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

• US 20100177950A1
• Filed: 07/27/2009
• Published: 07/15/2010
• Est. Priority Date: 07/25/2008
• Status: Active Grant

• Current Assignee: Champalimaud Foundation
• Original Assignee: Aureon Biosciences, Inc.
• Inventors: Fogarasi, Stephen, Vengrenyuk, Yevgen, Tabesh, Ali, Khan, Faisal, Donovan, Michael, Cordon-Cardo, Carlos, Fernandez, Gerardo, Costa, Jose, Mesa-Tejada, Ricardo
• Granted Patent: US 9,858,389 B2
• Time in Patent Office: Days
• US Class Current: 382/133
• CPC Class Codes: G16H 50/20 for computer-aided diagnosis, e.g. based on medical expert systems
• CPC Class Codes: G16H 50/30 for calculating health indices; for individual health risk assessment
• CPC Class Codes: G16H 50/50 for simulation or modelling of medical disorders
• CPC Class Codes: G16H 50/70 for mining of medical data, e.g. analysing previous cases of other patients

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 risk of prostate cancer progression in a patient, where the model is based on features including one or more (e.g., all) of preoperative PSA, dominant Gleason Grade, Gleason Score, at least one of a measurement of expression of AR in epithelial and stromal nuclei and a measurement of expression of Ki67-positive epithelial nuclei, a morphometric measurement of average edge length in the minimum spanning tree (MST) of epithelial nuclei, and a morphometric measurement of area of non-lumen associated epithelial cells relative to total tumor area. In some embodiments, the morphometric information is based on image analysis of tissue subject to multiplex immunofluorescence and may include characteristic(s) of a minimum spanning tree (MST) and/or a fractal dimension observed in the images.

Claims

1. Apparatus for evaluating a risk of progression of prostate cancer in a patient, the apparatus comprising:

a model predictive of prostate cancer progression configured to evaluate a dataset for a patient to thereby evaluate a risk of prostate cancer progression in the patient, wherein the model is based on one or more features selected from the following group of features;

preoperative PSA;

dominant Gleason Grade;

Gleason Score;

at least one of a measurement of expression of androgen receptor (AR) in epithelial nuclei and stromal nuclei and a measurement of expression of Ki67-positive epithelial nuclei;

a morphometric measurement of average edge length in the minimum spanning tree (MST) of epithelial nuclei; and

a morphometric measurement of area of non-lumen associated epithelial cells relative to total tumor area.

2. The apparatus of claim 1, wherein the dominant Gleason Grade comprises a dominant biopsy Gleason Grade (bGG).

3. The apparatus of claim 1, wherein the Gleason Score comprises a biopsy Gleason Score.

4. The apparatus of claim 1, wherein the measurement of the expression of androgen receptor (AR) in epithelial and stromal nuclei and the measurement of the expression of Ki67-positive epithelial nuclei form a combined feature, wherein the predictive model evaluates the measurement of the expression of androgen receptor (AR) in epithelial and stromal nuclei for the combined feature when a dominant Gleason Grade for the patient is less than or equal to 3, and evaluates the measurement of the expression of Ki67-positive epithelial nuclei for the combined feature when the dominant Gleason Grade for the patient is 4 or 5.

5. The apparatus of claim 1, wherein the morphometric measurement of average edge length in the minimum spanning tree (MST) of epithelial nuclei forms a combined feature with a dominant Gleason Grade, wherein the predictive model evaluates the measurement of average edge length in the minimum spanning tree (MST) of epithelial nuclei for the combined feature when the dominant Gleason Grade for the patient is less than or equal to 3, and evaluates the dominant Gleason Grade for the combined feature when the dominant Gleason Grade for the patient is 4 or 5.

6. The apparatus of claim 1, wherein based on the evaluation the model is configured to output a value indicative of a risk of prostate cancer progression in the patient.

7. The apparatus of claim 1, wherein the model is based on two features from the group.

8. The apparatus of claim 1, wherein the model is based on three features from the group.

9. The apparatus of claim 1, wherein the model is based on four features from the group.

10. The apparatus of claim 1, wherein the model is based on five features from the group.

11. The apparatus of claim 1, wherein the model is based on all of the features in the group.

12. The apparatus of claim 1, wherein the model is based on one or more features in the group and is further based on at least one additional clinical, molecular, or morphometric feature.

13. A method of evaluating a risk of progression of prostate cancer in a patient, the method comprising:

evaluating a dataset for a patient with a model predictive of prostate cancer progression, wherein the model is based on one or more features selected from the following group of features;

preoperative PSA;

dominant Gleason Grade;

Gleason Score;

at least one of a measurement of expression of androgen receptor (AR) in epithelial nuclei and stromal nuclei and a measurement of expression of Ki67-positive epithelial nuclei;

a morphometric measurement of average edge length in the minimum spanning tree (MST) of epithelial nuclei; and

a morphometric measurement of area of non-lumen associated epithelial cells relative to total tumor area;

thereby evaluating the risk of prostate cancer progression in the patient.

14. The method of claim 13, wherein the dominant Gleason Grade comprises a dominant biopsy Gleason Grade (bGG).

15. The method of claim 13, wherein the Gleason Score comprises a biopsy Gleason Score.

16. The method of claim 13, wherein the measurement of the expression of androgen receptor (AR) in epithelial and stromal nuclei and the measurement of the expression of Ki67-positive epithelial nuclei form a combined feature, wherein the evaluating comprises evaluating the measurement of the expression of androgen receptor (AR) in epithelial nuclei and stromal nuclei for the combined feature with the predictive model when a dominant Gleason Grade for the patient is less than or equal to 3, and evaluating the measurement of the expression of Ki67-positive epithelial nuclei for the combined feature with the predictive model when the dominant Gleason Grade for the patient is 4 or 5.

17. The method of claim 13, wherein the morphometric measurement of average edge length in the minimum spanning tree (MST) of epithelial nuclei forms a combined feature with a dominant Gleason Grade, wherein the evaluating comprises evaluating the measurement of average edge length in the minimum spanning tree (MST) of epithelial nuclei for the combined feature with the predictive model when the dominant Gleason Grade for the patient is less than or equal to 3, and evaluating the dominant Gleason Grade for the combined feature with the predictive model when the dominant Gleason Grade for the patient is 4 or 5.

18. The method of claim 13, further comprising outputting with the predictive model a value indicative of the risk of prostate cancer progression in the patient.

19. A computer readable medium comprising computer executable instructions recorded thereon for performing the method comprising:

evaluating a dataset for a patient with a model predictive of prostate cancer progression, wherein the model is based on one or more features selected from the following group of features;

preoperative PSA;

dominant Gleason Grade;

Gleason Score;

at least one of a measurement of expression of androgen receptor (AR) in epithelial nuclei and stromal nuclei and a measurement of expression of Ki67-positive epithelial nuclei;

a morphometric measurement of average edge length in the minimum spanning tree (MST) of epithelial nuclei; and

a morphometric measurement of area of non-lumen associated epithelial cells relative to total tumor area;

thereby evaluating the risk of prostate cancer progression in the patient.

20. The computer readable medium of claim 19 further comprising computer executable instructions recorded thereon for outputting with the predictive model a value indicative of the risk of prostate cancer progression in the patient.

21. Apparatus for evaluating a risk of occurrence of an outcome with respect to a medical condition in a patient, the apparatus comprising:

a model predictive of an outcome with respect to the medical condition, wherein the model is based on one or more computer-generated morphometric features generated from one or more images of tissue subject to multiplex immunofluorescence (IF), wherein the model is configured to;

receive a patient dataset for the patient; and

evaluate the patient dataset according to the model to produce a value indicative of the risk of occurrence of the outcome with respect to the medical condition in the patient.

22. The apparatus of claim 21, wherein the one or more computer-generated morphometric feature(s) comprises one or more measurements of the minimum spanning tree (MST) identified in the one or more images of tissue subject to multiplex immunofluorescence (IF).

23. The apparatus of claim 22, wherein the one or more measurements of the minimum spanning tree (MST) comprises one or more measurements of the MST of epithelial nuclei identified in the one or more images of tissue subject to multiplex immunofluorescence (IF).

24. The apparatus of claim 23, wherein the one or more measurements of the minimum spanning tree (MST) comprises average edge length in the MST of epithelial nuclei as identified in the one or more images of tissue subject to multiplex immunofluorescence (IF).

25. The apparatus of claim 21, wherein the one or more computer-generated morphometric features comprises one or more measurements of the fractal dimension (FD) measured in the one or more images of tissue subject to multiplex immunofluorescence (IF).

26. The apparatus of claim 25, wherein the one or more measurements of the fractal dimension (FD) comprises one or more measurements of the fractal dimension of one or more glands identified in the one or more images of tissue subject to multiplex IF.

27. The apparatus of claim 26, wherein the one or more measurements of the fractal dimension of one or more glands comprises one or more measurements of the fractal dimension of gland boundaries between glands and stroma.

28. The apparatus of claim 26, wherein the one or more measurements of the fractal dimension of one or more glands comprises one or more measurements of the fractal dimension of gland boundaries between glands and stroma and between glands and lumen.

29. The apparatus of claim 21, wherein the model is further based on one or more clinical features and one or more molecular features.

30. A method of evaluating a risk of occurrence of an outcome with respect a medical condition in a patient, the method comprising:

evaluating a dataset for a patient with a model predictive of an outcome with respect to the medical condition, wherein the model is based on one or more computer-generated morphometric feature(s) generated from one or more images of tissue subject to multiplex immunofluorescence (IF);

thereby evaluating the risk of occurrence of the outcome with respect to the medical condition in the patient.

31. The method of claim 30, wherein the one or more computer-generated morphometric features comprises one or more measurements of the minimum spanning tree (MST) identified in the one or more images of tissue subject to multiplex immunofluorescence (IF).

32. The method of claim 30, wherein the one or more computer-generated morphometric features comprises one or more measurements of the fractal dimension (FD) measured in the one or more images of tissue subject to multiplex immunofluorescence (IF).

33. A computer readable medium comprising computer executable instructions recorded thereon for performing the method comprising:

evaluating a dataset for a patient with a model predictive of an outcome with respect to a medical condition, wherein the model is based on one or more computer-generated morphometric features generated from one or more images of tissue subject to multiplex immunofluorescence (IF);

thereby evaluating the risk of occurrence of the medical condition in the patient.

34. The computer readable medium of claim 33, wherein the one or more computer-generated morphometric features comprises one or more measurements of the minimum spanning tree (MST) identified in the one or more images of tissue subject to multiplex immunofluorescence (IF).

35. The computer readable medium of claim 33, wherein the one or more computer-generated morphometric features comprises one or more measurements of the fractal dimension (FD) measured in the one or more images of tissue subject to multiplex immunofluorescence (IF).

36. Apparatus for identifying objects of interest in images of tissue, the apparatus comprising:

an image analysis tool configured to segment a tissue image into pathological objects comprising glands, wherein starting with lumens in the tissue image identified as seeds, the image analysis tool is configured to perform controlled region growing on the image comprising;

initiating growth around the lumen seeds in the tissue image thus encompassing epithelial cells identified in the image through said growth;

continuing growth of each gland around each lumen seed so long as the area of each successive growth ring is larger than the area of the preceding growth ring; and

discontinuing said growth of said gland when the area of a growth ring is less than the area of the preceding growth ring for said gland.

37. Apparatus for measuring the expression of one or more biomarkers in images of tissue subject to immunofluorescence (IF), the apparatus comprising:

an image analysis tool configured to;

measure within an image of tissue the intensity of a biomarker as expressed within a particular type of pathological object, wherein said measuring comprises determining a plurality of percentiles of the intensity of the biomarker as expressed within the particular type of pathological object; and

identify one of said plurality of percentiles as the percentile corresponding to a positive level of said biomarker in said pathological object.

38. The apparatus of claim 37, wherein said identifying one of said plurality of percentiles comprises identifying one of said plurality of percentiles based on an intensity in a percentile of another pathological object.

39. The apparatus of claim 37, wherein said image analysis tool is further configured to measure one or more features from said image of tissue, said one or more features comprising a difference of intensities of percentile values from said plurality of percentile values.

40. The apparatus of claim 39, wherein said one or more features comprising a difference of intensities of percentile values from said plurality of percentile values is normalized by an image threshold or another difference of intensities of percentile values.

41. Apparatus for identifying objects of interest in images of tissue, the apparatus comprising:

an image analysis tool configured to;

detect the presence of CD34 in an image of tissue subject to immunofluorescence (IF); and

based on said detection, detect and segment blood vessels which are in proximity to said CD34.