Fig. 1: Reciprocal pairs are enriched in BRCA1d and BRCA2d tumours.
From: Long-molecule scars of backup DNA repair in BRCA1- and BRCA2-deficient cancers
a, Schematic of exact and near reciprocality, using translocations as an example. Exactly reciprocal junctions link break ends that adjoin the same break point (schematic on the right), giving rise to a balanced translocation. Near-reciprocal junctions are associated with a gap segment (dark blue) that is lost (middle left) or gained (right examples). The gap segment polarity refers to whether the adjoining junctions connect to the gap segment (+ polarity; right two examples) or to its adjacent segments (− polarity, middle left example). The polarity determines whether there is a copy gain (+) or loss (− polarity) of the gap segment. Both (−) and (+) gap segments can give rise to quasi-balanced translocations; however, (+) gap segments are also equally consistent with a templated insertion (right). CN, copy number. b, Gap segment lengths and polarities of three canonical reciprocal pair patterns (right) plotted across BRCA1d, BRCA2d or HRP cases (left). Density is calculated as a Gaussian kernel normalized by the number of BRCA1d (n = 9), BRCA2d (n = 23) or HRP (n = 251) cases in each plot. c–e, Examples of rDups (c), rDels (d) and rDelDups (e) with violin plots showing their relative burdens across 15 BRCA1d, 13 BRCA2d and 236 HRP samples, which are independent from the data in b. P values obtained by Wald test on a gamma-Poisson regression model. f, Distribution of junction spans associated with different classes of reciprocal pair SVs. Note that junction span is distinct from gap segment length; the former refers to the genomic distance between the two break ends belonging to a junction, whereas the latter refers to the distance between reciprocal break ends belonging to distinct junctions.
