Fig. 1.

Tandem duplication phenotypes in 940 TCGA breast cancers. (A and B) TDP status was determined using genomic segments between 1 Kbp and 2 Mbp (A), or 2 Mbp and 10 Mbp (B), followed by Gaussian mixture modeling of the ratio of TDs to non-TD segments (total number of segments minus double the number of TD segments as per ref. 2). Odds ratio and P value represent Fisher’s exact test of BRCA1 mutation enrichment in the TDP subset of tumors. BRCA1 loss was defined as germ-line or somatic point mutation or deletion. TDP tumors are colored in red and non-TDP tumors in gray. All samples are denoted by an “x,” with the exception of tumors with BRCA1 loss, which are denoted by a square. (C) Bar plots illustrate the overlaps between the different TDP calling methods.