Figure 2.

In the BRCA2-Deficient Tumors, both sSNVs and Indels Had Distinctive Characteristics

(A) Tumors without biallelic BRCA2 mutations had nearly twice as many C>T sSNVs than any other substitution. C>T transitions represented a significantly smaller proportion of the substitutions in BRCA2-deficient tumors (Student’s t test p value = 0.0015).

(B) This signal is driven by a predilection in BRCA2-intact tumors for C>T substitutions within specific trinucleotide sequence contexts, particularly ACG, CCG, CCG, or TCT, where “C” is the substituted base.

(C) This pattern was absent in the three BRCA2-mutated tumors, which instead had closer to equal likelihood of each substitution and each trinucleotide sequence context.

(D) HR-competent tumors acquired somatic insertions and deletions at roughly the same rate, and these were overwhelmingly short, with 63.1% spanning a single base.

(E) In the setting of BRCA2 deficiency, deletions were more common than insertions and long deletions were common, accounting for more than 30% of all somatic indels in these tumors.

For all panels with error bars, these represent the standard deviation from the mean of all samples in that category.