Methods for identifying cancer patients at high risk of developing metastasis. The present invention relates to the field of biomedicine and cancer. Specifically, it relates to an in vitro method of prognosis or for predicting the risk of suffering from metastasis in a patient having localized cancer disease based on the differential presence of exons in circulating cell free DNA (cfDNA) in cancer patients.
. An in vitro method for identifying exons which are differentially present in patients having metastasis (DPE) with respect to patients having localized cancer disease, wherein said method comprises the following steps: i. quantifying individual exons by whole-exome sequencing of the circulating cell-free DNA (cfDNA) by next-generation sequencing in a blood, plasma or serum sample obtained from a cancer patient or group of patients with localized disease (N group); ii. quantifying individual exons by whole-exome sequencing of the cfDNA by next- generation sequencing in a blood, plasma or serum sample obtained from a cancer patient or group of patients with metastasized disease (M group); iii. comparing the quantification values in i) with the quantification values in ii) and identify as differentially present exons those which abundance differs in a statistically significant manner between both groups. The method according to claim 1 , wherein exome capturing for whole-exome sequencing is conducted by a method comprising hybridization of cfDNA in said blood, plasma or serum sample with probes substantially complementary to substantially all the coding DNA sequences in the patient's species genome. The method according to any of the precedent claims, wherein exon quantification is conducted by counting the number of sequence reads obtained by whole-exome sequencing that map to known exons when these are aligned to a reference genome sequence. The method according to any of the preceding claims, wherein quantification values of DPE have been normalized, preferably data normalization has been conducted by the trimmed mean of M values (TMM) method. An in vitro method of prognosis or for predicting the risk of suffering from metastasis in a patient having localized cancer disease, the method comprising: i. quantifying individual exons identified as differentially present in metastatic patients (DPE) according to a method as defined in any of claims 1 to 4 in a blood, plasma or serum sample obtained from said patient; and ii. comparing the quantification values in the patient's sample obtained in i) with the quantification values in a reference sample, wherein said reference sample is isolated from a patient or group of patients suffering from localized cancer disease; wherein when the quantification values in the patient's sample are increased or decreased in comparison with those in the reference sample the patient has a high risk of suffering from metastasis. 6. The method according to claim 5, wherein DPE are quantified by a method selected from the group consisting of next generation sequencing, quantitative PCR (qPCR), PCR- pyrosequencing, PCR-ELISA, DNA microarrays, branched DNA, dot-blot, Fluorescence In Situ Hybridization assay (FISH), and multiplex versions of said methods. 7. The method according to any of claims 5 or 6, wherein DPE are quantified by whole-exome sequencing using next generation sequencing. 8. The method according to any of the precedent claims, wherein said patient is a human patient. 9. The method according to any of the precedent claims, wherein said cancer is a solid tumor selected from the group consisting of lung cancer, sarcoma, malignant melanoma, mesothelioma, bladder carcinoma, prostate cancer, pancreas carcinoma, gastric carcinoma, ovarian cancer, hepatoma, breast cancer, colorectal cancer, kidney cancer, esophageal cancer, suprarenal cancer, parotid gland cancer, head and neck carcinoma, cervix cancer, mesothelioma and lymphoma. 10. The method according to any of the precedent claims, wherein said cancer is colorectal cancer, preferably adenocarcinoma. 1 1 . The method according to any of the precedent claims, wherein said differentially present exons are selected from the group consisting of the 379 exons found to be differentially present in colorectal cancer defined in Table 1 . 12. An in vitro method for selecting a treatment for a patient having localized cancer disease wherein said method comprises selecting a treatment according to the classification of said patient according to its prognosis or risk of metastasis by a method as defined in any of claims 5 to 1 1. 13. A method according to any of the preceding claims, wherein said method further comprises storing the method results in a data carrier, preferably wherein said data carrier is a computer readable medium. 14. A computer implemented method, wherein the method is as defined in any of claims 1 to 13. 15. Use of a kit for the prognosis or for predicting the risk of suffering from metastasis in a patient having localized cancer disease on the basis of the differential presence of exons in circulating cell-free DNA (cfDNA) according to a method of any of claims 5 to 13, said kit comprising: a) a reagent for quantifying individual exons in a blood, plasma or serum sample; b) optionally, instructions for the use of said reagent(s) in determining the levels of said exons, in a blood, plasma or serum sample.