Figure 4: Characterization and timing of chromosome 11 and 17 LOH in paediatric ACT.

(a) Microsatellite analysis of chromosome 11p15 in the WES cohort. All cases with available parental DNA demonstrated selective loss of maternal chromosome 11p15 (n=8, purple). (b) Temporal order of chromosome 11p and 17p cn-LOH and accumulation of SNVs in SJACT002. Scatter plots show MAFs of somatic SNVs and their genomic positions (individual dots) combined with two-dimensional (2D) density plots of AI values of germline heterozygous SNPs in cn-LOH regions of chromosomes 11p (left) and 17p (centre). At right, AI values in cn-LOH regions of chromosomes 11p and 17p were compared with the MAF distribution of somatic SNVs in genome-wide cn-LOH regions. (c) A three-dimensional (3D) scatter plot summarizes the temporal order of cn-LOH of chromosomes 11p and 17p and somatic SNV accumulation in paediatric ACTs. Shown are the median AI values for the chromosome 11p cn-LOH region, the median AI values for the chromosome 17p cn-LOH region and the median MAF of SNVs in genome-wide cn-LOH regions of 14 cases; SJACT002 and SJACT005 are labelled. See also Supplementary Fig. 7b.