Extended Data Table 2.

All genes differentially expressed in low-burden metastatic cells relative to primary tumour cells

Increased expression
Gene	Normal lineage	Fold change (low-burden/T)	*P value
TGFBR2	N/A	43.0	4.8×10−12
BCL2L1	basal/stem	30.1	2.2×10−11
EPHA4	N/A	27.0	4.5×10−14
AR	luminal	21.5	7.3×10−15
LGR5	basal/stem	17.6	4.6×10−13
IGFBP6	N/A	15.7	2.4×10−8
TGFB2	basal/stem	15.7	2.4×10−15
SOX2	N/A	14.5	2.8×10−11
BMI1	basal/stem	14.0	1.1×10−28
CXCL12	N/A	13.7	8.1×10−6
TWIST1	N/A	13.4	2.5×10−7
BCL2	basal/stem	12.3	1.3×10−10
NOTCH4	basal/stem	11.6	1.0×10−16
KRT5	basal/stem	10.8	6.1×10−8
POU5F1	N/A	10.5	1.8×10−6
TGFB1	N/A	8.1	7.1×10−5
THY1	N/A	7.4	2.3×10−5
CDKN1B	N/A	7.3	5.1×10−11
WNT2	N/A	6.6	6.7×10−6
SKP2	basal/stem	6.2	4.7×10−7
DAND5	N/A	6.1	2.2×10−9
PGR	basal/stem	5.8	9.4×10−5
CHEK1	basal/stem	5.6	2.3×10−5
CDH3	basal/stem	4.3	1.5×10−9
MTOR	basal/stem	3.8	1.0×10−4
TP73	N/A	3.5	5.1×10−7
TGFBR3	N/A	3.4	0.004
ESR2	basal/stem	3.3	0.002
ESR1	N/A	3.3	0.004
MAX	N/A	3.2	0.010
NTRK2	N/A	2.9	0.014
NOTCH3	basal/stem	2.9	0.040
FIGF	N/A	2.9	0.004
MME	basal/stem	2.4	0.017
TP63	basal/stem	2.3	0.017
TP53	basal/stem	2.2	0.003
MYCN	basal/stem	2.2	0.033
SNAI2	basal/stem	2.1	0.046
ITGA6	basal/stem	2.1	0.003
JAG1	basal/stem	1.9	0.057
ACTA2	basal/stem	1.8	0.004

Decreased expression
Gene	Normal lineage	Fold change (low-burden/T)	*P value
PTEN	luminal	−2.1	0.001
TGFBR1	N/A	−2.3	0.028
ERBB3	luminal	−2.3	0.004
CDH1	luminal	−2.6	0.059
CDK2	N/A	−3.5	0.001
MUC1	luminal	−3.9	0.007
VEGFA	N/A	−6.6	3.2× 10−5
CAV2	basal/stem	−7.5	2.3×10−5
MYC	N/A	−9.8	2.3×10−5
ITGB1	basal/stem	−11.2	9.1 ×10−26
PARP2	luminal prog.	−15.8	8.3×10−11
EMP1	luminal	−20.2	3.3×10−7
CD24	luminal	−28.7	1.7×10−12
VIM	N/A	−29.8	4.4×10−14

N/A, not part of 49-gene signature; that is, not differentially expressed in normal mammary lineages. P values: moderated t-test or Mann–Whitney U test, FDR corrected.