Computer-assisted analysis

• US 20060154236A1
• Filed: 11/11/2005
• Published: 07/13/2006
• Est. Priority Date: 11/11/2004
• Status: Abandoned Application

• Current Assignee: President and Fellows of Harvard College (Harvard Corporation)
• Original Assignee: President and Fellows of Harvard College (Harvard Corporation)
• Inventors: Wu, Lani, Slack, Michael D., Altschuler, Steven J.
• Application Number:
  US11/271,215
• Publication Number:
  US 20060154236A1
• Time in Patent Office: Days
• US Class Current: 435/4
• CPC Class Codes: G01N 33/5026 on cell morphology

Abstract

The present invention provides methods and systems for automated morphological analysis of cells also known as phenotypic screening. The inventive methods are particularly useful in the rapid analysis of cells required in a biological screen or in the screening for agents with a particular mechanism of action. Agents which cause a particular phenotype in the cells can be identified using the inventive quantitative morphometric analysis of cells. The data gathered using the inventive method can also be quantified and analyzed later for various trends and classifications (e.g., Kolmogorov-Smirnov statistics, titration-invariant similarity scores). Characteristics of cells which can be determined using this method include number of nuclei, size of cell, size of nuclei, number of the centrosomes, shape of cells, size of centrosomes, perimeter of nucleus, shape of nucleus, staining for a particular protein, staining for an organelle, pattern of staining, and degree of staining.

Claims

1. A method of cell analysis, the method comprising steps of:

providing cells for analysis;

contacting the cells with at least two agents over a range of titrations;

imaging the cells;

analyzing images of the cells for various visual characteristics;

quantitating the visual characteristics of the cells;

calculating a Kolmogorov-Smirnov statistic for a particular agent, titration, and descriptor as compared to untreated control cells based on a continuous distribution function of the quantitated visual characteristic;

calculating z-scores by normalizing the Kolmogorov-Smirnov statistic for all descriptors and titrations based on the variability of the quantitated visual characteristic;

defining a titration sub-series by shifting the starting point of the titration series over a range of possible shifts;

calculating an s-correlation for each pair of titration sub-series for two agents; and

determining the value of s that yields the highest correlation between two titration subseries.

2. The method of claim 1, wherein the step of determining further comprises normalizing the s-correlations using a Gaussian distribution.

3. The method of claim 1 further comprising:

clustering of agents based on the s-correlation.

4. The method of claim 1, wherein the characteristic is selected from the group consisting of eccentricity of cells, average number of nuclei per cell, average area of cells, average volume of cells, average number of centromeres per cell, average size of nuclei, average area of nuclei, average size of cells, perimeter of cell, perimeter of nucleus, average gray value of staining, degree of staining, pattern of staining, ratio of staining between nucleus and cytoplasm, and morphology.

5. The method of claim 1, wherein the step of calculating z-scores comprises dividing the Kolmogorov-Smirnov statistic by the standard deviation calculated for each descriptor based on a control, untreated population.

6. The method of claim 1, wherein the titrations are within the range of 1 pM agent to 10 mM agent.

7. The method of claim 1, wherein the titrations are within the range of 10 pM agent to 100 μ

M.

8. The method of claim 1, wherein the number of titrations is at least 5.

9. The method of claim 1, wherein each titration represents a 2-fold dilution.

10. The method of claim 1, wherein each titration represents a 3-fold dilution.

11. The method of claim 1, wherein each titration represents a 5-fold dilution.

12. A method of screening, the method comprising steps of:

providing a plurality of cell samples;

providing a plurality of test agents;

contacting one of the cell samples with one of the test agents over a range of titrations;

imaging the plurality of cell samples after a time period;

analyzing the images of the cell samples for various visual characteristics (descriptors);

quantitating the data for each descriptor, agent, and titration;

calculating a Kolmogorov-Smirnov statistic for a particular descriptor, agent, and titration as compared to untreated, control cells based on a continuous distribution function;

calculating z-scores by normalizing the Kolmogorov-Smirnov statistic for all sets of descriptors, agents, and titrations based on the variability of the descriptor;

defining a titration sub-series by shifting the starting point of the titration series over a range of possible shifts;

calculating an s-correlation for each pair of titration sub-series for two agents; and

determining the value of s that yields the highest correlation between two titration subseries.

13. The method of claim 12, wherein the step of determining further comprises normalizing the s-correlations using a Gaussian distribution.

14. The method of claim 12 further comprising clustering of agents based on the s-correlation.

15. The method of claim 12, further comprising selecting those test agents that achieve a certain characteristic of the cells upon exposure of the cells to the test agent.

16. The method of claim 12, wherein the plurality of cell samples comprises greater than 100 cell samples.

17. A method of calculating a titration-invariant similarity score, the method comprising steps of:

providing numerical data quantitating visual characteristics of samples of cells treated with at least two agents;

calculating a Kolmogorov-Smirnov statistic for a particular agent, titration, and descriptor as compared to untreated control cells based on a continuous distribution function of the quantitated visual characteristic;

calculating z-scores by normalizing the Kolmogorov-Smirnov statistic for all descriptors and titrations based on the variability of the quantitated visual characteristic;

defining a titration sub-series by shifting the starting point of the titration series over a range of possible shifts;

calculating an s-correlation for each pair of titration sub-series for two agents; and

determining the value of s that yields the highest correlation between two titration subseries.

18. The method of claim 17, wherein agents are compared.

19. The method of claim 17, wherein descriptors are compared.

20. The method of claim 17 further comprising clustering of compounds or descriptors based on the s-correlation.