Extended Data Fig. 3: Validation of inferred single cell CNV profiles and impact on marker gene expression. | Nature Cancer

Extended Data Fig. 3: Validation of inferred single cell CNV profiles and impact on marker gene expression.

From: Gradient of Developmental and Injury Response transcriptional states defines functional vulnerabilities underpinning glioblastoma heterogeneity

Extended Data Fig. 3

a, Spearman correlation between inferred scRNA-seq CNV score from averaged intra-GSC clusters (left; n = 56 clusters from 20 GSC cultures) or averaged samples (right; n = 20 GSC cultures) and log2 ratios from matched genes from WGS of GSC samples (n = 20 GSC cultures). Each point represents a gene within a given sample. b, Distribution of InferCNV scores for genes labelled as deletion (<0; n = 11,617 genes), neutral (0; n = 100,426 genes) or amplified (>0; n = 12,777 genes across) by GISTIC from corresponding WGS data. Gene counts per GISTIC CNV state represent a cumulative number of genes across 20 GSCs. Median scores for deletions (-0.15) and gains (0.17) used as cut offs to classify InferCNV scores as at least single copy gains or losses. Box plots within the violin plot represent the median, upper and lower quartiles of the distribution and whiskers represent 1.5-times interquartile range. Tips of the violin plot extend to the minimum and maximum values of the distribution. c, Visualization of single cell CNV calls averaged by intra-GSC cluster (denoted “_C#”), averaged by sample (“SampleAverage”) or results of matched WGS (“_WGS”). Samples (rows separated by solid lines) ordered by increasing cluster number. WGS CNV track below dashed line. Sample average above dashed line and cluster transcriptional profiles represent remaining rows. d, Binary heat map depicting chromosome arms (y-axis; sorted by genomic position) that are gained (red), deleted (blue) or copy-neutral (white) across intra-GSC clusters (x-axis; ordered alphabetically; n = 86 clusters from 29 GSC cultures). e, Proportion of cluster marker genes located within a variable CNV loci (y-axis) across intra-GSC clusters (x-axis; n = 69 clusters) from samples with variable cluster CNV profiles (n = 22 GSC cultures) as determined in Extended Data Fig. 3d. Clusters with significant (Fisher’s Exact Test p < 0.05) enrichment of marker genes within variable CNV loci are colored dark blue.

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