Strategies for analyzing spatial single cell data
Abstract/Contents
- Abstract
- There are multiple levels of heterogeneity within the tumor microenvironment from molecular heterogeneity, to heterogeneity in cellular populations. This heterogeneity is a major factor in differentiating tumors that progress from those that will remain indolent. One critically understudied aspect of heterogeneity in the tumor microenvironment is spatial context. Specifically, leveraging where cells are located and what is surrounding them in the tissue, to better understand tumor progression. While the number of studies profiling cancer through the lens of spatially constrained phenomena is growing, there is a lack of structure to which analyses adhere. As a result, assumptions made are often not clearly detailed, it is difficult to compare and contrast between study methodologies, and important tumoral contexts are often not considered. To this end I have 1) identified and defined four paradigms for the analysis of spatial single cell data; 2) framed spatial interactions in a tumor ecology context; 3) developed an algorithm to identify tumor level contexts; and 4) applied this algorithm to identify differential tumor responses to a hypoxic context and developed a novel spatial biomarker. This work helps to frame cancers as systems and tumoral phenomena as spatially-constrained contexts to better leverage spatial information to discriminate between tumors that will progress from those that remain indolent.
Description
| Type of resource | text |
|---|---|
| Form | electronic resource; remote; computer; online resource |
| Extent | 1 online resource. |
| Place | California |
| Place | [Stanford, California] |
| Publisher | [Stanford University] |
| Copyright date | 2021; ©2021 |
| Publication date | 2021; 2021 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Author | Boyce, Hunter Bryan |
|---|---|
| Degree supervisor | Altman, Russ |
| Degree supervisor | Mallick, Parag, 1976- |
| Thesis advisor | Altman, Russ |
| Thesis advisor | Mallick, Parag, 1976- |
| Thesis advisor | Gentles, Andrew J |
| Thesis advisor | West, Robert, (Data scientist) |
| Degree committee member | Gentles, Andrew J |
| Degree committee member | West, Robert, (Data scientist) |
| Associated with | Stanford University, Department of Biomedical Informatics |
Subjects
| Genre | Theses |
|---|---|
| Genre | Text |
Bibliographic information
| Statement of responsibility | Hunter Bryan Boyce. |
|---|---|
| Note | Submitted to the Department of Biomedical Informatics. |
| Thesis | Thesis Ph.D. Stanford University 2021. |
| Location | https://purl.stanford.edu/zm021bj6916 |
Access conditions
- Copyright
- © 2021 by Hunter Bryan Boyce
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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