Table 1.

SMG lists for the 3 main breast cancer clinical categories from TCGA data

ER+/HER2 (n = 330)Clinical HER2+ (n = 75)Triple negative (n = 86)
GeneCases, nLRTCTCases, nLRTCTCases, nLRTCT
PIK3CA14500230095.55E-093.22E-10
TP53680041006800
GATA345008000NANA
MAP3K136002NANA0NANA
CDH130002NANA1NANA
MLL328005NANA3NANA
MAP2K419001NANA1NANA
PTEN16000NANA1NANA
RUNX115001NANA0NANA
NCOR1131.10E-054.33E-071NANA1NANA
TBX3115.74E-124.91E-120NANA1NANA
AKT1112.75E-133.94E-121NANA0NANA
CTCF116.46E-042.31E-061NANA1NANA
NF1111.09E-021.39E-021NANA2NANA
PIK3R198.44E-071.82E-064NANA1NANA
FAM47C88.08E-032.96E-021NANA0NANA
CBFB71.32E-075.10E-080NANA1NANA
SF3B172.27E-031.07E-021NANA0NANA
TBL1XR166.33E-041.83E-051NANA1NANA
ZFP36L167.14E-051.27E-040NANA1NANA
FOXA162.51E-028.19E-031NANA1NANA
TLR464.54E-022.37E-021NANA0NANA
CDKN1B54.60E-065.94E-050NANA0NANA
GPS246.98E-033.73E-021NANA1NANA
OR6A243.67E-034.32E-030NANA0NANA
OR2L241.01E-028.19E-030NANA0NANA
RB13NANA1NANA42.77E-024.64E-02
PTPN223NANA46.57E-033.36E-020NANA

NOTE: NA indicates that after statistical adjustment for background mutation rates and gene size, the given mutations observed were not considered statistically significant. The list is focused on missense, nonsense, and frameshift mutations, and small insertions and deletions (indels). Structural mutations (large deletions, inversions, translocations, and amplifications) were not taken into account. LRT refers to the likelihood ratio test and CT to the convolution test, both of which are measures of likelihood of whether observations could have occurred by chance. Data in table from Koboldt et al. (6).