Patent ID: 11860164
Assignee: FRED HUTCHINSON CANCER CENTER
Field: Measurement (Instruments)
Classification: CPC G  Y | IPC G

Claim 0:
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.