Extended Data Fig. 8: TERT cis-activation by somatic non-coding variants in neuroblastoma.
From: Discovery of regulatory noncoding variants in individual cancer genomes by using cis-X
The analysis was based on 90 NBL primary tumor samples with matching RNA-seq and WGS from TARGET, 42 of which had positive immune cell infiltration signature based on prior analysis (Ma et al, Nature, 2018). (a) Samples with somatic copy number alterations (CNA, marked by red or blue blocks) or/and structural variations (SVs, marked by circles) at TERT locus. All except for one (PARAMT, marked #) were detected by cis-X as cis-activated candidates. Samples marked with * have immune cell infiltration signature. Samples highlighted in gray are used to illustrate allele-specific expression (ASE) below. (b) Examples of ASE detected in neuroblastoma with or without infiltrating immune cells. Variant allele fraction in DNA (by WGS) and RNA (by RNA-seq) of SNPs, depicted as bar graph, demonstrates that ASE analysis is not affected by the presence of immune cell infiltration signature in tumor samples.
