Systems and methods for treating, diagnosing and predicting the occurrence of a medical condition

Abstract

Clinical information, molecular information and/or computer-generated morphometric information is used in a predictive model for predicting the occurrence of a medical condition. In an embodiment, a model predicts whether a patient is likely to have a favorable pathological stage of prostate cancer, where the model is based on features including one or more (e.g., all) of preoperative PSA, Gleason Score, a measurement of expression of androgen receptor (AR) in epithelial and stromal nuclei and/or a measurement of expression of Ki67-positive epithelial nuclei, a morphometric measurement of a ratio of area of epithelial nuclei outside gland units to area of epithelial nuclei within gland units, and a morphometric measurement of area of epithelial nuclei distributed away from gland units. In some embodiments, quantitative measurements of protein expression in cell lines are utilized to objectively assess assay (e.g., multiplex immunofluorescence (IF)) performance and/or to normalize features for use within a predictive model.

1 - 27 . (canceled) 
     
     
         28 . The method of  claim 33 , further comprising determining the results of the multiplex immunofluorescence assay when the comparison indicates a deviation in the one or more measurements from the baseline levels of expression of the protein in the cell lines. 
     
     
         29 . The method of  claim 33 , further comprising the step of re-subjecting the at least one of the tissue cells for the one or more patients under consideration to the multiplex immunofluorescence assay when the comparison indicates a deviation in the one or more measurements from the baseline levels of expression of the protein in the cell lines. 
     
     
         30 . The method of  claim 33 , further comprising:
 normalizing the one or more measurements of protein expression from the one or more images thereof, based on at least one of the baseline levels of expression of the protein in the cell lines, the one or more measurements of the expression of the protein in the cells lines, one or more other measurements relating to the cell lines, or a combination thereof; and   utilizing the normalized one or more measurements for generating a predictive model or evaluation of a patient's risk with a final predictive model.   
     
     
         31 . The method of  claim 33 , wherein measuring with an image analysis tool one or more measurements of the expression of the protein in the cells lines comprises
 obtaining measurement values representing one or more of the following:   (1) mean biomarker intensity in a total cell nuclei population in a positive control;   (2) mean biomarker intensity in positive cell nuclei population, indicative of nuclei with intensity above a corresponding threshold in the positive control;   (3) percentage of positive cell nuclei in the positive control; and   (4) mean biomarker intensity in total cell nuclei population in a negative control.   
     
     
         32 . The method of  claim 33 , wherein:
 the reference cells comprise cultured cells with a known profile characteristic of a phenotype of a disease; and   the phenotype of the disease comprises one or more features measurable by quantitative immunofluorescence analysis.   
     
     
         33 . A method for validating multiplex immunofluorescence assay measurements, the method comprising:
 obtaining at least one baseline protein expression value for at least one target protein present in at least one member of a reference cell line using a multiplex immunofluorescence assay;   subjecting the at least one member of the reference cell line and at least one tissue cell for one or more patients under consideration to a multiplex immunofluorescence assay;   measuring, with an image analysis tool, the protein expression values of the at least one target protein in the at least one tissue cell and reference cell;   comparing the at least one baseline protein expression value to the measured protein expression values of the at least one tissue cell and reference cell to obtain a measurement deviation value; and   determining that the multiplex immunofluorescence assay performed on the one or more tissue cells for the one or more patients under consideration produced unreliable results based on the comparison.   
     
     
         34 . A system for validating multiplex immunofluorescence assay measurements, the system comprising:
 (1) a fluorescence imaging device configured to record:
 a. at least one baseline image of at least one member of a reference cell line subject to a multiplex immunofluorescence assay; and 
 b. at least one subject image of at least one member of the reference cell and at least one tissue cell for at least one patient subject to a multiplex immunofluorescence assay; 
   (2) at least one processor configured by code executing therein to perform the following:
 i. evaluate the baseline image to establish at least one baseline protein expression value for at least one target protein present in at least one member of the reference cell line; 
 ii. determine, using the subject image, the protein expression value of the at least one target protein in
 1. the at least one tissue cell; and 
 2. at least one member of the reference cell line; 
 
 iii. compare the at least one baseline protein expression value to the measured protein expression value of the at least one tissue cell and at least one member of the reference cell line to obtain a measurement deviation value; 
 iv. validate that the multiplex immunofluorescence assay performed on the one or more tissue cells for the one or more patients has produced reliable results based on the comparison. 
   
     
     
         35 . The system of  claim 34 , wherein the at least one processor is further configured to determine that the results of the multiplex immunofluorescence assay are unreliable where the measurement value for one or more protein expression values indicates a deviation in the one or more measurements from the baseline levels of expression of the protein in the cell lines. 
     
     
         36 . The system of  claim 35 , wherein a fluorescence imaging device is further configured to record a second subject image of the at least one of the tissue cells for the one or more patients and the reference cell line where the tissue and reference cells have been subject to a new multiplex immunofluorescence assay. 
     
     
         37 . The system of  claim 34 , wherein the at least one processor is further configured to:
 normalize the one or more measurements of protein expression from the one or more images thereof, based on (1) at least one of the baseline levels of expression of the protein in the reference cell line, (2) the one or more measurements of the expression of the protein in the reference cell line, (3) one or more other measurements relating to the reference cell line, or (4) a combination thereof; and   utilize the normalized one or more measurements to generate a predictive model or evaluation of a patient's risk with a final predictive model.   
     
     
         38 . The system of  claim 34 , wherein the image analysis tool is configured to obtain measurement values representing one or more of the following:
 (1) mean biomarker intensity in a total cell nuclei population in a positive control;   (2) mean biomarker intensity in positive cell nuclei population, indicative of nuclei with intensity above a corresponding threshold in the positive control;   (3) percentage of positive cells nuclei in the positive control; and   (4) mean biomarker intensity in total cell nuclei population in a negative control.   
     
     
         39 . The system of  claim 34 , wherein:
 the reference cell lines comprises cultured cells with a known profile characteristic of a phenotype of a disease; and the phenotype of the disease comprises one or more features measurable by quantitative immunofluorescence analysis.