Fig. 2: Overview tumor characteristics.

a Allelic imbalance (AI) segments in SNP-array data. From top-down, examples of chromosome 1 B-allele frequencies (BAF), mirrored BAF (mBAF) and Log R Ratios (LRR). Bottom, a schematic figure of the interpretation of the segments: black horizontal lines represent AI segments. Blue horizontal line represents LRR threshold −0.15. Blue dots represent the calculated breakpoints: I. When AI segment is at the end of the chromosome, only one breakpoint is counted for. II. If the LRR difference between adjacent copy-number segments is <0.1, the segments are considered contiguous and are counted as only two breakpoints. III. When the segment is not at the chromosome end and the LRR difference between both adjacent segments is >0.1, two breakpoints are calculated. b Typical allelic imbalance patterns in ULs. Representative examples of complex chromosomal rearrangement (CCR) patterns in different ULs. Only chromosomes affected by allelic imbalance changes are shown: Top: the majority of tumors with high breakpoint count are from tumors wild type (WT) for known MED12 mutations. Translocations between chr12 (HMGA2) and chr14 (RAD51B) are common. Middle: chromosomal rearrangements seen in MED12 tumors are typically more moderate. Bottom: whole-chromosome losses were predominantly detected in parous patients’ WT tumors. Blue line: deletion, green line: insertion, purple line: inversion, red line: duplication, black line: translocation, blue box: LOH/Loss, red box: Gain. c Average breakpoint number, total length of loss regions, total length of gain regions, and the combined length of loss and gain regions are presented for tumors from parous and nulliparous patients. The results are presented for all 1935 tumors (purple) and separately for MED12 (salmon) and WT (turquoise) tumors. 95% bootstrap confidence intervals are presented for the mean. In all comparisons, the mean length of tumor genome AI regions is higher in parous than nulliparous patients. Source data are provided.