Extended Data Fig. 8: Various measures of homologous recombination deficiency (HRD) across 23 cancer types in European Americans (EAs) and African Americans (AAs) from The Cancer Genome Atlas (TCGA).

HRD is quantified and presented via various scores. a, Number of (loss of heterozygosity) LOH events, (b) telomere allelic imbalance (AIL), (c) large-scale state transitions (LST), (d) scaled net sum of previous three defined as “genomic scar” and (e) mutation signature 3 contribution in AAs and EAs in various cancer types in TCGA where sample size for each cancer type is provided on the x-axis. First, cancer types are categorized by cell type or tissue of origin, if possible, where defined groups are pan-squamous (squamous cell derived tumors), pan-adeno (glandular structures in epithelial tissue derived tumors), pan-kidney (tumors originating in the kidney), and rest (referring to cancer types that cannot be categorized and includes LAML, THYM, GBM, LGG, SARC, BRCA, LIHC, OV, TCGT, THCA and UCEC; Refer here for reference to cancer types: https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/tcga-study-abbreviations). Second, additional categorization was performed based on tissue type (where solid is derived from solid tumors and neural-crest and Hema & Lymph—hematologic and lymphatic tumors). One-sided Wilcox Rank-sum test has been performed within each cancer type to test whether HRD is higher in AA than EA and significance before multiple testing correction is provided. Here, in the box plot, the center line denotes the median, the box indicates the interquartile range and the black line represents the rest of the distribution, except for points that are determined to be “outliers”, 1.5 times the interquartile range.