A Spatial Omnibus Test (SPOT) for Spatial Proteomic Data

Spatial proteomics can reveal the spatial organization of immune cells in the tumor immune microenvironment. Relating measures of spatial clustering, such as Ripley's K or Besag's L, to patient outcomes may offer important clinical insights. However, these measures require pre-specifying a...

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Bibliographic Details
Published in:Bioinformatics (Oxford, England) England), 2024-07, Vol.40 (7)
Main Authors: Samorodnitsky, Sarah, Campbell, Katie, Ribas, Antoni, C Wu, Michael
Format: Article
Language:English
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Summary:Spatial proteomics can reveal the spatial organization of immune cells in the tumor immune microenvironment. Relating measures of spatial clustering, such as Ripley's K or Besag's L, to patient outcomes may offer important clinical insights. However, these measures require pre-specifying a radius in which to quantify clustering, yet no consensus exists on the optimal radius which may be context-specific. We propose a SPatial Omnibus Test (SPOT) which conducts this analysis across a range of candidate radii. At each radius, SPOT evaluates the association between the spatial summary and outcome, adjusting for confounders. SPOT then aggregates results across radii using the Cauchy combination test, yielding an omnibus p-value characterizing the overall degree of association. Using simulations, we verify that the type I error rate is controlled and show SPOT can be more powerful than alternatives. We also apply SPOT to an ovarian and lung cancer study. An R package and tutorial is provided at https://github.com/sarahsamorodnitsky/SPOT.
ISSN:1367-4811
1367-4803
1367-4811
DOI:10.1093/bioinformatics/btae425