122515.14), C6orf48 (ENSG00000204387.12), USPL1 (ENSG00000132952.11), RBM39 (ENSG00000131051.22), MIS12 (ENSG00000167842.15), AFMID (ENSG00000183077.15), MACROD1 (ENSG00000133315.10), FN1 (ENSG00000115414.18), WBP1 (ENSG00000239779.6), XPO1 (ENSG00000082898.16), PTPN18 (ENSG00000072135.12), ARHGAP27 (ENSG00000159314.11), C16orf13 (ENSG00000130731.15), FCGRT (ENSG00000104870.12), DOCK6 (ENSG00000130158.13), EXOC7 (ENSG00000182473.21), BPTF (ENSG00000171634.17), PXN (ENSG00000089159.16), EXOC1 (ENSG00000090989.17), PLOD2 (ENSG00000152952.11), CD47 (ENSG00000196776.15), ARHGEF11 (ENSG00000132694.18), PBRM1 (ENSG00000163939.18), MAGI1 (ENSG00000151276.23), MBNL1 (ENSG00000152601.17), TNC (ENSG00000041982.15), ENAH (ENSG00000154380.17), BAZ2B (ENSG00000123636.17), RAI14 (ENSG00000039560.13), FNIP1 (ENSG00000217128.11), MAP3K7 (ENSG00000135341.17), ERBIN (ENSG00000112851.14), SULF2 (ENSG00000196562.14), SORBS1 (ENSG00000095637.21), SRSF6 (ENSG00000124193.14), WASH3P (ENSG00000185596.16), OPA1 (ENSG00000198836.9), GOLGB1 (ENSG00000173230.15), APLP2 (ENSG00000084234.16), CPNE1 (ENSG00000214078.12), WIPF1 (ENSG00000115935.17), ATG9A (ENSG00000198925.11), NUBP2 (ENSG00000095906.16), ANO1 (ENSG00000131620.17), AURKA (ENSG00000087586.17), EPB41L3 (ENSG00000082397.17), KALRN(ENSG00000160145.15), ADAM15 (ENSG00000143537.13), KRAS (ENSG00000133703.11), SLC39A14 (ENSG00000104635.13), MYO9A (ENSG00000066933.15), TPM1 (ENSG00000140416.20), MYO6 (ENSG00000196586.13), KIAA1217 (ENSG00000120549.17), GIT2 (ENSG00000139436.20), MYL6 (ENSG00000092841.18), MYH11 (ENSG00000133392.17), NUMB (ENSG00000133961.20), TEAD1 (ENSG00000187079.16), SPAG9 (ENSG00000008294.20), FAT1 (ENSG00000083857.13), TNS1 (ENSG00000079308.17), ESYT2 (ENSG00000117868.15), SLMAP (ENSG00000163681.14), AKAP9 (ENSG00000127914.16), RUBCN (ENSG00000145016.15), ATP2B4 (ENSG00000058668.14), LRRFIP2 (ENSG00000093167.17), TBC1D23 (ENSG00000036054.12), EHBP1 (ENSG00000115504.14), SLK (ENSG00000065613.13), WDFY3 (ENSG00000163625.15), SMARCC2 (ENSG00000139613.11), KIF13A (ENSG00000137177.19), MPRIP (ENSG00000133030.20), LRRFIP1 (ENSG00000124831.18), NIN (ENSG00000100503.23), RPS24 (ENSG00000138326.19), ACTN1 (ENSG00000072110.13), CTNND1 (ENSG00000198561.13), CD44 (ENSG00000026508.18), APBB2 (ENSG00000163697.16), SEC31A(ENSG00000138674.16), SYTL2 (ENSG00000137501.17), MYOF (ENSG00000138119.16), NAV2 (ENSG00000166833.19), GAB1 (ENSG00000109458.8), PLEKHM2(ENSG00000116786.12), CLSTN1 (ENSG00000171603.16), GOLGA4(ENSG00000144674.16), PBX1 (ENSG00000185630.18) and FKBP14 (ENSG00000106080.10).

[0071] Another embodiment of the application relates to a method for predicting outcome in a colorectal cancer subject using PSI values, the method being based on the occurrence of at least one alternative splicing event, preferably at least one exon skipping event, the method comprising the steps of:

[0072] a) collecting a sample from a tumor of a subject suffering from a cancer, preferably the cancer is an epithelial cell-derived cancer;

[0073] b) determining PSI values;

[0074] c) converting the PSI values to determine an indication of disease outcome.

[0075] In step a), a sample is collected from a tumor of a subject suffering from a cancer.

[0076] Suitable samples comprise tumor tissue or cells from a subject suffering from an epithelial cell-derived cancer. The sample preferably comprises a biopsy sample, such as a tumor biopsy, primary tissue, metastatic tissue. In particular, the sample can be obtained by needle biopsy, image-guided biopsy, surgical (resection) biopsy, shave / punch biopsy, endoscopic biopsy, laparoscopic biopsy, and combinations thereof.

[0077] In step b) of the method according to the application, PSI values are determined.

[0078] The PSI value represents the percent inclusion of an exon, calculated / determined by dividing the number of reads from the upstream and downstream splice junctions of the alternatively spliced exon and / or from the alternatively spliced exon itself, referred to as inclusive reads, by the total number of reads from all splice junctions within the splice site, including both inclusive reads and skipping reads, which are reads from the splice junction connecting the exon upstream of the alternatively spliced exon to the exon downstream of the alternatively spliced exon. Inclusive reads and skipping reads are normalized using the effective length of the splice isoform, which is a mathematical conversion of the sequencing read length and exon length.

[0079] For example, PSI values can be estimated from RNA-Seq data using computational tools such as rMATS-turbo (https: / / github.com / Xinglab / rmats-turbo) or MISO (https: / / miso.readthedocs.io / en / fastmiso / ).

[0080] There are multiple ways to convert PSI values to determine disease outcomes.

[0081] One option is to convert the calculated PSI values to CMS probabilities through a mathematical conversion. Preferably, the calculated PSI values are converted to CMS probability estimates through a mathematical conversion that is the dot product of the PSI values with their corresponding weights derived from the reference dataset, specifically as follows:

[0082] PSI and Θ are the vector representations of the PSI values of the new sample and their associated weights related to consensus molecular subtypes, respectively, which are estimated on the reference dataset through a penalized multinomial logistic regression model.

[0083] .

[0084] z is a linear combination of the PSI values and their corresponding weights, and β0is an intercept derived from the reference dataset for each CMS.

[0085] .

[0086] z is converted to a probability for each CMS using a Logistic function, where e is a mathematical constant (approximately equal to 2.718):

[0087] .

[0088] Another possible method of converting the PSI values into a CMS classification involves measuring the distance between the PSI values of the sample and the median PSI of each CMS in the reference dataset. By ordering these distances, the CMS with the smallest distance is assigned to the sample. For n PSI values, the CMS can be assigned in the following way:

[0089]

[0090] .

[0091] In step c) of the method according to the application, the tumor is classified as CMS1, CMS2, CMS3 or CMS4 by converting the PSI values to determine an indication of disease outcome. Preferably, the PSI values are converted to determine an indication of disease outcome to decide whether the subject receives an anti-tumor therapy and / or disease progression monitoring.

[0092] The identification of CMS1 is as defined above.

[0093] The identification of CMS2 is as defined above.

[0094] The identification of CMS3 is as defined above.

[0095] The identification of CMS4 is as defined above.

[0096] Preferably, the alternative splicing event is based on at least one exon skipping event on at least one gene, in particular at least 50 genes, especially at least 116 genes, selected from the group consisting of ITGAE (ENSG00000083457.11), CCNDBP1 (ENSG00000166946.13), CPT1B (ENSG00000205560.12), CDC16 (ENSG00000130177.14), PTPN6 (ENSG00000111679.16), ACCS (ENSG00000110455.13), EXOSC9 (ENSG00000123737.12), ZNF611 (ENSG00000213020.9), MRRF (ENSG00000148187.17), NUP153 (ENSG00000124789.11), WARS (ENSG00000140105.17), D2HGDH (ENSG00000180902.17), LUC7L (ENSG00000007392.16), EPB41 (ENSG00000159023.20), DGUOK (ENSG00000114956.19), MDM4 (ENSG00000198625.12), PTP4A2 (ENSG00000184007.19), MKNK2 (ENSG00000099875.14), CCDC112 (ENSG00000164221.12), FRYL (ENSG00000075539.14), CEP78 (ENSG00000148019.13), FNBP1 (ENSG00000187239.16), ECT2 (ENSG00000114346.13), ANKRD26 (ENSG00000107890.16), ZMIZ2 (ENSG00000122515.14), C6orf48 (ENSG00000204387.12), USPL1 (ENSG00000132952.11), RBM39 (ENSG00000131051.22), MIS12 (ENSG00000167842.15), AFMID (ENSG00000183077.15), MACROD1 (ENSG00000133315.10), FN1 (ENSG00000115414.18), WBP1 (ENSG00000239779.6), XPO1 (ENSG00000082898.16), PTPN18 (ENSG00000072135.12), ARHGAP27(ENSG00000159314.11), C16orf13 (ENSG00000130731.15), FCGRT(ENSG00000104870.12), DOCK6 (ENSG00000130158.13), EXOC7 (ENSG00000182473.21),BPTF (ENSG00000171634.17), PXN (ENSG00000089159.16), EXOC1(ENSG00000090989.17), PLOD2 (ENSG00000152952.11), CD47 (ENSG00000196776.15),ARHGEF11 (ENSG00000132694.18), PBRM1 (ENSG00000163939.18), MAGI1(ENSG00000151276.23), MBNL1 (ENSG00000152601.17), TNC (ENSG00000041982.15),ENAH (ENSG00000154380.17), BAZ2B (ENSG00000123636.17), RAI14(ENSG00000039560.13), FNIP1 (ENSG00000217128.11), MAP3K7(ENSG00000135341.17), ERBIN (ENSG00000112851.14), SULF2 (ENSG00000196562.14),SORBS1 (ENSG00000095637.21), SRSF6 (ENSG00000124193.14), WASH3P(ENSG00000185596.16), OPA1 (ENSG00000198836.9), GOLGB1 (ENSG00000173230.15),APLP2 (ENSG00000084234.16), CPNE1 (ENSG00000214078.12), WIPF1(ENSG00000115935.17), ATG9A (ENSG00000198925.11), NUBP2 (ENSG00000095906.16),ANO1 (ENSG00000131620.17), AURKA (ENSG00000087586.17), EPB41L3(ENSG00000082397.17), KALRN (ENSG00000160145.15), ADAM15(ENSG00000143537.13), KRAS (ENSG00000133703.11), SLC39A14(ENSG00000104635.13), MYO9A (ENSG00000066933.15), TPM1 (ENSG00000140416.20),MYO6 (ENSG00000196586.13), KIAA1217 (ENSG00000120549.17), GIT2(ENSG00000139436.20), MYL6 (ENSG00000092841.18), MYH11 (ENSG00000133392.17),NUMB (ENSG00000133961.20), TEAD1 (ENSG00000187079.16), SPAG9(ENSG00000008294.20), FAT1 (ENSG00000083857.13), TNS1 (ENSG00000079308.17),ESYT2 (ENSG00000117868.15), SLMAP (ENSG00000163681.14), AKAP9(ENSG00000127914.16), RUBCN (ENSG00000145016.15), ATP2B4(ENSG00000058668.14), LRRFIP2 (ENSG00000093167.17), TBC1D23(ENSG00000036054.12), EHBP1 (ENSG00000115504.14), SLK (ENSG00000065613.13),WDFY3 (ENSG00000163625.15), SMARCC2 (ENSG00000139613.11), KIF13A(ENSG00000137177.19), MPRIP (ENSG00000133030.20), LRRFIP1(ENSG00000124831.18), NIN (ENSG00000100503.23), RPS24 (ENSG00000138326.19),ACTN1 (ENSG00000072110.13), CTNND1 (ENSG00000198561.13), CD44(ENSG00000026508.18), APBB2 (ENSG00000163697.16), SEC31A (ENSG00000138674.16), SYTL2 (ENSG00000137501.17), MYOF (ENSG00000138119.16), NAV2 (ENSG00000166833.19), GAB1 (ENSG00000109458.8), PLEKHM2 (ENSG00000116786.12), CLSTN1 (ENSG00000171603.16), GOLGA4 (ENSG00000144674.16), PBX1 (ENSG00000185630.18) and FKBP14 (ENSG00000106080.10).

[0097] In the method of the present application, advantageously, a rating scale can be established using the PSI value based on the occurrence of at least one alternative splicing event. Advantageously, this rating scale can be used to decide whether a subject is likely to develop an adverse outcome. In particular, the PSI value can be used to classify a tumor as CMS1, CMS2, CMS3 or CMS4. Furthermore, it can be decided whether the subject should be subjected to an anti-tumor therapy and / or monitoring of disease progression. This method allows for a decision to be made at a very early stage of the disease, while markers used in the current most advanced staging schemes (e.g. the presence of other tumor markers or metastases) are usually not yet detectable at this time.

[0098] Another embodiment of the present application relates to a kit for predicting the outcome of a subject suffering from colorectal cancer by means of a PSI value based on the occurrence of at least one alternative splicing event. The kit comprises means / tools for determining the PSI value.

[0099] Preferably, the alternative splicing is based on at least one exon skipping event. In particular, the at least one exon skipping event occurs in at least one, in particular at least 50, especially at least 116 genes selected from the group consisting of ITGAE (ENSG00000083457.11), CCNDBP1 (ENSG00000166946.13), CPT1B (ENSG00000205560.12), CDC16 (ENSG00000130177.14), PTPN6 (ENSG00000111679.16), ACCS (ENSG00000110455.13), EXOSC9 (ENSG00000123737.12), ZNF611 (ENSG00000213020.9), MRRF (ENSG00000148187.17), NUP153 (ENSG00000124789.11), WARS (ENSG00000140105.17), D2HGDH (ENSG00000180902.17), LUC7L (ENSG00000007392.16), EPB41 (ENSG00000159023.20), DGUOK (ENSG00000114956.19), MDM4 (ENSG00000198625.12), PTP4A2 (ENSG00000184007.19), MKNK2 (ENSG00000099875.14), CCDC112 (ENSG00000164221.12), FRYL (ENSG00000075539.14), CEP78 (ENSG00000148019.13), FNBP1 (ENSG00000187239.16), ECT2 (ENSG00000114346.13), ANKRD26 (ENSG00000107890.16), ZMIZ2 (ENSG00000122515.14), C6orf48 (ENSG00000204387.12), USPL1 (ENSG00000132952.11), RBM39 (ENSG00000131051.22), MIS12 (ENSG00000167842.15), AFMID (ENSG00000183077.15), MACROD1 (ENSG00000133315.10), FN1 (ENSG00000115414.18), WBP1 (ENSG00000239779.6), XPO1 (ENSG00000082898.16), PTPN18 (ENSG00000072135.12), ARHGAP27 (ENSG00000159314.11), C16orf13 (ENSG00000130731.15), FCGRT (ENSG00000104870.12), DOCK6 (ENSG00000130158.13), EXOC7 (ENSG00000182473.21), BPTF (ENSG00000171634.17), PXN (ENSG00000089159.16), EXOC1 (ENSG00000090989.17), PLOD2 (ENSG00000152952.11), CD47 (ENSG00000196776.15), ARHGEF11 (ENSG00000132694.18), PBRM1 (ENSG00000163939.18), MAGI1 (ENSG00000151276.23), MBNL1 (ENSG00000152601.17), TNC (ENSG00000041982.15), ENAH (ENSG00000154380.17), BAZ2B (ENSG00000123636.17), RAI14 (ENSG00000039560.13), FNIP1 (ENSG00000217128.11), MAP3K7 (ENSG00000135341.17), ERBIN (ENSG00000112851.14), SULF2 (ENSG00000196562.14), SORBS1 (ENSG00000095637.21), SRSF6 (ENSG00000124193.14), WASH3P (ENSG00000185596.16), OPA1 (ENSG00000198836.9), GOLGB1 (ENSG00000173230.15), APLP2 (ENSG00000084234.16), CPNE1 (ENSG00000214078.12), WIPF1 (ENSG00000115935.17), ATG9A (ENSG00000198925.11), NUBP2 (ENSG00000095906.16), ANO1 (ENSG00000131620.17), AURKA (ENSG00000087586.17), EPB41L3 (ENSG00000082397.17), KALRN(ENSG00000160145.15), ADAM15 (ENSG00000143537.13), KRAS (ENSG00000133703.11), SLC39A14 (ENSG00000104635.13), MYO9A (ENSG00000066933.15), TPM1 (ENSG00000140416.20), MYO6 (ENSG00000196586.13), KIAA1217 (ENSG00000120549.17), GIT2 (ENSG00000139436.20), MYL6 (ENSG00000092841.18), MYH11 (ENSG00000133392.17), NUMB (ENSG00000133961.20), TEAD1 (ENSG00000187079.16), SPAG9 (ENSG00000008294.20), FAT1 (ENSG00000083857.13), TNS1 (ENSG00000079308.17), ESYT2 (ENSG00000117868.15), SLMAP (ENSG00000163681.14), AKAP9 (ENSG00000127914.16), RUBCN (ENSG00000145016.15), ATP2B4 (ENSG00000058668.14), LRRFIP2 (ENSG00000093167.17), TBC1D23 (ENSG00000036054.12), EHBP1 (ENSG00000115504.14), SLK.

[0100] The identification of CMS1 is as defined above.

[0101] The identification of CMS2 is as defined above.

[0102] The identification of CMS3 is as defined above.

[0103] The identification of CMS4 is as defined above.

[0104] Another embodiment of the application is the use of a PSI value based on the occurrence of an alternative splicing event as an outcome marker for a colorectal cancer patient. Preferably, the alternative splicing event is at least one exon skipping event.

[0105] The identification of CMS1 is as defined above.

[0106] The identification of CMS2 is as defined above.

[0107] The identification of CMS3 is as defined above.

[0108] The identification of CMS4 is as defined above.

[0109] Preferably, the alternative splicing event is based on at least one exon skipping event on at least one gene, in particular at least 50 genes, especially at least 116 genes, selected from the group consisting of ITGAE (ENSG00000083457.11), CCNDBP1 (ENSG00000166946.13), CPT1B (ENSG00000205560.12), CDC16 (ENSG00000130177.14), PTPN6 (ENSG00000111679.16), ACCS (ENSG00000110455.13), EXOSC9 (ENSG00000123737.12), ZNF611 (ENSG00000213020.9), MRRF (ENSG00000148187.17), NUP153 (ENSG00000124789.11), WARS (ENSG00000140105.17), D2HGDH (ENSG00000180902.17), LUC7L (ENSG00000007392.16), EPB41 (ENSG00000159023.20), DGUOK (ENSG00000114956.19), MDM4 (ENSG00000198625.12), PTP4A2 (ENSG00000184007.19), MKNK2 (ENSG00000099875.14), CCDC112 (ENSG00000164221.12), FRYL (ENSG00000075539.14), CEP78 (ENSG00000148019.13), FNBP1 (ENSG00000187239.16), ECT2 (ENSG00000114346.13), ANKRD26 (ENSG00000107890.16), ZMIZ2 (ENSG00000122515.14), C6orf48 (ENSG00000204387.12), USPL1 (ENSG00000132952.11), RBM39 (ENSG00000131051.22), MIS12 (ENSG00000167842.15), AFMID (ENSG00000183077.15), MACROD1 (ENSG00000133315.10), FN1 (ENSG00000115414.18), WBP1 (ENSG00000239779.6), XPO1 (ENSG00000082898.16), PTPN18 (ENSG00000072135.12), ARHGAP27(ENSG00000159314.11), C16orf13 (ENSG00000130731.15), FCGRT(ENSG00000104870.12), DOCK6 (ENSG00000130158.13), EXOC7 (ENSG00000182473.21),BPTF (ENSG00000171634.17), PXN (ENSG00000089159.16), EXOC1(ENSG00000090989.17), PLOD2 (ENSG00000152952.11), CD47 (ENSG00000196776.15),ARHGEF11 (ENSG00000132694.18), PBRM1 (ENSG00000163939.18), MAGI1(ENSG00000151276.23), MBNL1 (ENSG00000152601.17), TNC (ENSG00000041982.15),ENAH (ENSG00000154380.17), BAZ2B (ENSG00000123636.17), RAI14(ENSG00000039560.13), FNIP1 (ENSG00000217128.11), MAP3K7(ENSG00000135341.17), ERBIN (ENSG00000112851.14), SULF2 (ENSG00000196562.14),SORBS1 (ENSG00000095637.21), SRSF6 (ENSG00000124193.14), WASH3P(ENSG00000185596.16), OPA1 (ENSG00000198836.9), GOLGB1 (ENSG00000173230.15),APLP2 (ENSG00000084234.16), CPNE1 (ENSG00000214078.12), WIPF1(ENSG00000115935.17), ATG9A (ENSG00000198925.11), NUBP2 (ENSG00000095906.16),ANO1 (ENSG00000131620.17), AURKA (ENSG00000087586.17), EPB41L3(ENSG00000082397.17), KALRN (ENSG00000160145.15), ADAM15(ENSG00000143537.13), KRAS (ENSG00000133703.11), SLC39A14(ENSG00000104635.13), MYO9A (ENSG00000066933.15), TPM1 (ENSG00000140416.20),MYO6 (ENSG00000196586.13), KIAA1217 (ENSG00000120549.17), GIT2(ENSG00000139436.20), MYL6 (ENSG00000092841.18), MYH11 (ENSG00000133392.17),NUMB (ENSG00000133961.20), TEAD1 (ENSG00000187079.16), SPAG9(ENSG00000008294.20), FAT1 (ENSG00000083857.13), TNS1 (ENSG00000079308.17),ESYT2 (ENSG00000117868.15), SLMAP (ENSG00000163681.14), AKAP9(ENSG00000127914.16), RUBCN (ENSG00000145016.15), ATP2B4(ENSG00000058668.14), LRRFIP2 (ENSG00000093167.17), TBC1D23(ENSG00000036054.12), EHBP1 (ENSG00000115504.14), SLK (ENSG00000065613.13),WDFY3 (ENSG00000163625.15), SMARCC2 (ENSG00000139613.11), KIF13A(ENSG00000137177.19), MPRIP (ENSG00000133030.20), LRRFIP1(ENSG00000124831.18), NIN (ENSG00000100503.23), RPS24 (ENSG00000138326.19),ACTN1 (ENSG00000072110.13), CTNND1 (ENSG00000198561.13), CD44(ENSG00000026508.18), APBB2 (ENSG00000163697.16), SEC31A (ENSG00000138674.16), SYTL2 (ENSG00000137501.17), MYOF (ENSG00000138119.16), NAV2 (ENSG00000166833.19), GAB1 (ENSG00000109458.8), PLEKHM2 (ENSG00000116786.12), CLSTN1 (ENSG00000171603.16), GOLGA4 (ENSG00000144674.16), PBX1 (ENSG00000185630.18) and FKBP14 (ENSG00000106080.10).

[0110] Another embodiment of the application is a method for treating a patient with colorectal cancer using PSI values based on alternative splicing events, the method comprising the steps of:

[0111] d) collecting a sample from a tumor of a patient having cancer, preferably cancer of epithelial cell origin;

[0112] e) determining the PSI values;

[0113] f) converting the PSI values to determine an indication of disease outcome.

[0114] Preferably, the alternative splicing event is at least one exon skipping event.

[0115] The identification of CMS1 is as defined above.

[0116] The identification of CMS2 is as defined above.

[0117] The identification of CMS3 is as defined above.

[0118] The identification of CMS4 is as defined above.

[0119] Preferably, the alternative splicing event is based on at least one exon skipping event on at least one gene, in particular at least 50 genes, especially at least 116 genes, selected from the group consisting of ITGAE (ENSG00000083457.11), CCNDBP1 (ENSG00000166946.13), CPT1B (ENSG00000205560.12), CDC16 (ENSG00000130177.14), PTPN6 (ENSG00000111679.16), ACCS (ENSG00000110455.13), EXOSC9 (ENSG00000123737.12), ZNF611 (ENSG00000213020.9), MRRF (ENSG00000148187.17), NUP153 (ENSG00000124789.11), WARS (ENSG00000140105.17), D2HGDH (ENSG00000180902.17), LUC7L (ENSG00000007392.16), EPB41 (ENSG00000159023.20), DGUOK (ENSG00000114956.19), MDM4 (ENSG00000198625.12), PTP4A2 (ENSG00000184007.19), MKNK2 (ENSG00000099875.14), CCDC112 (ENSG00000164221.12), FRYL (ENSG00000075539.14), CEP78 (ENSG00000148019.13), FNBP1 (ENSG00000187239.16), ECT2 (ENSG00000114346.13), ANKRD26 (ENSG00000107890.16), ZMIZ2 (ENSG00000122515.14), C6orf48 (ENSG00000204387.12), USPL1 (ENSG00000132952.11), RBM39 (ENSG00000131051.22), MIS12 (ENSG00000167842.15), AFMID (ENSG00000183077.15), MACROD1 (ENSG00000133315.10), FN1 (ENSG00000115414.18), WBP1 (ENSG00000239779.6), XPO1 (ENSG00000082898.16), PTPN18 (ENSG00000072135.12), ARHGAP27(ENSG00000159314.11), C16orf13 (ENSG00000130731.15), FCGRT(ENSG00000104870.12), DOCK6 (ENSG00000130158.13), EXOC7 (ENSG00000182473.21),BPTF (ENSG00000171634.17), PXN (ENSG00000089159.16), EXOC1(ENSG00000090989.17), PLOD2 (ENSG00000152952.11), CD47 (ENSG00000196776.15),ARHGEF11 (ENSG00000132694.18), PBRM1 (ENSG00000163939.18), MAGI1(ENSG00000151276.23), MBNL1 (ENSG00000152601.17), TNC (ENSG00000041982.15),ENAH (ENSG00000154380.17), BAZ2B (ENSG00000123636.17), RAI14(ENSG00000039560.13), FNIP1 (ENSG00000217128.11), MAP3K7(ENSG00000135341.17), ERBIN (ENSG00000112851.14), SULF2 (ENSG00000196562.14),SORBS1 (ENSG00000095637.21), SRSF6 (ENSG00000124193.14), WASH3P(ENSG00000185596.16), OPA1 (ENSG00000198836.9), GOLGB1 (ENSG00000173230.15),APLP2 (ENSG00000084234.16), CPNE1 (ENSG00000214078.12), WIPF1(ENSG00000115935.17), ATG9A (ENSG00000198925.11), NUBP2 (ENSG00000095906.16),ANO1 (ENSG00000131620.17), AURKA (ENSG00000087586.17), EPB41L3(ENSG00000082397.17), KALRN (ENSG00000160145.15), ADAM15(ENSG00000143537.13), KRAS (ENSG00000133703.11), SLC39A14(ENSG00000104635.13), MYO9A (ENSG00000066933.15), TPM1 (ENSG00000140416.20),MYO6 (ENSG00000196586.13), KIAA1217 (ENSG00000120549.17), GIT2(ENSG00000139436.20), MYL6 (ENSG00000092841.18), MYH11 (ENSG00000133392.17),NUMB (ENSG00000133961.20), TEAD1 (ENSG00000187079.16), SPAG9(ENSG00000008294.20), FAT1 (ENSG00000083857.13), TNS1 (ENSG00000079308.17),ESYT2 (ENSG00000117868.15), SLMAP (ENSG00000163681.14), AKAP9(ENSG00000127914.16), RUBCN (ENSG00000145016.15), ATP2B4(ENSG00000058668.14), LRRFIP2 (ENSG00000093167.17), TBC1D23(ENSG00000036054.12), EHBP1 (ENSG00000115504.14), SLK (ENSG00000065613.13),WDFY3 (ENSG00000163625.15), SMARCC2 (ENSG00000139613.11), KIF13A(ENSG00000137177.19), MPRIP (ENSG00000133030.20), LRRFIP1(ENSG00000124831.18), NIN (ENSG00000100503.23), RPS24 (ENSG00000138326.19),ACTN1 (ENSG00000072110.13), CTNND1 (ENSG00000198561.13), CD44(ENSG00000026508.18), APBB2 (ENSG00000163697.16), SEC31A (ENSG00000138674.16), SYTL2 (ENSG00000137501.17), MYOF (ENSG00000138119.16), NAV2 (ENSG00000166833.19), GAB1 (ENSG00000109458.8), PLEKHM2 (ENSG00000116786.12), CLSTN1 (ENSG00000171603.16), GOLGA4 (ENSG00000144674.16), PBX1 (ENSG00000185630.18) and FKBP14 (ENSG00000106080.10).

[0120] Advantageously, in the method of the present application, a rating scale can be established by using the PSI value based on the occurrence of at least one alternative splicing event. Advantageously, this rating scale can be used to decide whether a subject is likely to develop an adverse outcome. In particular, the PSI value can be used to classify a tumor as CMS1, CMS2, CMS3 or CMS4. Furthermore, it can be decided whether an anti-tumor treatment and / or monitoring of disease progression should be performed on the subject. This method allows for a decision to be made at a very early stage of the disease, when markers used in the current most advanced staging schemes (e.g. the presence of other tumor markers or metastases) are usually not yet detectable.

[0121] Exemplary embodiments

[0122] 1. A colorectal cancer subtype identifier that classifies a tumor by a PSI value based on the occurrence of at least one alternative splicing event.

[0123] 2. The colorectal cancer subtype identifier according to embodiment 1, wherein the alternative splicing event is at least one exon skipping event.

[0124] 3. The colorectal cancer subtype identifier according to any of the preceding embodiments, for classifying a tumor as CMS1, CMS2, CMS3 or CMS4.

[0125] 4. The colorectal cancer subtype identifier according to any one of embodiments 1 to 3, wherein for identifying CMS1 there is at least one exon skipping event, wherein the exon skipping event is selected from: in exon of ITGAE, genomic coordinates chr17:3723287-3723383; in exon of CCNDBP1, genomic coordinates chr15:43194080-43194137; in exon of CPT1B, genomic coordinates chr22:50573807-50573921; in exon of CDC16, genomic coordinates chr13:114236644-114236699; in exon of PTPN6, genomic coordinates chr12:6951458-6951520; in exon of PTPN6, genomic coordinates chr12:6951463-6951520; in exon of ACCS, genomic coordinates chr11:44073446-44073517; in exon of EXOSC9, genomic coordinates chr4:121816143-121816194; in exon of EXOSC9, genomic coordinates chr4:121816368-121816447; in exon of ZNF611, genomic coordinates chr19:52707468-52707542; in exon of MRRF, genomic coordinates chr9:122285779-122285946; in exon of NUP153, genomic coordinates chr6:17668974-17669028; in exon of WARS, genomic coordinates chr14:100375282-100375350; in exon of WARS, genomic coordinates chr14:100375282-100375403; in exon of WARS, genomic coordinates chr14:100375282-100375406; in exon of D2HGDH, genomic coordinates chr2:241748864-241749929; in exon of LUC7L, genomic coordinates chr16:228332-228402; in exon of EPB41, genomic coordinates chr1:29058588-29058645; in exon of DGUOK, genomic coordinates chr2:73938909-73939022; in exon of MDM4, genomic coordinates chr1:204537429-204537497; in exon of MDM4, genomic coordinates chr1:204537458-204537497; in exon of PTP4A2, genomic coordinates chr1:31915894-31915987;MKNK2 in an exon with genomic coordinates of chr19:2039630-2039856; CCDC112 in an exon with genomic coordinates of chr5: 115269702-115269798; FRYL in an exon with genomic coordinates of chr4:48593929-48594016; CEP78 in an exon with genomic coordinates of chr9:78265858-78265906; FNBP1 in an exon with genomic coordinates of chr9: 129923843-129923996; FNBP1 in an exon with genomic coordinates of chr9: 129923843-129924026; ECT2 in an exon with genomic coordinates of chr3: 172752149-172752472; ECT2 in an exon with genomic coordinates of chr3: 172755482-172755575; ANKRD26 in an exon with genomic coordinates of chr10: 27044156-27044190; ZMIZ2 in an exon with genomic coordinates of chr7: 44760150-44760228; C6orf48 in an exon with genomic coordinates of chr6: 31836423-31836517; or USPL1 in an exon with genomic coordinates of chr13: 30621072-30621239.

[0126] 5. The colorectal cancer subtype identifier according to any one of embodiments 1 to 3, wherein for identifying CMS2 there is at least one exon skipping event, wherein the exon skipping event is selected from: in exon of ZMIZ2, genomic coordinates chr7:44760150-44760228; in exon of C6orf48, genomic coordinates chr6:31836423-31836517; in exon of USPL1, genomic coordinates chr13:30621072-30621239; in exon of RBM39, genomic coordinates chr20:35740524-35740597; in exon of MIS12, genomic coordinates chr17:5488195-5488589; in exon of AFMID, genomic coordinates chr17:78204655-78204741; in exon of MACROD1, genomic coordinates chrll:63998837-63998872; in exon of FN1, genomic coordinates chr2:215380810-215381080; in exon of WBP1, genomic coordinates chr2:74459477-74459562; in exon of XPO1, genomic coordinates chr2:61525269-61525333; in exon of PTPN18, genomic coordinates chr2:130359232-130359309; in exon of ARHGAP27, genomic coordinates chr17:45404268-45404334; in exon of C16orf13, genomic coordinates chr16:635280-635340; in exon of C16orf13, genomic coordinates chr16:635517-635774; in exon of C16orf13, genomic coordinates chr16:635611-635774.

[0127] 6. The colorectal cancer subtype identifier according to any one of embodiments 1 to 3, wherein for identifying CMS3 there is at least one exon skipping event present, wherein the exon skipping event is selected from: in exon with genomic coordinates chr 16:635280-635340 of C16orf13; in exon with genomic coordinates chr 16:635517-635774 of C16orf13; in exon with genomic coordinates chr 16:635611-635774 of C16orf13; in exon with genomic coordinates chr 20:56388686-56388784 of AURKA; in exon with genomic coordinates chr 18:5394676-5394793 of EPB41L3; in exon with genomic coordinates chr 3:124637207-124637303 of KALRN; in exon with genomic coordinates chr 1:155061903-155061975 of ADAM15; in exon with genomic coordinates chr 12:25215436-25215560 of KRAS; in exon with genomic coordinates chr 8:22412036-22412206 of SLC39A14; in exon with genomic coordinates chr 15:71951776-71951896 of MYO9A; in exon with genomic coordinates chr 15:63044026-63044152 of TPM1; in exon with genomic coordinates chr 15:63061197-63061273 of TPM1; in exon with genomic coordinates chr 15:63061712-63061788 of TPM1; in exon with genomic coordinates chr 6:75894813-75894840 of MYO6; in exon with genomic coordinates chr 6:75898372-75898411 of MYO6; in exon with genomic coordinates chr 10:24494499-24494604 of KIAA1217; in exon with genomic coordinates chr 10:24542692-24542770 of KIAA1217; in exon with genomic coordinates chr 10:24542882-24544481 of KIAA1217; in exon with genomic coordinates chr 12:109945259-109945349 of GIT2; in exon with genomic coordinates chr 12:56160625-56160670 of MYL6; in exon with genomic coordinates chr 11:57789036-57789155 of CTNND1; in exon with genomic coordinates chr 11:57791384-57791673 of CTNND1.In an exon of CTNND1, genomic coordinates chrll:57791491-57791673; CD44, genomic coordinates chrll:35208104-35208206; CD44, genomic coordinates chrll:35211245-35211449; APBB2, genomic coordinates chr4:40935076-40935139; SEC31A, genomic coordinates chr4:82830936-82830975; SEC31A, genomic coordinates chr4:82830936-82830975; SEC31A, genomic coordinates chr4:82842139-82842481; SEC31A, genomic coordinates chr4:82842184-82842481; SYTL2, genomic coordinates chrll:85717482-85717530; MYOF, genomic coordinates chr10:93392916-93392955; NAV2, genomic coordinates chrll:20051288-20051333; GAB1, genomic coordinates chr4:143434087-143434168; PLEKHM2, genomic coordinates chr 1 : 15721328-15721388; CLSTN1, genomic coordinates chr 1 : 9737497-9737554; CLSTN1, genomic coordinates chr 1 : 9756480-9756510; GOLGA4, genomic coordinates chr3:37361242-37361305; PBX1, genomic coordinates chr 1 : 164820071-164820184; FKBP14, genomic coordinates chr7:30020212-30020304; or XPO1, genomic coordinates chr2:61525269-61525333.

[0128] 7. The colorectal cancer subtype identifier according to any one of embodiments 1 to 3, wherein for identifying CMS4 there is at least one exon skipping event, wherein the exon skipping event is selected from: in exon with genomic coordinates chr15:71951776-71951896 of MYO9A; in exon with genomic coordinates chr15:63044026-63044152 of TPM1; in exon with genomic coordinates chr15:63061197-63061273 of TPM1; in exon with genomic coordinates chr15:63061712-63061788 of TPM1; in exon with genomic coordinates chr6:75894813-75894840 of MYO6; in exon with genomic coordinates chr6:75898372-75898411 of MYO6; in exon with genomic coordinates chr10:24494499-24494604 of KIAA1217; in exon with genomic coordinates chr10:24542692-24542770 of KIAA1217; in exon with genomic coordinates chr10:24542882-24544481 of KIAA1217; in exon with genomic coordinates chr12:109945259-109945349 of GIT2; in exon with genomic coordinates chr12:56160625-56160670 of MYL6; in exon with genomic coordinates chr17:67875555-67875744 of BPTF; in exon with genomic coordinates chr16:15708802-15708841 of MYH11; in exon with genomic coordinates chr14:73279280-73279424 of NUMB; in exon with genomic coordinates chr11:12878888-12878900 of TEAD1; in exon with genomic coordinates chr17:50975862-50975901 of SPAG9; in exon with genomic coordinates chr4:186590367-186590403 of FAT1; in exon with genomic coordinates chr2:217830366-217830390 of TNS1; in exon with genomic coordinates chr7:158752780-158752843 of ESYT2; in exon with genomic coordinates chr3:57925844-57925934 of SLMAP; in exon with genomic coordinates chr7:91992157-91992211 of AKAP9; in exon with genomic coordinates chr3:197691073-197691148 of RUBCN.ATP2B4 in exons with genomic coordinates chr1 :203733222-203733400; LRRFIP2 in exons with genomic coordinates chr3:37091466-37091538; TBC1 D23 in exons with genomic coordinates chr3: 100311832-100311877; EHBP1 in exons with genomic coordinates chr2:62987930-62988038; SLK in exons with genomic coordinates chr10: 104010815-104010908; WDFY3 in exons with genomic coordinates chr4:84726860-84726911 ; SMARCC2 in exons with genomic coordinates chr12:56164302-56164368; KIF13A in exons with genomic coordinates chr6:17771113-17771218; MPRIP in exons with genomic coordinates chr17: 17180606-17180669; LRRFIP1 in exons with genomic coordinates chr2:237769625-237769818; NIN in exons with genomic coordinates chr14:50756491-50758630; RPS24 in exons with genomic coordinates chr10:78040203-78040225; ACTN1 in exons with genomic coordinates chr14:68878988-68879069; CTNND1 in exons with genomic coordinates chr11 :57789036-57789155; CTNND1 in exons with genomic coordinates chr11 :57791384-57791673; CTNND1 in exons with genomic coordinates chr11 :57791491-57791673; CD44 in exons with genomic coordinates chr11 :35208104-35208206; CD44 in exons with genomic coordinates chr11 :35211245-35211449; APBB2 in exons with genomic coordinates chr4:40935076-40935139; SEC31A in exons with genomic coordinates chr4:82830936-82830975; SEC31A in exons with genomic coordinates chr4:82830936-82830975; SEC31A in exons with genomic coordinates chr4:82842139-82842481 ; SEC31A in exons with genomic coordinates chr4:82842184-82842481 ; SYTL2 in exons with genomic coordinates chr11 :85717482-85717530;MYOF, in an exon with genomic coordinates chr10:93392916-93392955; NAV2, in an exon with genomic coordinates chrll:20051288-20051333; GAB1, in an exon with genomic coordinates chr4:143434087-143434168; PLEKHM2, in an exon with genomic coordinates chrl:15721328-15721388; CLSTN1, in an exon with genomic coordinates chrl:9737497-9737554; CLSTN1, in an exon with genomic coordinates chrl:9756480-9756510; GOLGA4, in an exon with genomic coordinates chr3:37361242-37361305; PBX1, in an exon with genomic coordinates chrl: 164820071-164820184; FKBP14, in an exon with genomic coordinates chr7:30020212-30020304.

[0129] 8. The colorectal cancer subtype identifier according to any of the preceding embodiments, wherein for distinguishing CMS2 and CMS3 from CMS1 and CMS4 there is at least one exon skipping event, wherein the exon skipping event is selected from the group consisting of: in exon with genomic coordinates chr19:49521694-49521813 of FCGRT; in exon with genomic coordinates chr19:11229297-11229390 of DOCK6; in exon with genomic coordinates chr17:76090328-76090397 of EXOC7; in exon with genomic coordinates chr17:67875555-67875744 of BPTF; in exon with genomic coordinates chr12:120224642-120224727 of PXN; in exon with genomic coordinates chr4:55888887-55888932 of EXOC1 ; in exon with genomic coordinates chr3:146077861-146077924 of PLOD2; in exon with genomic coordinates chr3:108049618-108049651 of CD47; in exon with genomic coordinates chr3:108050577-108050602 of CD47; in exon with genomic coordinates chr1 :156938417-156938513 of ARHGEF11 ; in exon with genomic coordinates chr3:52558248-52558413 of PBRM1 ; in exon with genomic coordinates chr3:65448021-65448057 of MAGI1 ; in exon with genomic coordinates chr3:152446703-152446757 of MBNL1 ; in exon with genomic coordinates chr9:115064646-115064919 of TNC; in exon with genomic coordinates chr1 :225504990-225505053 of ENAH; in exon with genomic coordinates chr2:159397073-159397100 of BAZ2B; in exon with genomic coordinates chr5:34813573-34813660 of RAI14; in exon with genomic coordinates chr5:131710577-131710661 of FNIP1 ; in exon with genomic coordinates chr6:90544551-90544632 of MAP3K7; in exon with genomic coordinates chr5:66068876-66069020 of ERBIN; in exon with genomic coordinates chr20:47659398-47659452 of SULF2; in exon with genomic coordinates chr10:95414493-95414655 of SORBS1 ;SORBS1, in an exon with genomic coordinates chr10:95414493-95414862.

[0130] 9. The colorectal cancer subtype identifier according to any of the preceding embodiments, wherein for differentiating CMS2 and CMS4 from CMS1 and CMS3, there is at least one exon skipping event, wherein the exon skipping event is selected from the group consisting of: SRSF6, in an exon with genomic coordinates chr20:43459152-43459420; WASH3P, in an exon with genomic coordinates chr15:101972595-101972694; OPA1, in an exon with genomic coordinates chr3:193626091-193626202; GOLGB1, in an exon with genomic coordinates chr3:121719645-121719753; GOLGB1, in an exon with genomic coordinates chr3:121719645-121719768; APLP2, in an exon with genomic coordinates chr11:130137255-130137291; CPNE1, in an exon with genomic coordinates chr20:35658929-35659014; WIPF1, in an exon with genomic coordinates chr2:174597600-174597858; ATG9A, in an exon with genomic coordinates chr2:219228433-219228482; NUBP2, in an exon with genomic coordinates chr16:1786737-1786955; ANO1, in an exon with genomic coordinates chr11:70111125-70111191.

[0131] 10. The colorectal cancer subtype identifier according to any of the preceding embodiments, wherein the alternative splicing event is based on at least one exon skipping event on at least one gene selected from the group consisting of ITGAE, CCNDBP1, CPT1B, CDC16, PTPN6, ACCS, EXOSC9, ZNF611, MRRF, NUP153, WARS, D2HGDH, LUC7L, EPB41, DGUOK, MDM4, PTP4A2, MKNK2, CCDC112, FRYL, CEP78, FNBP1, ECT2, ANKRD26, ZMIZ2, C6orf48, USPL1, RBM39, MIS12, AFMID, MACROD1, FN1, WBP1, XPO1, PTPN18, ARHGAP27, C16orf13, FCGRT, DOCK6, EXOC7, BPTF, PXN, EXOC1, PLOD2, CD47, ARHGEF11, PBRM1, MAGI1, MBNL1, TNC, ENAH, BAZ2B, RAI14, FNIP1, MAP3K7, ERBIN, SULF2, SORBS1, SRSF6, WASH3P, OPA1, GOLGB1, APLP2, CPNE1, WIPF1, ATG9A, NUBP2, ANO1, AURKA, EPB41L3, KALRN, ADAM15, KRAS, SLC39A14, MYO9A, TPM1, MYO6, KIAA1217, GIT2, MYL6, MYH11, NUMB, TEAD1, SPAG9, FAT1, TNS1, ESYT2, SLMAP, AKAP9, RUBCN, ATP2B4, LRRFIP2, TBC1D23, EHBP1, SLK, WDFY3, SMARCC2, KIF13A, MPRIP, LRRFIP1, NIN, RPS24, ACTN1, CTNND1, CD44, APBB2, SEC31A, SYTL2, MYOF, NAV2, GAB1, PLEKHM2, CLSTN1, GOLGA4, PBX1, and FKBP14.

[0132] 11. A method for predicting outcome in a subject having colorectal cancer, the method being based on the occurrence of at least one alternative splicing event using a PSI value, wherein the method comprises the steps of:

[0133] a) collecting a sample from a tumor of a subject having cancer;

[0134] b) determining a PSI value;

[0135] c) converting the PSI value to determine a disease outcome indication.

[0136] 12. The method according to embodiment 11, wherein the alternative splicing event is at least one exon skipping event.

[0137] 13. The method according to embodiment 12, wherein the at least one exon skipping event is at least one exon skipping event on at least one gene selected from the group consisting of ITGAE, CCNDBP1, CPT1B, CDC16, PTPN6, ACCS, EXOSC9, ZNF611, MRRF, NUP153, WARS, D2HGDH, LUC7L, EPB41, DGUOK, MDM4, PTP4A2, MKNK2, CCDC112, FRYL, CEP78, FNBP1, ECT2, ANKRD26, ZMIZ2, C6orf48, USPL1, RBM39, MIS12, AFMID, MACROD1, FN1, WBP1, XPO1, PTPN18, ARHGAP27, C16orf13, FCGRT, DOCK6, EXOC7, BPTF, PXN, EXOC1, PLOD2, CD47, ARHGEF11, PBRM1, MAGI1, MBNL1, TNC, ENAH, BAZ2B, RAI14, FNIP1, MAP3K7, ERBIN, SULF2, SORBS1, SRSF6, WASH3P, OPA1, GOLGB1, APLP2, CPNE1, WIPF1, ATG9A, NUBP2, ANO1, AURKA, EPB41L3, KALRN, ADAM15, KRAS, SLC39A14, MYO9A, TPM1, MYO6, KIAA1217, GIT2, MYL6, MYH11, NUMB, TEAD1, SPAG9, FAT1, TNS1, ESYT2, SLMAP, AKAP9, RUBCN, ATP2B4, LRRFIP2, TBC1D23, EHBP1, SLK, WDFY3, SMARCC2, KIF13A, MPRIP, LRRFIP1, NIN, RPS24, ACTN1, CTNND1, CD44, APBB2, SEC31A, SYTL2, MYOF, NAV2, GAB1, PLEKHM2, CLSTN1, GOLGA4, PBX1, and FKBP14.

[0138] 14. The method according to embodiment 11, wherein the tumor is classified as CMS1, CMS2, CMS3, or CMS4 by converting the PSI values to determine disease outcome indication.

[0139] 15. The method according to embodiment 11, wherein by converting the PSI values to determine an indication of disease outcome, it is decided whether to subject the subject to anti-tumor therapy and / or monitoring of disease progression.

[0140] 16. A kit for predicting outcome of a subject suffering from colorectal cancer, wherein the prediction is based on the occurrence of at least one alternative splicing event, preferably at least one exon skipping event, on at least one gene selected from the group consisting of ITGAE, CCNDBP1, CPT1B, CDC16, PTPN6, ACCS, EXOSC9, ZNF611, MRRF, NUP153, WARS, D2HGDH, LUC7L, EPB41, DGUOK, MDM4, PTP4A2, MKNK2, CCDC112, FRYL, CEP78, FNBP1, ECT2, ANKRD26, ZMIZ2, C6orf48, USPL1, RBM39, MIS12, AFMID, MACROD1, FN1, WBP1, XPO1, PTPN18, ARHGAP27, C16orf13, FCGRT, DOCK6, EXOC7, BPTF, PXN, EXOC1, PLOD2, CD47, ARHGEF11, PBRM1, MAGI1, MBNL1, TNC, ENAH, BAZ2B, RAI14, FNIP1, MAP3K7, ERBIN, SULF2, SORBS1, SRSF6, WASH3P, OPA1, GOLGB1, APLP2, CPNE1, WIPF1, ATG9A, NUBP2, ANO1, AURKA, EPB41L3, KALRN, ADAM15, KRAS, SLC39A14, MYO9A, TPM1, MYO6, KIAA1217, GIT2, MYL6, MYH11, NUMB, TEAD1, SPAG9, FAT1, TNS1, ESYT2, SLMAP, AKAP9, RUBCN, ATP2B4, LRRFIP2, TBC1D23, EHBP1, SLK, WDFY3, SMARCC2, KIF13A, MPRIP, LRRFIP1, NIN, RPS24, ACTN1, CTNND1, CD44, APBB2, SEC31A, SYTL2, MYOF, NAV2, GAB1, PLEKHM2, CLSTN1, GOLGA4, PBX1 and FKBP14, wherein the kit comprises means / tools for determining the PSI values.

[0141] 17. Use of at least one PSI value based on alternative splicing occurrence as a marker of outcome of a subject suffering from colorectal cancer.

[0142] 18. A method of treating a subject having colorectal cancer, the method using a PSI value based on alternative splicing occurrence, comprising the steps of:

[0143] d) collecting a sample from a tumor of a subject having cancer;

[0144] e) determining at least one PSI value;

[0145] f) transforming the PSI value to determine a disease outcome indication.

[0146] 19. The method according to embodiment 18, wherein the tumor is classified as CMS1, CMS2, CMS3 or CMS4 by transforming the PSI value to determine a disease outcome indication.

[0147] 20. The method according to embodiment 11 or 18, wherein the subject is a human.

[0148] The application will be further illustrated in the following examples, but the scope of the application is not to be limited to the specific examples described. The application includes all combinations of the features described and in particular the preferred features, as long as these features are not mutually exclusive. BRIEF DESCRIPTION OF DRAWINGS

[0149] Using data from colorectal cancer patients, specifically detectable alternative splicing events (AS) present in 675 human colorectal cancers (data from Indivumed Inc / GmbH, Indivumed cohort), the CMS identifier was constructed and validated. Using two different expression profile-based classifiers, CMS Caller (Eide et al., Sci Rep. 2017; 7(1): 16618) and CMS Classifier (Guinney et al., Nat Med. 2015; 21(11): 1350-6), CMS labels were generated for the entire cohort. Using unsupervised clustering, the strength of association between different types of AS and CMS was measured. To construct the classifiers, ground-truth for CMS labels was derived from expression data quantified at the gene level. Feature selection was performed by bootstrapping and L1 penalty estimation. The resulting feature space was used to train multiple logistic regression models, where training used the Indivumed cohort containing 300 CRCs. The performance of the models was evaluated on unseen CRCs from two independent sources. A colorectal cancer subtype identifier (CRCi) was developed based on 29 exon skipping events that accurately classified unseen tumors (Indivumed AUC = 0.95; TCGA AUC = 0.93) and outperformed expression-based CMS classifiers.

[0150] Figure 1 Exon skipping events strongly associated with consensus molecular subtypes (CMS) of colorectal cancer.

[0151] (A) Distribution of CMS labels identified by two independent expression-based methods in the Indivumed colorectal cancer cohort (n=429).

[0152] (B) Strength of association between clusters obtained after NMF consensus clustering and CMS based on percent spliced in (PSI) values from alternative splicing events. Strength of association was determined by Cramer's V (a measure of effect size for the Chi-Squared test of independence).

[0153] (C) Distribution of samples on NMF clusters ordered by their relationship to CMS (n=429).

[0154] Figure 2 Performance of the colorectal cancer subtype identifier (CRCi).

[0155] Receiver operating characteristic curves showing the performance of CRCi on (A) a randomly selected test cohort (Indivumed, n = 129) and (B) a validation cohort (TCGA, n = 99).

[0156] Figure 3: CRCi reflects known molecular signatures better than expression-based methods in the subtype classification of discordant samples.

[0157] (A) Expression-based nearest neighbor CMS classification of discordant tumor samples using two expression-based classifiers.

[0158] (B) Heatmap of CMS-associated molecular signatures showing the -loglO transformed P-values of the competitive gene set test in the consensus cohort. Black indicates downregulation, white indicates upregulation.

[0159] (C) Heatmap of CMS-associated molecular signatures showing the -loglO transformed P-values from the competitive gene set test comparing a given subtype in the consensus or discordant cohort to all other consensus subtypes.

[0160] (D) Cosine similarity calculated based on transformed P-values from the competitive gene set test comparing a given subtype in the consensus and discordant cohort to all other subtypes in the consensus cohort.

[0161] Figure 4 RT-PCR validation of key exon skipping events associated with CRCi. Scatter plot showing the strength of the correlation between the PSI values estimated by RT-PCR (reverse transcription polymerase chain reaction) and RNA-Seq in tumor samples (n = 16) from colorectal cancer patients, as measured by the Pearson correlation coefficient.

[0162] Figure 5: (A) RT-PCR detection of key exon skipping events associated with CRCi.

[0163] RNA samples extracted from 16 colorectal cancer samples were used to detect 6 key exon skipping events. Samples 1-4, 5-8, 9-12, and 13-16 were classified as CMS1, CMS2, CMS3, and CMS4, respectively. Boxes indicate the number of exons included in the amplicon, with skipped exons indicated by white boxes and constitutive exons indicated by black boxes. To detect TPM1 alternative splicing, which is characterized by the inclusion of mutually exclusive exons involving two equal-length exons, two different sets of primers were designed to assess the expression of these variants. OAT mRNA expression was used as a standard for normalization in separate PCR reactions (OAT amplicon indicated by dashed boxes).

[0164] (B) OAT mRNA expression as a normalizing standard in independent PCR reactions for detecting TPM1 variants. Boxplots show the expression of OAT in tumors grouped by CMS (n=429).

[0165] Figure 6 : There is a correlation between the PSI values of CRCi between human colorectal cancer samples and human colorectal cancer cell lines.

[0166] (A) Scatterplot showing the correlation between the median PSI values estimated for 29 exon skipping events of the CRCi model in colorectal tumors (n=429) and colorectal cancer cell lines (n=46). The strength of the correlation is measured by the Pearson correlation coefficient.

[0167] (B) RT-PCR for 6 key exon skipping events using RNA extracted from colorectal cancer cell lines. Lovo cell line was classified as CMS1, NCIH-508 cell line as CMS2, HT-29 cell line as CMS3, NCIH-747 and HCT116 cell lines as CMS4.

Claims

1. A colorectal cancer subtype identifier that classifies a tumor by a PSI value based on the occurrence of at least one alternative splicing event.

2. The colorectal cancer subtype identifier according to claim 1, wherein the alternative splicing event is at least one exon skipping event.

3. The colorectal cancer subtype identifier according to any one of the preceding claims, for classifying a tumor as CMS1, CMS2, CMS3 or CMS4.

4. The colorectal cancer subtype identifier according to any one of claims 1 to 3, wherein for identifying CMS1 there is at least one exon skipping event, wherein the exon skipping event is selected from: in exon of ITGAE, genomic coordinates chr17:3723287-3723383; in exon of CCNDBP1, genomic coordinates chr15:43194080-43194137; in exon of CPT1B, genomic coordinates chr22:50573807-50573921; in exon of CDC16, genomic coordinates chr13:114236644-114236699; in exon of PTPN6, genomic coordinates chr12:6951458-6951520; in exon of PTPN6, genomic coordinates chr12:6951463-6951520; in exon of ACCS, genomic coordinates chr11:44073446-44073517; in exon of EXOSC9, genomic coordinates chr4:121816143-121816194; in exon of EXOSC9, genomic coordinates chr4:121816368-121816447; in exon of ZNF611, genomic coordinates chr19:52707468-52707542; in exon of MRRF, genomic coordinates chr9:122285779-122285946; in exon of NUP153, genomic coordinates chr6:17668974-17669028; in exon of WARS, genomic coordinates chr14:100375282-100375350; in exon of WARS, genomic coordinates chr14:100375282-100375403; in exon of WARS, genomic coordinates chr14:100375282-100375406; in exon of D2HGDH, genomic coordinates chr2:241748864-241749929; in exon of LUC7L, genomic coordinates chr16:228332-228402; in exon of EPB41, genomic coordinates chr1:29058588-29058645; in exon of DGUOK, genomic coordinates chr2:73938909-73939022; in exon of MDM4, genomic coordinates chr1:204537429-204537497; in exon of MDM4, genomic coordinates chr1:204537458-204537497; in exon of PTP4A2, genomic coordinates chr1:31915894-31915987.MKNK2 in an exon with genomic coordinates of chr19:2039630-2039856; CCDC112 in an exon with genomic coordinates of chr5:115269702-115269798; FRYL in an exon with genomic coordinates of chr4:48593929-48594016; CEP78 in an exon with genomic coordinates of chr9:78265858-78265906; FNBP1 in an exon with genomic coordinates of chr9:129923843-129923996; FNBP1 in an exon with genomic coordinates of chr9:129923843-129924026; ECT2 in an exon with genomic coordinates of chr3:172752149-172752472; ECT2 in an exon with genomic coordinates of chr3:172755482-172755575; ANKRD26 in an exon with genomic coordinates of chr10:27044156-27044190; ZMIZ2 in an exon with genomic coordinates of chr7:44760150-44760228; C6orf48 in an exon with genomic coordinates of chr6:31836423-31836517; or USPL1 in an exon with genomic coordinates of chr13:30621072-30621239.

5. The colorectal cancer subtype identifier according to any one of claims 1 to 3, wherein for identifying CMS2 there is at least one exon skipping event, wherein the exon skipping event is selected from the group consisting of: ZMIZ2, in an exon with genomic coordinates chr7:44760150-44760228; C6orf48, in an exon with genomic coordinates chr6:31836423-31836517; USPL1, in an exon with genomic coordinates chr13:30621072-30621239; RBM39, in an exon with genomic coordinates chr20:35740524-35740597; MIS12, in an exon with genomic coordinates chr17:5488195-5488589; AFMID, in an exon with genomic coordinates chr17:78204655-78204741; MACROD1, in an exon with genomic coordinates chrll:63998837-63998872; FN1, in an exon with genomic coordinates chr2:215380810-215381080; WBP1, in an exon with genomic coordinates chr2:74459477-74459562; XPO1, in an exon with genomic coordinates chr2:61525269-61525333; PTPN18, in an exon with genomic coordinates chr2:130359232-130359309; ARHGAP27, in an exon with genomic coordinates chr17:45404268-45404334; C16orf13, in an exon with genomic coordinates chr16:635280-635340; C16orf13, in an exon with genomic coordinates chr16:635517-635774; C16orf13, in an exon with genomic coordinates chr16:635611-635774.

6. The colorectal cancer subtype identifier of any one of claims 1 to 3, wherein for identifying CMS3 there is at least one exon skipping event present, wherein the exon skipping event is selected from: in exon of C16orf13, genomic coordinates chr l6:635280-635340; in exon of C16orf13, genomic coordinates chr l6:635517-635774; in exon of C16orf13, genomic coordinates chr l6:635611-635774; in exon of AURKA, genomic coordinates chr20:56388686-56388784; in exon of EPB41L3, genomic coordinates chr l8:5394676-5394793; in exon of KALRN, genomic coordinates chr3: 124637207-124637303; in exon of ADAM15, genomic coordinates chr l: 155061903- 155061975; in exon of KRAS, genomic coordinates chr l2:25215436-25215560; in exon of SLC39A14, genomic coordinates chr8:22412036-22412206; in exon of MYO9A, genomic coordinates chr l5:71951776-71951896; in exon of TPMl, genomic coordinates chr l5:63044026-63044152; in exon of TPMl, genomic coordinates chr l5:63061197-63061273; in exon of TPMl, genomic coordinates chr l5:63061712-63061788; in exon of MYO6, genomic coordinates chr6:75894813-75894840; in exon of MYO6, genomic coordinates chr6:75898372-75898411; in exon of KIAA1217, genomic coordinates chr l0:24494499-24494604; in exon of KIAA1217, genomic coordinates chr l0:24542692-24542770; in exon of KIAA1217, genomic coordinates chr l0:24542882-24544481; in exon of GIT2, genomic coordinates chr l2: 109945259- 109945349; in exon of MYL6, genomic coordinates chr l2:56160625-56160670; in exon of CTNNDl, genomic coordinates chr l l:57789036-57789155; in exon of CTNNDl, genomic coordinates chr l l:57791384-57791673.In an exon of CTNND1, genomic coordinates chrll:57791491-57791673; CD44, genomic coordinates chrll:35208104-35208206; CD44, genomic coordinates chrll:35211245-35211449; APBB2, genomic coordinates chr4:40935076-40935139; SEC31A, genomic coordinates chr4:82830936-82830975; SEC31A, genomic coordinates chr4:82830936-82830975; SEC31A, genomic coordinates chr4:82842139-82842481; SEC31A, genomic coordinates chr4:82842184-82842481; SYTL2, genomic coordinates chrll:85717482-85717530; MYOF, genomic coordinates chr10:93392916-93392955; NAV2, genomic coordinates chrll:20051288-20051333; GAB1, genomic coordinates chr4:143434087-143434168; PLEKHM2, genomic coordinates chr1:15721328-15721388; CLSTN1, genomic coordinates chr1:9737497-9737554; CLSTN1, genomic coordinates chr1:9756480-9756510; GOLGA4, genomic coordinates chr3:37361242-37361305; PBX1, genomic coordinates chr1:164820071-164820184; FKBP14, genomic coordinates chr7:30020212-30020304; or XPO1, genomic coordinates chr2:61525269-61525333.

7. The colorectal cancer subtype identifier of any one of claims 1 to 3, wherein for identifying CMS4 there is at least one exon skipping event, wherein the exon skipping event is selected from: in exon with genomic coordinates chr15:71951776-71951896 of MYO9A; in exon with genomic coordinates chr15:63044026-63044152 of TPM1; in exon with genomic coordinates chr15:63061197-63061273 of TPM1; in exon with genomic coordinates chr15:63061712-63061788 of TPM1; in exon with genomic coordinates chr6:75894813-75894840 of MYO6; in exon with genomic coordinates chr6:75898372-75898411 of MYO6; in exon with genomic coordinates chr10:24494499-24494604 of KIAA1217; in exon with genomic coordinates chr10:24542692-24542770 of KIAA1217; in exon with genomic coordinates chr10:24542882-24544481 of KIAA1217; in exon with genomic coordinates chr12:109945259-109945349 of GIT2; in exon with genomic coordinates chr12:56160625-56160670 of MYL6; in exon with genomic coordinates chr17:67875555-67875744 of BPTF; in exon with genomic coordinates chr16:15708802-15708841 of MYH11; in exon with genomic coordinates chr14:73279280-73279424 of NUMB; in exon with genomic coordinates chr11:12878888-12878900 of TEAD1; in exon with genomic coordinates chr17:50975862-50975901 of SPAG9; in exon with genomic coordinates chr4:186590367-186590403 of FAT1; in exon with genomic coordinates chr2:217830366-217830390 of TNS1; in exon with genomic coordinates chr7:158752780-158752843 of ESYT2; in exon with genomic coordinates chr3:57925844-57925934 of SLMAP; in exon with genomic coordinates chr7:91992157-91992211 of AKAP9; in exon with genomic coordinates chr3:197691073-197691148 of RUBCN.ATP2B4 in exons with genomic coordinates chr1 :203733222-203733400; LRRFIP2 in exons with genomic coordinates chr3:37091466-37091538; TBC1 D23 in exons with genomic coordinates chr3: 100311832-100311877; EHBP1 in exons with genomic coordinates chr2:62987930-62988038; SLK in exons with genomic coordinates chr10: 104010815-104010908; WDFY3 in exons with genomic coordinates chr4:84726860-84726911 ; SMARCC2 in exons with genomic coordinates chr12:56164302-56164368; KIF13A in exons with genomic coordinates chr6:17771113-17771218; MPRIP in exons with genomic coordinates chr17: 17180606-17180669; LRRFIP1 in exons with genomic coordinates chr2:237769625-237769818; NIN in exons with genomic coordinates chr14:50756491-50758630; RPS24 in exons with genomic coordinates chr10:78040203-78040225; ACTN1 in exons with genomic coordinates chr14:68878988-68879069; CTNND1 in exons with genomic coordinates chr11 :57789036-57789155; CTNND1 in exons with genomic coordinates chr11 :57791384-57791673; CTNND1 in exons with genomic coordinates chr11 :57791491-57791673; CD44 in exons with genomic coordinates chr11 :35208104-35208206; CD44 in exons with genomic coordinates chr11 :35211245-35211449; APBB2 in exons with genomic coordinates chr4:40935076-40935139; SEC31A in exons with genomic coordinates chr4:82830936-82830975; SEC31A in exons with genomic coordinates chr4:82830936-82830975; SEC31A in exons with genomic coordinates chr4:82842139-82842481 ; SEC31A in exons with genomic coordinates chr4:82842184-82842481 ; SYTL2 in exons with genomic coordinates chr11 :85717482-85717530;MYOF, in an exon with genomic coordinates chr10:93392916-93392955; NAV2, in an exon with genomic coordinates chrll:20051288-20051333; GAB1, in an exon with genomic coordinates chr4:143434087-143434168; PLEKHM2, in an exon with genomic coordinates chrl:15721328-15721388; CLSTN1, in an exon with genomic coordinates chrl:9737497-9737554; CLSTN1, in an exon with genomic coordinates chrl:9756480-9756510; GOLGA4, in an exon with genomic coordinates chr3:37361242-37361305; PBX1, in an exon with genomic coordinates chrl: 164820071-164820184; FKBP14, in an exon with genomic coordinates chr7:30020212-30020304.

8. The colorectal cancer subtype identifier according to any of the preceding claims, wherein for distinguishing CMS2 and CMS3 from CMS1 and CMS4 there is at least one exon skipping event, wherein the exon skipping event is selected from the group consisting of: in exon with genomic coordinates chr19:49521694-49521813 of FCGRT; in exon with genomic coordinates chr19:11229297-11229390 of DOCK6; in exon with genomic coordinates chr17:76090328-76090397 of EXOC7; in exon with genomic coordinates chr17:67875555-67875744 of BPTF; in exon with genomic coordinates chr12:120224642-120224727 of PXN; in exon with genomic coordinates chr4:55888887-55888932 of EXOC1 ; in exon with genomic coordinates chr3:146077861-146077924 of PLOD2; in exon with genomic coordinates chr3:108049618-108049651 of CD47; in exon with genomic coordinates chr3:108050577-108050602 of CD47; in exon with genomic coordinates chr1 :156938417-156938513 of ARHGEF11 ; in exon with genomic coordinates chr3:52558248-52558413 of PBRM1 ; in exon with genomic coordinates chr3:65448021-65448057 of MAGI1 ; in exon with genomic coordinates chr3:152446703-152446757 of MBNL1 ; in exon with genomic coordinates chr9:115064646-115064919 of TNC; in exon with genomic coordinates chr1 :225504990-225505053 of ENAH; in exon with genomic coordinates chr2:159397073-159397100 of BAZ2B; in exon with genomic coordinates chr5:34813573-34813660 of RAI14; in exon with genomic coordinates chr5:131710577-131710661 of FNIP1 ; in exon with genomic coordinates chr6:90544551-90544632 of MAP3K7; in exon with genomic coordinates chr5:66068876-66069020 of ERBIN; in exon with genomic coordinates chr20:47659398-47659452 of SULF2; in exon with genomic coordinates chr10:95414493-95414655 of SORBS1 ;SORBS1, in an exon with genomic coordinates chr10:95414493-95414862; 9. The colorectal cancer subtype identifier according to any of the preceding claims, wherein for the discrimination of CMS2 and CMS4 from CMS1 and CMS3 there is at least one exon skipping event, wherein the exon skipping event is selected from the group consisting of: SRSF6, in exons with genomic coordinates chr20:43459152-43459420; WASH3P, in exons with genomic coordinates chr15:101972595-101972694; OPAl, in exons with genomic coordinates chr3:193626091-193626202; GOLGB1, in exons with genomic coordinates chr3:121719645-121719753; GOLGB1, in exons with genomic coordinates chr3:121719645-121719768; APLP2, in exons with genomic coordinates chrll:130137255-130137291; CPNE1, in exons with genomic coordinates chr20:35658929-35659014; WIPF1, in exons with genomic coordinates chr2:174597600-174597858; ATG9A, in exons with genomic coordinates chr2:219228433-219228482; NUBP2, in exons with genomic coordinates chr16:1786737-1786955; ANOl, in exons with genomic coordinates chrll:70111125-70111191.

10. The colorectal cancer subtype identifier according to any of the preceding claims, wherein the alternative splicing event is based on at least one exon skipping event on at least one gene selected from the group consisting of ITGAE, CCNDBP1, CPT1B, CDC16, PTPN6, ACCS, EXOSC9, ZNF611, MRRF, NUP153, WARS, D2HGDH, LUC7L, EPB41, DGUOK, MDM4, PTP4A2, MKNK2, CCDC112, FRYL, CEP78, FNBP1, ECT2, ANKRD26, ZMIZ2, C6orf48, USPL1, RBM39, MIS12, AFMID, MACROD1, FN1, WBP1, XPO1, PTPN18, ARHGAP27, C16orf13, FCGRT, DOCK6, EXOC7, BPTF, PXN, EXOC1, PLOD2, CD47, ARHGEF11, PBRM1, MAGI1, MBNL1, TNC, ENAH, BAZ2B, RAI14, FNIP1, MAP3K7, ERBIN, SULF2, SORBS1, SRSF6, WASH3P, OPA1, GOLGB1, APLP2, CPNE1, WIPF1, ATG9A, NUBP2, ANO1, AURKA, EPB41L3, KALRN, ADAM15, KRAS, SLC39A14, MYO9A, TPM1, MYO6, KIAA1217, GIT2, MYL6, MYH11, NUMB, TEAD1, SPAG9, FAT1, TNS1, ESYT2, SLMAP, AKAP9, RUBCN, ATP2B4, LRRFIP2, TBC1D23, EHBP1, SLK, WDFY3, SMARCC2, KIF13A, MPRIP, LRRFIP1, NIN, RPS24, ACTN1, CTNND1, CD44, APBB2, SEC31A, SYTL2, MYOF, NAV2, GAB1, PLEKHM2, CLSTN1, GOLGA4, PBX1 and FKBP14.

11. A method for predicting outcome in a subject suffering from colorectal cancer, the method being based on the occurrence of at least one alternative splicing event using a PSI value, wherein the method comprises the steps of: a) collecting a sample from a tumor of a subject suffering from cancer; b) determining a PSI value; c) converting the PSI value to determine an indication of disease outcome. ​ ​ ​ 12. The method according to claim 11, wherein the alternative splicing event is at least one exon skipping event, in particular wherein the at least one exon skipping event is at least one exon skipping event on at least one gene selected from the group consisting of ITGAE, CCNDBP1, CPT1B, CDC16, PTPN6, ACCS, EXOSC9, ZNF611, MRRF, NUP153, WARS, D2HGDH, LUC7L, EPB41, DGUOK, MDM4, PTP4A2, MKNK2, CCDC112, FRYL, CEP78, FNBP1, ECT2, ANKRD26, ZMIZ2, C6orf48, USPL1, RBM39, MIS12, AFMID, MACROD1, FN1, WBP1, XPO1, PTPN18, ARHGAP27, C16orf13, FCGRT, DOCK6, EXOC7, BPTF, PXN, EXOC1, PLOD2, CD47, ARHGEF11, PBRM1, MAGI1, MBNL1, TNC, ENAH, BAZ2B, RAI14, FNIP1, MAP3K7, ERBIN, SULF2, SORBS1, SRSF6, WASH3P, OPA1, GOLGB1, APLP2, CPNE1, WIPF1, ATG9A, NUBP2, ANO1, AURKA, EPB41L3, KALRN, ADAM15, KRAS, SLC39A14, MYO9A, TPM1, MYO6, KIAA1217, GIT2, MYL6, MYH11, NUMB, TEAD1, SPAG9, FAT1, TNS1, ESYT2, SLMAP, AKAP9, RUBCN, ATP2B4, LRRFIP2, TBC1D23, EHBP1, SLK, WDFY3, SMARCC2, KIF13A, MPRIP, LRRFIP1, NIN, RPS24, ACTN1, CTNND1, CD44, APBB2, SEC31A, SYTL2, MYOF, NAV2, GAB1, PLEKHM2, CLSTN1, GOLGA4, PBX1 and FKBP14.

13. The method according to claim 11, wherein the tumor is classified as CMS1, CMS2, CMS3 or CMS4 by converting the PSI values to determine disease outcome indication.

14. The method according to claim 11, wherein it is decided whether to subject the subject to an anti-tumor treatment and / or monitoring of disease progression by converting the PSI values to determine a disease outcome indication.

15. A kit for predicting the outcome of a subject suffering from colorectal cancer, wherein the prediction is based on the occurrence of at least one alternative splicing event, preferably at least one exon skipping event, on at least one gene selected from the group consisting of ITGAE, CCNDBP1, CPT1B, CDC16, PTPN6, ACCS, EXOSC9, ZNF611, MRRF, NUP153, WARS, D2HGDH, LUC7L, EPB41, DGUOK, MDM4, PTP4A2, MKNK2, CCDC112, FRYL, CEP78, FNBP1, ECT2, ANKRD26, ZMIZ2, C6orf48, USPL1, RBM39, MIS12, AFMID, MACROD1, FN1, WBP1, XPO1, PTPN18, ARHGAP27, C16orf13, FCGRT, DOCK6, EXOC7, BPTF, PXN, EXOC1, PLOD2, CD47, ARHGEF11, PBRM1, MAGI1, MBNL1, TNC, ENAH, BAZ2B, RAI14, FNIP1, MAP3K7, ERBIN, SULF2, SORBS1, SRSF6, WASH3P, OPA1, GOLGB1, APLP2, CPNE1, WIPF1, ATG9A, NUBP2, ANO1, AURKA, EPB41L3, KALRN, ADAM15, KRAS, SLC39A14, MYO9A, TPM1, MYO6, KIAA1217, GIT2, MYL6, MYH11, NUMB, TEAD1, SPAG9, FAT1, TNS1, ESYT2, SLMAP, AKAP9, RUBCN, ATP2B4, LRRFIP2, TBC1D23, EHBP1, SLK, WDFY3, SMARCC2, KIF13A, MPRIP, LRRFIP1, NIN, RPS24, ACTN1, CTNND1, CD44, APBB2, SEC31A, SYTL2, MYOF, NAV2, GAB1, PLEKHM2, CLSTN1, GOLGA4, PBX1 and FKBP14, wherein the kit comprises means / instruments for determining the PSI values.

16. Use of at least one PSI value based on alternative splicing occurrence as a marker of outcome for a subject having colorectal cancer.

17. A method of treating a subject having colorectal cancer, the method using PSI values based on alternative splicing occurrence, comprising the steps of: d) collecting a sample from a tumor of a subject having cancer; e) determining at least one PSI value; f) transforming the PSI value to determine a disease outcome indication, preferably wherein by transforming the PSI value to determine a disease outcome indication, the tumor is classified as CMS1, CMS2, CMS3, or CMS4.

18. The method of claim 11 or 17, wherein the subject is a human.

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