Markers, methods and systems for identifying cell populations, diagnosing, monitoring, predicting and treating conditions

1. A method for identifying a specific cell population comprising:

a) providing single-cell flow or mass cytometry biomarker expression data from two or more cell samples, wherein the biomarkers are associated with a cell phenotype;

b) growing an exhaustive annotation forest of partition trees of the biomarker expression data for each cell sample, the partition trees comprising 1-dimensional, depth-3 gating strategies, constrained by shape;

c) estimating annotation boundaries for one or more biomarkers within each cell sample by averaging over gates drawn for each biomarker over the entire annotation forest;

d) calculating a depth score for each biomarker to quantify how well-gated each biomarker is in each cell sample;

e) selecting biomarkers having a high distribution of depth score across cell samples;

f) standardizing a number of annotation boundaries for each selected biomarker and their associated cell phenotype;

g) relaxing the depth-3 constrained shape for each cell sample;

h) searching the 1-dimensional, relaxed depth-3 gating strategies to discover and select phenotypes present in each cell sample;

i) assigning a phenotypic score to each selected phenotype that quantifies cell homogeneity in each cell sample with that phenotype;

j) selecting one or more high-scoring phenotypes for annotation; and

k) producing an annotated count matrix that displays the numbers of cells from each cell sample for each selected high-scoring phenotype.

2. The method of claim 1 , wherein the cell sample is a patient sample.

3. The method of claim 2 , wherein the patient sample is a blood sample.

4. The method of claim 1 , wherein the method is used to identify biomarkers associated with a particular condition or disease.

5. The method of claim 1 , wherein the method is used to diagnosis a subject with a particular condition or disease.

6. The method of claim 1 , wherein the method is used to monitor the effectiveness of a particular treatment and/or monitor a subject's disease progression associated with a particular condition or disease.

7. The method of claim 1 , wherein the method is used to predict a subject's response to treatment for a particular condition or disease.

8. The method of claim 4 , wherein the particular condition or disease is Merkel cell carcinoma.

9. The method of claim 8 , wherein Merkel cell carcinoma is of viral origin.