Abstract: The invention relates to methods of breast tumor analysis relying on the detection of expression levels of specific genes. Such methods find application in, amongst other, predicting the response of a breast cancer patient to immunotherapy or to immunogenic therapy, and in following up such responses. The expression levels of the genes can thus be used in determining which breast cancer patients are most likely to respond to immunotherapy or immunogenic therapy. The genes serving as biomarkers are individually highly performant in predicting the response of a breast tumor to immunotherapy or to immunogenic therapy, but are weak in predicting the response of melanoma to immunotherapy or to immunogenic therapy. Diagnostic kits are likewise part of the invention.

Abstract: The present application relates to the field of cancer, particular to hypoxic tumors. It was found that hypoxia is an important driver for hypermethylation of (promoters of) tumor suppressor genes. As this hypermethylation is a stable signature that is also present in circulating tumor DNA in peripheral blood, detecting this methylation pattern is a surrogate marker for tumor hypoxia. This can be used to adapt therapy as well.

Abstract: The field of the invention generally relates to cancer, including methods for diagnosing, prognosing, and treating cancer. In particular, the field of the invention relates to novel signatures of unique sets of point mutations involving a change of a cytosine or a guanidine, and methods, systems, and components thereof based upon the novel signature for identifying tumor samples having increased tumor mutational burden (TMB). Both the signatures and the methods, systems, and components thereof may be utilized for identifying cancer patients, microsatellite stable-cancer patients in particular, who will effectively respond to immune checkpoint blockade therapy.

Abstract: Described are methods of analyzing cell free DNA based on combining analysis of cfDNA methylation with analysis of the cfDNA nucleosome footprint and/or with analysis of cfDNA copy number alteration. The diagnostic performance of these methods, in particular relating to early or earlier stage diseases or disorders, is increased compared to the diagnostic performance of the individual cfDNA analysis methods.

Abstract: The present invention relates to biomarkers for predicting the risk of developing chronic allograft injury in a patient, and means and methods for (post-transplant) preservation of allografts and transplantation organs. In particular, a method to predict the risk of developing chronic allograft injury in a patient is presented based on age-related increase of methylation of CpGs. In particular, the allograft is a kidney.

Abstract: The present application relates to the field of cancer, particular to hypoxic tumors. It was found that hypoxia is an important driver for hypermethylation of (promoters of) tumor suppressor genes. As this hypermethylation is a stable signature that is also present in circulating tumor DNA in peripheral blood, detecting this methylation pattern is a surrogate marker for tumor hypoxia. This can be used to adapt therapy as well.

Abstract: The invention relates to methods of tumor analysis relying on the detection of expression of or of changes in the expression levels of specific retrotransposons. Such methods find application in, amongst other, predicting the response of a tumor to immunotherapy or to immunogenic therapy, and in following up such responses. The expression levels of specific retrotransposons can thus be used in determining which patients are most likely to respond to immunotherapy or immunogenic therapy. Corresponding diagnostic kits are likewise part of the invention.

Abstract: The present invention concerns the use of interleukin-8 (IL-8) as a biomarker for predicting the outcome of the treatment with aflibercept, or ziv-aflibercept of a patient suspected to suffer from a cancer.

Abstract: The present invention relates to the identification of a specific set of CpG biomarkers for predicting the risk of developing chronic allograft injury in a patient, and means and methods for preservation of allografts and transplantation organs. In particular, a method to predict the risk of developing chronic allograft injury in a patient is presented based on cold-ischemia induced hypermethylation of CpGs as an important driver for downregulation of (promoters of) genes essential for organ preservation. Specifically, a CpG biomarker signature for hypermethylation of renal allograft organs caused by hypoxia and ischemia pre-implantation revealed treatment options of ischemia-associated chronic allograft injury and preservation of donor kidneys.

Abstract: Described are mismatch repair (MMR?) deficient tumors. Markers are presented herein having a high sensitivity to detect whether a tumor is mismatch repair deficient or not. The markers are particularly mutations in microsatellite regions. Accordingly, methods and materials are provided for diagnosing microsatellite instability of a tumor. Such a method comprises determining the presence of these markers. Further, kits are provided to detect the presence of these markers (or subsets thereof) in a sample.

Abstract: The present invention concerns the use of interleukin-8 (IL-8) as a biomarker for predicting the outcome of the treatment with aflibercept, or ziv-aflibercept of a patient suspected to suffer from a cancer.

Abstract: Described are mismatch repair (MMR-)deficient tumors. Markers are presented herein having a high sensitivity to detect whether a tumor is mismatch repair deficient or not. The markers are particularly mutations in microsatellite regions. Accordingly, methods and materials are provided for diagnosing microsatellite instability of a tumor. Such a method comprises determining the presence of these markers. Further, kits are provided to detect the presence of these markers (or subsets thereof) in a sample.

Abstract: The present application relates to the field of cancer, particularly to colorectal cancer (CRC). A panel of biomarkers is presented herein that can be used to cluster CRC samples into distinct genetic subtypes. It further relates to the use of the clustering method on patients treated with an anti-VEGF therapy and the identification of anti-VEGF responsive genetic subtypes.

Abstract: The present invention concerns the use of interleukin-8 (IL-8) as a biomarker for predicting the outcome of the treatment with aflibercept, or ziv-aflibercept of a patient suspected to suffer from a cancer.

Abstract: The present application relates to the field of cancer, particularly to mismatch repair (MMR?) deficient tumors. New markers are presented herein that have a high sensitivity to detect whether a tumor is mismatch repair deficient or not. The markers are particularly mutations in microsatellite regions. Accordingly, methods are provided for diagnosing microsatellite instability of a tumor, comprising determining the presence of these markers. Further, kits are provided to detect the presence of these markers (or subsets thereof) in a sample.

Abstract: The present application relates to the field of cancer, particular to hypoxic tumors. It was found that hypoxia is an important driver for hypermethylation of (promoters of) tumor suppressor genes. As this hypermethylation is a stable signature that is also present in circulating tumor DNA in peripheral blood, detecting this methylation pattern is a surrogate marker for tumor hypoxia. This can be used to adapt therapy as well.

Abstract: The present invention concerns the use of interleukin-8 (IL-8) as a biomarker for predicting the outcome of the treatment with aflibercept, or ziv-aflibercept of a patient suspected to suffer from a cancer.

Abstract: The invention is concerned with a method of determining whether a patient is more suitably treated by a therapy with an angiogenesis inhibitor, such as bevacizumab, by determining the genotype of VEGFR-1 gene. The invention further relates to a pharmaceutical composition comprising an angiogenesis inhibitor, such as bevacizumab, for the treatment of a patient suffering from cancer based on the genotype of VEGFR-1 gene. The invention further relates to a method for improving the treatment effect of chemotherapy of a patient suffering from cancer by adding an angiogenesis inhibitor, such as bevacizumab, based on the genotype of VEGFR-1 gene.

Abstract: Described are mismatch repair (MMR-)deficient tumors. Markers are presented herein having a high sensitivity to detect whether a tumor is mismatch repair deficient or not. The markers are particularly mutations in microsatellite regions. Accordingly, methods and materials are provided for diagnosing microsatellite instability of a tumor. Such a method comprises determining the presence of these markers. Further, kits are provided to detect the presence of these markers (or subsets thereof) in a sample.

Abstract: The invention is concerned with a method of determining whether a patient is more suitably treated by a therapy with an angiogenesis inhibitor, such as bevacizumab, by determining the genotype of VEGFR-1 gene. The invention further relates to a pharmaceutical composition comprising an angiogenesis inhibitor, such as bevacizumab, for the treatment of a patient suffering from cancer based on the genotype of VEGFR-1 gene. The invention further relates to a method for improving the treatment effect of chemotherapy of a patient suffering from cancer by adding an angiogenesis inhibitor, such as bevacizumab, based on the genotype of VEGFR-1 gene.