Fig. 5

Allelic imbalance is detectable in spatial transcriptomics data. A, B We counted the number of reads mapping to each allele of heterozygous SNPs from each spot. To identify SNPs with mono-allelic expression, we plotted the fraction of reads mapping to each allele as a function of total read coverage. As expected, the reads from genes with low expression often came from one allele; however, genes with high expression tended to express both alleles with a notable exception highlighted in B–D. A SNPs from chromosomal arm 3q of tumor spots, for which there was loss of heterozygosity evident in tumor DNA sequencing data (see Additional file 2: Fig. S1B). B A SNP from the immunoglobulin heavy chain (IGH) locus at chromosome 14q32 in which expression favors one allele. C DNA and RNA sequencing read alignments surrounding the IGH SNP. A total of three heterozygous SNPs occurred in this region. Note the heterozygosity in the DNA sequencing data, while the RNA sequencing data shows mono-allelic expression at all three sites. D Spots with greater than 25 × coverage and > 90% of reads mapping to the minor allele of the IGH SNP are projected onto the tissue, where they tend to overlie immune cells