Visualization tools for digital PCR data

Patent metadata

Field	Value
Publication number	US-11417037-B2
Application number	US-202016937634-A
Country	US
Kind code	B2
Filing date	Jul 24, 2020
Priority date	Nov 7, 2012
Publication date	Aug 16, 2022
Grant date	Aug 16, 2022

Abstract

A method for generating a data visualization is provided. The method includes displaying a representation of a portion of detected data from a substrate to a user. The method further includes generating a data quality value for the portion of detected data and displaying, along with the representation of the portion of detected data, an indication of data quality value for the portion of detected data. The method further includes selecting, by the user, a quality value threshold, and displaying an adjusted indication of data quality value for the portion of detected data meeting the quality value threshold.

First claim

What is claimed is:

1. A method for generating a data visualization for emission data from a biological analysis system, the method comprising:
generating data quality values for emission data from a plurality of reaction sites on a substrate, the emission data indicating presence or absence of a target product of a biological assay reaction at the plurality of reaction sites;
setting a quality value threshold to an initial quality value threshold;
displaying, on a graphical user interface (GUI), a first data visualization comprising a positional representation of the plurality of reaction sites from at least a portion of the substrate, wherein the positional representation of the first data visualization simultaneously indicates relative data quality of the plurality of reaction sites of the at least the portion of the substrate based on a comparison of the data quality values of the plurality of the reaction sites from at least the portion of the substrate to the initial quality value threshold;
displaying, on the GUI with the first data visualization, an interactive tool, the interactive tool being manipulatable to adjust the initial quality value threshold to an adjusted quality value threshold;
receiving, via the interactive tool, a selection of the adjusted quality value threshold; and
in response to receiving the selection of the adjusted quality value threshold, dynamically altering the first data visualization displayed on the GUI to a second data visualization, the second data visualization comprising the positional representation of the plurality of reaction sites from the at least the portion of the substrate, wherein the positional representation of the second data visualization simultaneously indicates relative data quality of the plurality of reaction sites from at least the portion of the substrate based on a comparison of the data quality values of the plurality of reaction sites and the adjusted quality value threshold.

2. The method of claim 1 , further comprising displaying on the GUI one or more scatter plots of at least some of the emission data for the plurality of reactions sites from at least the portion of the substrate, wherein the one or more scatter plots indicate presence or absence of differing target reaction products of a reaction at the plurality of reaction sites.

3. The method of claim 2 , wherein axes of the one or more scatter plots indicate emission intensity from differing dyes used in the biological assay reaction.

4. The method of claim 1 , wherein the first and second data visualizations comprise a heat map.

5. The method of claim 1 , further comprising displaying on the GUI one or more histograms of the emission data for the plurality of reaction sites from at least the portion of the substrate, wherein the one or more histograms indicate a number of the plurality of reactions sites meeting the initial and/or the adjusted quality value threshold.

6. The method of claim 1 , wherein the emission data comprises fluorescence data.

7. The method of claim 1 , wherein the emission data indicating presence or absence of a target product of a biological assay reaction comprises emission data indicating presence or absence of one or more amplified target nucleic acid products of a polymerase chain reaction.

8. The method of claim 1 , wherein the plurality of reaction sites is at least 20,000 reaction sites.

9. The method of claim 1 , wherein the plurality of reaction sites is at least 40,000 reaction sites.

10. The method of claim 1 , wherein the relative data quality of the first and second data visualizations is indicated by differing colors depicted in the positional representations of the plurality of reaction sites from at least the portion of the substrate.

11. The method of claim 1 , wherein reactions sites comprising quality values below the initial quality value threshold in the first data visualization and the adjusted quality value threshold in the second data visualization are depicted with a first color and reaction sites comprising quality value above the initial quality value threshold in the first data visualization and the adjusted quality value threshold in the second data visualization are depicted with a second color.

12. The method of claim 1 , further comprising displaying on the GUI a third data visualization comprising another positional representation of the plurality of reaction sites from at least the portion of the substrate, wherein the positional representation of the third data visualization indicates presence or absence of the target product for each of the plurality of reaction sites from at least the portion of the substrate.

13. A biological analysis system, the system comprising:
a processor; and
a memory encoded with instructions to:
generate data quality values for emission data from a plurality of reaction sites on a substrate, the emission data indicating presence or absence of a target product of a biological assay reaction at the plurality of reaction sites,
set a quality value threshold to an initial quality value threshold,
display, on a graphical user interface (GUI), a first data visualization comprising a positional representation of the plurality of reaction sites from at least a portion of the substrate, wherein the positional representation of the first data visualization simultaneously indicates relative data quality of the plurality of reaction sites of the at least the portion of the substrate based on a comparison of the data quality values of the plurality of reaction sites from at least the portion of the substrate to the initial quality value threshold,
display, on the GUI with the first data visualization, an interactive tool, the interactive tool being manipulatable to adjust the initial quality value threshold to an adjusted quality value threshold,
receive, via the interactive tool, a selection of the adjusted quality value threshold, and
in response to receiving the selection of the adjusted quality value threshold, dynamically alter the first data visualization to a second data visualization, the second data visualization comprising the positional representation of the plurality of reaction sites from the at least the portion of the substrate, wherein the positional representation of the second data visualization simultaneously indicates relative data quality of the plurality of reaction sites from at least the portion of the substrate based on a comparison of the data quality values of the plurality of reaction sites and the adjusted quality value threshold.

14. The system of claim 13 , wherein the emission data comprises fluorescence data.

15. The system of claim 13 , wherein the emission data indicating presence or absence of a target product of a biological assay reaction comprises emission data indicating presence or absence of one or more amplified target nucleic acid products of a polymerase chain reaction.

16. The system of claim 13 , wherein the memory is further encoded with instructions to display the first and second data visualizations such that reactions sites comprising quality values below the initial quality value threshold in the first data visualization and the adjusted quality value threshold in the second data visualization are depicted with a first color and reaction sites comprising quality value above the initial quality value threshold in the first data visualization and the adjusted quality value threshold in the second data visualization are depicted with a second color.

17. The system of claim 13 , wherein the first and second data visualizations compri

Assignees

• Life Technologies Corp

Inventors

• Leong Harrison
• Majumdar Nivedita Sumi
• Marks Jeffrey A
• Straub Theodore E
• Talbot Ryan J
• Bodner Kevin S
• Hoard David

Classifications

• G06T11/23

  using straight lines or curves · CPC title

• G06T11/26 Primary

  Drawing of charts or graphs · CPC title

• G16B25/20 Primary

  Polymerase chain reaction [PCR]; Primer or probe design; Probe optimisation · CPC title

• G16B45/00

  ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks · CPC title

• G06T11/206 Primary

  Physics · mapped topic