Approach to detect chromosomal rearrangements from mate-pair genomic DNA sequencing data. (Top) schematic of bioinformatic algorithm. False-positive calls were minimized using filters based on quality of mapping, quality of nearby sequence in the reference genome, and a mask developed from noncancerous samples (see “Mate-pair data mapping and bioinformatic analysis”). Candidate abnormalities were supported by at least 4 mate pairs with reads mapping > 15 kb apart. Events were classified as recurrent abnormalities when they shared breakpoints within 1 Mb in 2 or more cases. (Bottom) numbers of read pairs or rearrangement events after executing each step of the algorithm, shown for individual cases and as the sum of all cases.