Supplementary Table 1
Gene Variant New in
Breast CA
Freq (#) COSMIC ID Percent of total aberrations (%)**
Targetable Rx
EGFR Amplification 1 N/A 1% +
PTEN Deletion/LOH 1 1% +
APC S1465R + 1 26699 1% +
APC A1358V + 1 1541289 1% +
ATM V410A + 2 1% +
BRAF G469A + 1 460 1% +
BRAF G596S + 1 27560 1% +
CDH1 Q346* 1 19524 1%
CDH1 D367fs*26 + 1 1%
HER2(ERBB2) Amplification 2 N/A 2% +
HER2(ERBB2) V777M + 1 14064 1% +
ERBB4 Q598K + 1 1% +
ERBB4 K137N + 1 1% +
FGFR1 Amplification 3 3% +
FGFR3 F384L + 1 724 1% +
JAK3 V722I + 2 34213 2% ? (unlikely)
VEGFR2(KDR) Q472H + 21 149673 21% ??
KIT M541L + 7 28026 7% ? (unlikely)
KRAS G12D 1 521 1% +
KRAS Q61K + 1 549, 87298 1% +
MET M362T + 1 1% ? (unlikely)
MET N375S + 2 2% ? (unlikely)
PIK3CA E542K 5 760 5% +
PIK3CA E545K 2 763 2% +
PIK3CA Q60K 1 12579 1% +
PIK3CA H1047R 5 775 5% +
PIK3CA N345K 1 754 1% +
PIK3CA I139M + 4 4% +
PIK3CA E453K 1 12584 1% +
PIK3CA Q546R 1 12459 1% +
SMO A401V + 1 1%
STK11 F157Lfs*8 + 1 1% +
STK11 F354L 1 21360 1% +
STK11 R331Q + 1 1% +
TP53 R273H 1 10660 1%
TP53 F338fs*7 1 1%
TP53 R342* 2 11073 2%
TP53 P72R 17 250061 N/A: Common
polymorphism
TP53 F109_R110dup + 1 1%
TP53 E285K 1 10722 1%
TP53 F134C 1 43949 1%
TP53 R175H 1 10648 1%
TP53 Y163H + 1 43846 1%
TP53 H193R 1 10742 1%
TP53 I195T 2 11089 2%
Supplementary Table 1
Gene Site New in
Breast CA
Freq (#) COSMIC ID Percent of total aberrations (%)
Targetable RX
TP53 R213* 1 10654 1%
TP53 R248W 3 10656 3%
TP53 Y234C 1 10725 1%
TP53 E285K 1 10722 1%
TP53 E294* 1 10856 1%
TP53 E298* 1 10710 1%
TP53 V272E + 1 44580 1%
TP53 C135fs*35 + 1 1%
TP53 C176W + 1 11114 1%
VHL Amplification + 1 N/A 1%
TOTAL n= 58/102** n= 119 42/102**
(57%) (41%)
** Excluding TP53 P72R (n=17), classified as VUS, but known to be a common polymorphism (SNP), has now been shown to have no association to breast cancer risk/biology.
SNPs (Single Nucleotide Polymorphisms) or possible SNPs are boxed in red. These were all classified among VUS and further characterized as follows:
- JAK3 V722I: dbSNP rsID = rs3213409; PolyPhen2 Class:score = benign: 0.001
- KDR/VEGFR2: dbSNP rsID = rs1870377; PolyPhen2 Class:score = possibly-damaging: 0.955 - KIT M541L: dbSNP rsID = rs3822214; PolyPhen 2 Class:score = benign: 0.012
- MET M362T: dbSNP rsID = rs77523018; PolyPhen 2 Class:score = benign: 0.007 - SMO A410V: dbSNP rsID = rs117663825; PolyPhen 2 Class:score = unknown
- TP53 P72R: dbSNP rsID = rs104522; PolyPhen 2 Class:score = possibly damaging: 0.745
