Predicting total nucleic acid yield and dissection boundaries for histology slides
A method for qualifying a specimen prepared on one or more hematoxylin and eosin (H&E) slides by assessing an expected yield of nucleic acids for tumor cells and providing associated unstained slides for subsequent nucleic acid analysis is provided.
1. A computer-implemented method for predicting an expected yield of nucleic acid from tumor cells within a dissection boundary on a histology slide, the method comprising:
receiving a digital image of the histology slide at an image-based nucleic acid yield prediction system having one or more processors;
identifying, using the one or more processors, tumor cells of the histology slide from the digital image using a trained cell segmentation model, wherein the trained cell segmentation model is a pixel-resolution three-dimensional classification model trained to classify a cell interior, a cell border and a cell interior, and defining a dissection boundary of the histology slide and corresponding to the identified tumor cells; and
predicting, using the one or more processors, the expected yield of nucleic acid for the tumor cells within the dissection boundary by providing the digital image to a machine learning model trained on images of a plurality of histology slides having labeled dissection boundaries and labeled total nucleic yield, the plurality of histology slides associated with imaging features.
2. The method of claim 1 , wherein the imaging features comprises tumor shape features, cell shape features, and/or cell texture features.
3. The method of claim 1 , wherein the imaging features comprises tumor shape features in the form of tumor area, tumor perimeter, tumor circularity, tumor density, and/or number of tumors.
4. The method of claim 1 , wherein the imaging features comprises cell shape features in the form of cell area, cell perimeter, cell circularity, and/or cell density.
5. The method of claim 1 , wherein the imaging features comprises cell texture features in the form of RGB texture patterns, grayscale texture patterns, gradient and/or features.
6. The method of claim 1 , further comprising:
accepting an associated unstained slide of the histology slide for next-generation sequencing when the predicted expected yield of nucleic acid exceeds a minimum threshold.
7. The method of claim 6 , wherein the minimum threshold is 50 ng.
8. The method of claim 1 , wherein when the predicted expected yield of nucleic acid fails to satisfy a target total nucleic acid yield:
identifying a number of associated unstained slides that satisfies the target total nucleic acid yield; and
accepting the number of associated unstained slides for next-generation sequencing.
9. The method of claim 8 , wherein the target total nucleic acid yield is selected from a range between and including 50 ng-2000 ng.
10. The method of claim 8 , wherein the associated unstained slides are flagged for scrapping.
11. The method of claim 8 , wherein the associated unstained slides comprise tissue from the same formalin-fixed paraffin embedded specimen.
12. The method of claim 8 , further comprising superimposing, using a viewer, the dissection boundary mask over the digital image of the associated unstained slides to visually indicate to a user which tumor cells to scrape.
13. The method of claim 8 , further comprising:
generating a tumor area mask that defines the dissection boundary by providing the digital image of the histology slide to a model trained on a plurality of histology slide having dissection labels.
14. The method of claim 13 , wherein a viewer superimposes the tumor area mask over the digital image to visually indicate to a user which tumor cells to scrape.
15. The method of claim 1 , wherein predicting the expected yield of nucleic acid for the tumor cells within the dissection boundary further comprises:
counting the number of tumor cells identified within the dissection boundary and multiplying the count by a tumor cell average nucleic acid yield and adjusting to account for the identified imaging features.
16. The method of claim 1 , wherein predicting the expected yield of nucleic acid for the tumor cells within the dissection boundary further comprises:
calculating the surface area of the dissection boundary and multiplying the surface area by a dissection boundary average nucleic acid yield and adjusting to account for the identified imaging features.
17. The method of claim 1 , wherein identifying tumor cells of the histology slide from the digital image using the trained cell segmentation model comprises:
applying, using the one or more processors, a plurality of tile images formed from the digital image to the trained cell segmentation model and, for each tile, assigning a cell classification to one or more pixels within the tile image.
18. The method of claim 17 , wherein assigning the cell classification to one or more pixels within the tile image comprises:
identifying, using the one or more processors, the one or more pixels as a cell interior, a cell border, or a cell exterior and classifying the one or more pixels as the cell interior, the cell border, or the cell exterior.
19. A computing device configured to predict an expected yield of nucleic acid from tumor cells within a dissection boundary on a histology slide, the computing device comprising:
one or more memories; and
one or more processors configured to,
receive a digital image of the histology slide at an image-based nucleic acid yield prediction system having one or more processors;
identify, using the one or more processors, tumor cells of the histology slide from the digital image using a trained cell segmentation model, wherein the trained cell segmentation model is a pixel-resolution three-dimensional classification model trained to classify a cell interior, a cell border and a cell interior, and defining a dissection boundary of the histology slide and corresponding to the identified tumor cells; and
predict the expected yield of nucleic acid for the tumor cells within the dissection boundary by providing the digital image to a machine learning model trained on images of a plurality of histology slides having labeled dissection boundaries and labeled total nucleic yield, the plurality of histology slides associated with imaging features.
20. A computer system for predicting an expected yield of nucleic acid from tumor cells within a dissection boundary on a histology slide, the computer system comprising one or more processors configured to:
receive a digital image of the histology slide at an image-based nucleic acid yield prediction system having one or more processors;
identify, using the one or more processors, tumor cells of the histology slide from the digital image using a trained cell segmentation model, wherein the trained cell segmentation model is a pixel-resolution three-dimensional classification model trained to classify a cell interior, a cell border and a cell interior, and define a dissection boundary of the histology slide and corresponding to the identified tumor cells; and
predict the expected yield of nucleic acid for the tumor cells within the dissection boundary by providing the digital image to a machine learning model trained on images of a plurality of histology slides having labeled dissection boundaries and labeled total nucleic yield, the plurality of histology slides associated with imaging features.