Extended Data Fig. 1: Additional information on different types of SCNA and the BISCUT method.
From: Cancer aneuploidies are shaped primarily by effects on tumour fitness
(a) Empirical examples of low centromeric mechanical bias (1q telomere-bounded deletions, for which the ratio of breakpoints occurring in the centromere over those occurring in the arm is less than 1), and high centromeric mechanical bias (5p telomere-bounded amplifications, for which the centromere/arm breakpoint ratio is much greater than 1). Within the chromosome arm, bins are 1 Mb large. (b) Mean amplification and deletion breakpoint density within chromosome arms, aggregated across all tumors and all chromosome arms (n = 67; binned by Mb), versus breakpoint density within all centromeres (values in breakpoints per megabase). Error bars represent the 95% confidence interval for the mean. C/A Ratio represents centromeric breaks over arm breaks. (c) Comparison of length distributions of telomere-bounded, centromere-bounded, and interstitial amplifications and deletions, aggregated across all chromosome arms. (d) Example depicting BISCUT’s recursion steps. From top to bottom: BISCUT detects peaks iteratively, walking both left and right if a significant peak is detected, with the new boundaries including the detected peak. If a peak is not detected, overlaps with a previous peak, or there are fewer than 4 samples, the analysis is stopped. See Fig. 2c and Methods for details.
