System and method for label selection

Patent metadata

Field	Value
Publication number	US-10876953-B2
Application number	US-201615744030-A
Country	US
Kind code	B2
Filing date	Jul 13, 2016
Priority date	Jul 15, 2015
Publication date	Dec 29, 2020
Grant date	Dec 29, 2020

Abstract

Methods and systems for performing a flow cytometry experiment can include evaluating one or more assignments of labels to a plurality of markers. Evaluating assignments of labels can include evaluating condition numbers for at least one spillover matrix. The method can further include selecting labels based at least in part on the evaluation of condition numbers. Methods and systems for performing a flow cytometry experiment can also include inputting data regarding markers, cell populations, labels, and cytometer configuration for a flow cytometry experiment, assigning labels to at least some of the markers, and running the flow cytometry experiment.

First claim

What is claimed is:

1. A method for performing a flow cytometer experiment having a panel of fluorescent labels and a plurality of cell populations with a plurality of markers, each of the cell populations expressing a subset of the plurality of markers, comprising:
inputting to a computer system biological data assigning subsets of the plurality of markers to each of the plurality of cell populations;
inputting, retrieving, or selecting marker density characteristics for at least some of the markers;
inputting, retrieving, or selecting configuration data for a flow cytometer;
inputting, retrieving, or selecting emission spectrum data for a plurality of labels;
assigning labels to at least some of the markers;
generating one or more spillover matrices having entries S ij ;
with the computer system, evaluating a condition number of one or more spillover matrices for the assigned labels to at least some of the plurality of markers, the one or more spillover matrices having entries S ij , wherein S ij corresponds to the response of a detector i to a label j wherein generating the spillover matrices and evaluating the condition numbers are performed separately for each cell population;
with the computer system, displaying one or more results of the evaluating;
optionally repeating the assigning labels, evaluating one or more of the assignments, and displaying one or more results;
selecting a panel of reagents for use in a flow cytometry experiment based on the generated spillover matrices and evaluated condition numbers for the spillover matrices, each reagent comprising one of the plurality of labels attached to a detector molecule; and
running a flow cytometry experiment with the flow cytometer using the selected panel of reagents.

2. The method of claim 1 , wherein assigning labels to at least some of the markers is performed manually.

3. The method of claim 1 , wherein the plurality of labels comprises p labels having p corresponding emission spectra, wherein the plurality of markers comprises a total of n markers to be labeled, wherein assigning labels to at least some of the markers comprises:
generating, one or more spillover matrices having entries S ij , wherein S ij corresponds to the response of a detector i to a label j;
evaluating the condition numbers of the one or more spillover matrices for at least one selection of n or fewer of the p labels; and
selecting labels for at least some of the n markers based at least in part on the evaluating.

4. The method of claim 3 , further comprising determining a first population of the sample having the greatest number of markers of all of the cell populations within the sample, wherein evaluating the condition numbers of the spillover matrices for at least one selection of n or fewer of the p labels is first performed for different combinations of a number of the p labels corresponding to the number of markers of the first population.

5. The method of claim 3 , wherein assigning labels comprises determining a subset of the labels having the lowest condition number for the first population.

6. The method of claim 4 , wherein generating the spillover matrices for the assignment of labels, evaluating the condition numbers, and selecting labels are performed sequentially for one or more of the remaining cell populations in descending order of the number of markers in each cell population, wherein the labels available for a marker in a population are limited to the labels previously for populations having the same marker.

7. The method of claim 6 , further comprising repeating generating the spillover matrices for the assignment of labels, evaluating the condition numbers, and selecting labels sequentially for one or more of the remaining cell populations with every cell population used as a first remaining cell population in the sequence.

8. The method of claim 3 , further comprising summarizing all selections of labels, and wherein selecting labels comprises determining the selection of labels having the smallest overall condition number.

9. The method of claim 1 , further comprising, with a computer system, displaying a hierarchical visual representation of at least some of the one or more cell populations, wherein the hierarchy is based at least in part on the subsets of the markers expressed by each of the one or more cell populations.

10. The method of claim 9 , wherein the displaying a hierarchical visual representation of at least some of the plurality of cell populations comprises providing a modifiable population tree.

11. The method of claim 1 , further comprising optionally repeating the assigning labels and evaluating one or more assignments.

12. The method of claim 1 , wherein the inputting, retrieving, or selecting marker density characteristics comprises inputting, retrieving, or selecting relative density classifications for co-expressed markers.

13. The method of claim 1 , further comprising inputting, retrieving, or selecting relative brightness classifications for the plurality of labels.

14. The method of claim 1 , wherein the configuration data for the flow cytometer comprises one or more of excitation laser specifications, detector specifications, filter specifications, and filter window specifications.

15. The method of claim 1 , further comprising selecting one or more reagents and with the computer system, ordering the one or more reagents.

Assignees

• Becton Dickinson Co

Inventors

• Ren ran
• Xu Heng
• Semyonova Maria
• Jaimes Maria
• Stall Alan M

Classifications

• G01N15/1459

  the analysis being performed on a sample stream · CPC title

• G01N2015/1006

  for cytology · CPC title

• C12Q1/04

  Determining presence or kind of microorganism; Use of selective media for testing antibiotics or bacteriocides; Compositions containing a chemical indicator therefor {(C12Q1/6897 takes precedence)} · CPC title

• G01N2015/1477

  Multiparameters · CPC title

• G01N15/1425 Primary

  using an analyser being characterised by its control arrangement · CPC title