Biological data annotation and visualization

Patent metadata

Field	Value
Publication number	US-2016357905-A1
Application number	US-201514730032-A
Country	US
Kind code	A1
Filing date	Jun 3, 2015
Priority date	Jun 3, 2015
Publication date	Dec 8, 2016
Grant date	—

Abstract

Identification of regions-of-interest within cell maps is disclosed. In certain embodiments, identification of the regions-of interest is based on the use of biomarkers selected based on nucleic acid sequence data. The nucleic acid sequence data may be acquired for a homogeneous or heterogeneous set of cells present in the respective tissue sample.

First claim

1 . A method for interactively evaluating image and data for a tissue sample, comprising:
acquiring nucleic acid sequence data for a portion of a tissue sample; selecting a plurality of probes based on the nucleic acid sequence data; generating a cell map comprising an image of the tissue sample on which biomarker expression data generated using the selected probes is displayed; and identifying one or more spatially localized regions-of-interest within the cell map, wherein the regions-of-interest correspond to spatial locations of cells expressing targets of the probes selected based on the nucleic acid sequence data.

2 . The method of claim 1 , wherein selecting the plurality of probes is part of a gene set enrichment analysis performed on the nucleic acid sequence data.

3 . The method of claim 1 , wherein the nucleic acid sequence data is acquired for a tumor, lesion, or abnormality within the tissue sample.

4 . The method of claim 1 , wherein the nucleic acid sequence data comprises mutation information associated with a subset of cells of the tissue sample.

5 . The method of claim 1 , wherein the nucleic acid sequence data is acquired from a homogeneous sample derived from a localized region within the tissue sample.

6 . The method of claim 1 , wherein the nucleic acid sequence data is acquired from a heterogeneous sample derived from the tissue sample without a spatial context linked to the tissue sample.

7 . The method of claim 1 , wherein the plurality of probes comprise labeled or tagged antibodies.

8 . The method of claim 1 , wherein the nucleic acid sequence data is specific to a sequencing region taken from the tissue sample.

9 . The method of claim 1 , wherein the cell map comprises a multiplexed image of the tissue sample.

10 . The method of claim 1 , further comprising:
acquiring additional nucleic acid sequence data for the one or more spatially localized regions of interest; selecting additional probes based on the additional nucleic acid sequence data; generating an updated cell map comprising an updated image of the tissue sample exposed to the additional probes; and identifying one or more additional regions-of-interest within the updated cell map, wherein the additional regions-of-interest correspond to spatial locations of cells expressing targets of the probes selected based on the additional nucleic acid sequence data.

11 . A method for interactively evaluating image and data for a tissue sample, comprising:
acquiring sequence data for one or more mutations present in a tissue sample; selecting a plurality of immunofluorescent (IF) probes based on the sequence data; generating one or more multiplexed images of the tissue sample using the plurality of IF probes; identifying one or more regions-of-interest within the one or more multiplexed images based on the presence of the IF probes.

12 . The method of claim 11 , wherein the sequence data is acquired for spatially localized regions of the tissue sample.

13 . The method of claim 11 , wherein the sequence data is acquired for a homogeneous cell mixture derived from the tissue sample.

14 . The method of claim 11 , wherein the plurality of IF probes represent a limited subset of available probes.

15 . The method of claim 11 , wherein the one or more identified regions-of-interest correspond to the spatial locations of the one or more mutations within the tissue sample.

16 . A processor-based system, comprising:
one or both of a memory or storage device storing one or more executable routines for the analysis of region-specific nucleic acid sequence data and cellular or sub-cellular biomarker data; one or more processors configured to execute the one or more executable routines which, when executed, cause acts to be performed comprising:
generating a cell map comprising an image of a tissue sample exposed to a plurality of probes, wherein the plurality of probes are selected based on sequence data acquired for the tissue sample; and
displaying one or more fields-of-view within the cell map, wherein the fields-of-view displays cells exhibiting one or more mutations associated with the sequence data.

17 . The processor-based system of claim 16 , wherein the one or more executable routines, when executed, perform a gene set enrichment analysis on the sequence data as part of the selection of the plurality of probes.

18 . The processor-based system of claim 16 , wherein the sequence data is acquired for a tumor, lesion, or abnormality within the tissue sample.

19 . The processor-based system of claim 16 , wherein the plurality of probes comprise labeled or tagged antibodies.

20 . The processor-based system of claim 16 , wherein the sequence data is specific to a sequencing region taken from the tissue sample.

Assignees

• Gen Electric

Inventors

• Sarachan Brion Daryl
• Graf John Frederick
• Gerdes Michael John

Classifications

• G16B45/00 Primary

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

• G16B25/00

  ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression · CPC title

• C12Q1/6841

  In situ hybridisation · CPC title

• G01N21/6428

  Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes" (in vivo A61B5/00; immunoassay G01N33/53) · CPC title

• G01N21/6486

  Measuring fluorescence of biological material, e.g. DNA, RNA, cells (G01N21/6428 takes precedence) · CPC title