Weighted genome instability index (wGII) analysis

To assess chromosomal instability, the weighted Genome Instability Index (wGII) was calculated using segmentation files [55]. First, the ploidy of each tumor was assigned as the median copy number accounting for the length of segments. For each chromosome, GII was calculated as the fraction of the genome presenting aberrant copy numbers (differing more than 0.3) relative to baseline ploidy. The wGII of the tumor was calculated as the mean fraction of aberration across all 22 chromosomes, such that all chromosomes influence the score equally regardless of size. The association between genetic ancestry and wGII was evaluated using a linear regression model where the dependent variable was wGII and the independent variable was AA status (AA as 1 and EA as 0), adjusting for the propensity score.