Within-subject and between-subject correlations in Nanostring DSP spatial genomics data

Music City Center 

The function of cytokine interactions in initiating and advancing pancreatic cancer was studied with GeoMx® dsp spatial sequencing data using PDAC FFPE samples from 15 patients in up to 5 regions of interest (ROIs) of one tumor each for two cell types: CAFs vs ductal. Usually, each ROI was exposed on two of the eight slides used. One goal is to study within-subject (across ROIs in each subject) and between-subject correlations among the expression levels between cytokines of interest and other genes. The correlations could be strong between the changes in two variables within a patient and/or among the average expression levels between patients. Challenges arise from crossed and nested effects among ROIs, slides and patients. We applied methods proposed by Bland and Altman: within-subject correlations were derived from ANCOVA with fixed effects for the subject by slide interaction, and between-subject correlations used weighted averages weighting by number of ROIs. A false discovery rate criterion was used to identify correlations. The identified correlations aligned well with previous hypotheses. This work was in part funded by NIH-P01 and the Salk Cancer Center Support Grant.

Spatial genomics

Spatial sequencing

Gene expression

Pancreatic cancer 

Biopharmaceutical Section