Table 3.

Antigens, Primary Antibodies, Clone, Source, Optimal Dilution, and Scoring System Used for Each Immunohistochemical Marker

Antigen	Antibody	Clone	Source	Antigen retrieval	Dilution/incubation time	Distribution	Scoring system	Cut-offs
ER	Mouse MAb anti-ERα	SP1	Dako-Cytomation	Citrate pH6	1:150	Nuclear	Allred score	≥3 (Positive)
					30 min
ER	Mouse MAb anti-ERα	EP1	Dako-Cytomation	Citrate pH6	1:80	Nuclear	% Positive cells	≥1% (Positive)
					30 min
PR	Mouse MAb anti-PR	PgR636	Dako-Cytomation	Citrate pH6	1:125	Nuclear	% Positive cells	≥1% (Positive)
					30 min
HER2	Rabbit antihuman c-erbB2	Polyclonal	Dako-Cytomation	None	1:400	Membrane	See text	See text
					60 min
BRCA1	BRCA1	MS110	Calbiochem	Citrate pH6	1:100	Nuclear	% of positive cells	<25% (Negative)
					60 min
ATM	Rabbit MAb anti-ATM	Y170	Abcam	Citrate pH6	1:100	Nuclear	% of positive cells	<25% (Negative)
					18 h
ATR	Mouse MAb Anti-ATR	1E9	Novus Biologicals	Citrate pH6	1:20	Nuclear	H-score	≥60 (High)
					18 h
Chk2	Rabbit polyclonal anti-Chk2	Ab47433	Abcam	Citrate pH6	1:100	Nuclear	H-score	≥100 (High)
					60 min
pChk1	Rabbit anti-pChk1	Ab58567	Abcam	Citrate pH6	1:140	Nuclear	H-score	≥50 (High)
					60 min
DNA-PKcs	Mouse MAb Anti-	3H6	Abcam	Citrate pH6	1:1000	Nuclear	H-score	>260 (High)
					20 min
PARP1	Mouse MAb Anti-PARP1	7D3-6	BD Pharmingen	Citrate pH6	1:1000	Nuclear	% of positive cells	≥10% (Positive)
SMUG1	goat MAb anti-SMUG1		Acris Antibody GmbH	Citrate pH6	1/200	Nuclear	H-score	>35 (Positive)
					15 min
APE1	Rabbit polyclonal anti-APE1	NB100-101	Novus Biologicals	Citrate pH6	1:500	Nuclear	H-score	≥100 (Positive)
					60 min
XRCC1	Mouse MAb Anti-XRCC1	33-2-5	Thermo Scientific	Citrate pH6	1:200	Nuclear	% of positive cells	≥10% (Positive)
					20 min
FEN1	rabbit polyclonal anti-FEN1	NBP1-67924	Novus Biologicals	Citrate pH6	1:200	Nuclear	H-score	≥100 (Positive)
					15 min
TOP2A	Mouse MAb	KiS1	Dako-Cytomation	Citrate pH6	1:150	Nuclear/cytoplasmic	% of positive cells	>25% (Positive)
p53	Mouse MAb anti p53	DO7	Novocastra	Citrate pH6	1: 50	Nuclear	% of positive cells	≤20% (Negative)
					60 min			>20% (High)
Ki67	Mouse MAb anti-Ki-67	MIB1	Dako-Cytomation	Citrate pH6	1:300	Nuclear	% of positive cells	<10% (Low)
								10%–30% (Moderate)
								>30% (High)

ATM, ataxia telangiectasia mutated; ATR, ataxia telangiectasia mutated and Rad3 related; BRCA1, breast cancer susceptibility gene 1; DNA-PKcs, DNA-dependent protein kinase catalytic subunit; ER, estrogen receptor; PARP1, poly (ADP-ribose) polymerase 1.