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Table 1 Somatic alterations by region in breast cancer re-sequence analysis

From: Somatic sequence alterations in twenty-one genes selected by expression profile analysis of breast carcinomas

Gene

Nonsynonymous

Synonymous

5'

IVS

3'

Indel

TP53a

R110P, F113V, A138V (2), Y163C, Y163H, H193T, I195T, V216M, S241A, R249M, I251S, D259Y, R273C (3)

  

IVS1+75A>G

IVS6-2A>G

IVS7-1G>T

 

7 bp @ G286

22 bp @ L189

GATA3a

R366X, R366L

  

IVS2-281C>G

Ex5+311C>G

CA @ IVS3-3

A @ T315

CAV1

 

D143D

-2768A>C

-1446T>A

-596A>G

 

Ex3-3G>C

 

CDH1

D777N

M282I (2)

A563A

 

IVS3+128T>C

IVS3+260A>G

IVS7+47T>C

IVS7+2049T>A

IVS8-175G>A

 

CCGG @ Ex3+19

A @ Ex345

G @ Ex7+15

AAGT @ IVS13+3

ESR1

H6Y

M264I

 

Ex1+139G>C

 

Ex8+2144T>A

 

FBXW7

E117K

  

IVS1-1641A>C

  

FOXA1

  

-3717G>A

   

FOXC1

  

-2713G>T

-1770C>T

 

+936G>A

+940G>A

 

FZD7

 

L23L

L26L

G409G

-1387G>C

   

MYBL2

   

IVS7+15A>G

IVS8-14C>G

IVS12+28G>C

  

PIN1

 

S38S

 

IVS2+3447G>A

IVS2+3419G>A

IVS2+3370T>C

  

RB1CC1

R1514C

S1424S

L1511L

-31467C>A

-30224C>G

IVS1+5248T>G

IVS1+6068A>G

IVS11+97T>C

IVS11-36C>T

IVS15+1535C>G

IVS21-16G>A

  

RERG

  

Ex1+63G>T

IVS2+27438T>G

IVS2-30415C>T

 

CTTdel @ IVS2-7163

STK6 b

 

A172A

E175E

 

IVS4-35A>G

IVS9-33A>G

  

TP53I3

M180K

P102P

    

XBP1

R232K

 

-2339G>C

IVS4-11G>A

  
  1. Eighty-seven unique somatic alterations were identified by sequence analysis in 16 of 21 genes analyzed (TP53, GATA3, CAV1, CDH1, ESR1, FBXW7, FOXA1, FOXC1, FZD7, MYBL2, PIN1, RB1CC1, RERG, STK6, TP53I3, and XBP1). No somatic alterations were detected in five genes (CDK5, NQO1, PIM1, PLK1, and RARRES3). All alterations were observed singly in bidirectional sequence analysis; numbers in parentheses indicates the number of unique tumor samples with somatic alterations. Intronic analysis restricted to regions including 100 bp on either side of exonic junctions and evolutionarily conserved regions between mouse and human (>75% similarity over 200 bp). aMost of the nonsynonymous mutations and deletions in TP53 and GATA3 were previously reported [4,19]. bIn the analysis of STK6 (also known as STK15), additional alterations were observed at six sites within the target 5' region but lie in the adjacent gene CSTF1 (-7698C>T, -7648A>G, -7105C>T, -5992A>G, -4868A>G, and -4221G>A). None of the variants result in nonsynonymous alterations in the coding region of CSTF.
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Breast Cancer Research

ISSN: 1465-542X

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