Biomarker method

A method for determining efficacy of a treatment in a subject, the method comprising:

• I. quantifying a first spatial distribution of cells or sub-cellular structures in the subject before the treatment, at least in part by:
• a. obtaining, using an imaging technique that allows spatial mapping of biomarker positivity, first image data corresponding to an image of a first tissue sample of a patient and comprising a first set of N biomarkers, wherein the first image data represents a spatial map of the first set of N biomarkers;
• b. processing, by one or more processors, the first image data to obtain a first set of coordinates, wherein each coordinate of the first set of coordinates denotes the location of a cell or sub-cellular structure represented by a biomarker or combination of biomarkers of the first set of N biomarkers;
• and
• c. processing, by the one or more processors, the first set of coordinates into a two-dimensional symmetric (2N−1)×(2N−1) or 2N×2N matrix (D1), wherein each element (i, j) of the D1 matrix indicates the frequency of a cell or sub-cellular structure represented by a first biomarker, or combination of biomarkers, of the first set of N biomarkers (i) being observed within a first interaction distance, dI 1 of a cell or sub-cellular structure represented by a second biomarker or combination of biomarkers (j) of the first set of N biomarkers, wherein i and j may be the same or different, and wherein the first set of coordinates obtained in step I.b. is a set of (x,y) coordinates;
• II. applying the treatment to the subject;
• III. quantifying a second spatial distribution of cells or sub-cellular structures in the subject after the treatment, at least in part by:
• a. obtaining, using the imaging technique, second image data corresponding to an image of a second tissue sample of the subject taken after the treatment and comprising a second set of N biomarkers, wherein the second image data represents a spatial map of the second set of N biomarkers;
• b. processing, by the one or more processors, the second image data to obtain a second set of coordinates, wherein each coordinate of the second set of coordinates denotes the location of a cell or sub-cellular structure represented by a biomarker or combination of biomarkers of the second set of N biomarkers;
• and
• c. processing, by the one or more processors, the second set of coordinates into a two-dimensional symmetric (2N−1)×(2N−1) or 2N×2N matrix (D2), wherein each element (i, j) of the D2 matrix indicates the frequency of a cell or sub-cellular structure represented by a first biomarker, or combination of biomarkers, of the second set of N biomarkers (i) being observed within a second interaction distance, dI 2, of a cell or sub-cellular structure represented by a second biomarker or combination of biomarkers (j) of the second set of N biomarkers, wherein i and j may be the same or different, and wherein the second set of coordinates obtained in step III.b. is a second set of (x,y) coordinates;
• and
• IV. comparing the quantified first spatial distribution determined in step I with the quantified second spatial distribution determined in step III in order to determine efficacy of the treatment in the subject.