Abstract: This disclosure provides kits and methods for detecting markers in a sample from a subject with unknown status and generating a risk assessment of the presence or absence of cancer, such as colorectal cancer. In embodiments, a kit comprises at least five reagents, each specifically binding to one of at least five polypeptides in a sample from the subject. The polypeptides include at least ferritin, keratin 1-10, IL-8, CEA, and LI CAM. The kit further includes at least one standard comprising a known amount of at least one of the polypeptides. The kit can also include computer readable media comprising instructions to analyze the detected amounts of the at least four polypeptides along with FIT concentration and age using a machine learning algorithm to determine whether a subject has an increased risk of the presence of colorectal cancer.

Abstract: This disclosure provides kits and methods for detecting markers in a sample from a subject with unknown status and generating a risk assessment of the presence or absence of cancer, such as colorectal cancer. In embodiments, a kit comprises at least two reagents, each specifically binding to one of at least two polypeptides in a sample from the subject. The polypeptides include IL-8 and ferritin. The kit further includes at least one standard comprising a known amount of at least one of the polypeptides. The kit can also include computer readable media comprising instructions to analyze the detected amounts of the at least two polypeptides using a machine learning algorithm to determine whether a subject has an increased risk of the presence of colorectal cancer.

Abstract: The present invention provides compositions and methods having improved specificity and sensitivity for the pre-operative assessment of ovarian tumors (e.g., symptomatic and asymptomatic adnexal mass) in a variety of subjects (e.g., pre- and post-menopausal women) having a variety of ovarian cancer types (e.g., low malignant potential, intermediate malignant potential, high malignant potential).

Abstract: The present invention provides compositions and methods that provide a high degree of sensitivity and a high degree of specificity for the non-invasive assessment of endometriosis in women having a variety of endometriosis types (e.g., endometriosis, endometriotic cysts, endometrioma, or another benign condition of the endometrium) and at a variety of disease states (e.g., early and late stage).

Abstract: The present invention provides compositions and methods that provide a high degree of sensitivity and a high degree of specificity for the preoperative assessment of ovarian tumors in an African American subject (e.g., pre- and post-menopausal women) having a variety of ovarian cancer types (e.g., clear cell/mucinous, low malignant potential, high malignant potential) and at a variety of disease states (e.g., early and late stage).

Abstract: This disclosure provides kits and methods for detecting markers in a sample from a subject with unknown status and generating a risk assessment of the presence or absence of cancer, such as colorectal cancer. In embodiments, a kit comprises at least four reagents, each specifically binding to one of at least four polypeptides in a sample from the subject. The polypeptides include GDF15, keratin 1-10, and two or more of hepsin, IL-8, CEA, L1CAM, MCP-1, and OPG. The kit further includes at least one standard comprising a known amount of at least one of the polypeptides. The kit can also include computer readable media comprising instructions to analyze the detected amounts of the at least four polypeptides using a machine learning algorithm to determine whether a subject has an increased risk of the presence of colorectal cancer.

Abstract: We disclose a method of screening a mammal for a cancer associated with methylation of promoters of tumor-suppressor genes by collecting a sample of a body fluid or tissue of the mammal containing free DNA; isolating the free DNA from the sample; amplifying at least a portion of the promoter of each of a plurality of turner-suppressor genes associated with the cancer from the free DNA, to yield a plurality of amplified promoters; and quantifying methylation of each of the plurality of amplified promoters, to yield a methylation quantity. The method can have a high sensitivity and high specificity and can thus reduce the proportion of unneeded biopsies. It can also be performed with minimal invasiveness and discomfort to a patient.

Abstract: Systematic comparisons of breast ductal fluid samples obtained by nipple aspiration from women with unilateral breast cancer revealed significant differences in ductal fluid protein expression between the breast with cancer and the breast without cancer in each patient. This study demonstrates that breast ductal fluid contains over 1000 separate protein species and suggests that ductal fluids from breast cancer patients may be useful for high-throughput biomarker discovery.

Abstract: The present invention provides a method for assessing stem cell transplant in a protein-containing sample using multi-dimensional protein separation. Such multi-dimensional separation techniques include chromatography, electrophoresis and mass spectrometry. A protein-containing sample may comprise body fluids such as blood and serum but may also include a cell, tissue or organ. Identification of a protein present in the donor and the transplant recipient but not in the recipient sample before transplant indicates that the stem cell is grafted.

Abstract: A method of diagnosing a cancerous condition in a female includes analyzing ductal secretions from each breast of a female subject in which differences in the protein profiles of the two samples are indicative of a cancerous condition. Protein samples are preferable analyzed by two dimensional gel electrophoresis or by microarrays. Identification of cancer markers and monitoring progression and treatment of cancers, and especially breast cancer are also dislcosed.

Abstract: Systematic comparisons of breast ductal fluid samples obtained by nipple aspiration from women with unilateral breast cancer revealed significant differences in ductal fluid protein expression between the breast with cancer and the breast without cancer in each patient. This study demonstrates that breast ductal fluid contains over 1000 separate protein species and suggests that ductal fluids from breast cancer patients may be useful for high-throughput biomarker discovery.

Abstract: Peptides derived from prostate specific antigen (PSA) that correspond to the immunodominant epitopes found in the native antigen are disclosed. These peptides were identified using a method that predicts continuous, immunodominant epitopes. Anti-PSA antibodies, methods for their production and their use in diagnostic assays also are disclosed.

Abstract: The present invention relates to identifying protein epitopes and more particularly to a novel method for identifying, determining the location, optimal length of amino acid residues and immunobiological potency of protein epitopes by applying a custom negative cosine function fit algorithm to a protein hydropathy scale. This fit analysis is supplemented with experimental immunobiological data. The amino acid sequence of the protein epitopes of the present invention exhibit a hydrophobic-hydrophilic-hydrophobic hydropathy pattern of an approximately fixed length in a given protein.

Abstract: Peptides derived from prostate specific antigen (PSA) that correspond to the immunodominant epitopes found in the native antigen are disclosed. These peptides were identified using a method that predicts continuous, immunodominant epitopes. Anti-PSA antibodies, methods for their production and their use in diagnostic assays also are disclosed.