Nature research paper: ERα-associated translocations underlie oncogene amplifications in breast cancer
. An exemplary case of multi-chromosomal chromothripsis . The SVs are distributed more-or-less evenly in the involved chromosomes without sparing one arm.. Chromosomes showing typical features of chromothripsis. The SVs are distributed evenly on two chromosome arms, and the rearrangements are more-or-less random, in contrast to the asymmetric footprint of TB amplification.a
. ‘Dual-LOH’ pattern of the bridge arms in the tumors with TB amplification. Both bridge arms in each case show substantial loss of heterozygosity . Notably, the bridge arm segments proximal to the TB amplification often show complex copy-number pattern with segmental loss or gain by one copy. This is likely due to the unequal breakpoints between the sister dicentrics. Depending on the location of the break, some segments can be duplicated or lost in a daughter cell after the bridge resolution..
. Replication timing and amplification boundaries. Violin plots show the replication timing weighted average values in 100-Kbp bins. The box plot in the center of the violin indicates median , first and third quartiles , and 1.5× of interquartile range . Comparisons were made by one-sided Wilcoxon’s rank sum test.. Fraction of 100-Kbp bins overlapping with various epigenomic features in the background and in the recurrent hotspots of amplification boundaries .
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