Supplemental Figure 1: Box and whisker plots of cell-free DNA concentration and cell-free DNA integrity (cfDI) in three different metastasis groups (non-visceral metastasis, liver metastasis and non-liver visceral metastasis) estimated from ALU and LINE1 targets: (a) for ALU cfDNA concentration; (b) for ALU cfDI; (c) for LINE1 cfDNA concentration and (d) for LINE1 cfDI.

Supplemental Figure 2: Prognostic value of cfDNA integrity kinetics by Kaplan-Meier curve of overall survival and progression free survival of MBCBL patients stratified by (a) ALU cfDI kinetics. 0: < median, 1: > median, (b) LINE1 cfDI kinetics. 0: < median, 1: > median, (c) log2ALUcfDNA concentration kinetics. 0: < median, 1: > median, (d) log2LINE1cfDNA concentration kinetics. 0: < median, 1: > median.

Supplemental Figure 3: Prognostic value of cfDNA integrity kinetics by Kaplan-Meier curve of overall survival and progression free survival of MBC1C patients stratified by (a) ALU cfDI kinetics. 0: < median, 1: > median, (b) LINE1 cfDI kinetics. 0: < median, 1: > median, (c) log2ALUcfDNA concentration kinetics. 0: < median, 1: > median, (d) log2LINE1cfDNA concentration kinetics. 0: < median, 1: > median.

Supplemental Table 1: cell-free DNA concentration (cfDNA conc) and cell-free DNA integrity (cfDI) change according to specific type of metastatic breast cancer. Statistically significant P < 0.05 is highlighted in bold.

Type / Number / Group / ALU / LINE1
cfDI / cfDNA conc (ng/uL) / cfDI / cfDNA conc (ng/uL)
Mean±SD / Mean±SD / Mean±SD / Mean±SD
Luminal A / n=150 / MBCBL / 0.55±0.20 / 0.46±1.34 / 0.48±0.20 / 0.66±2.33
MBC1C / 0.63±0.20 / 0.27±0.51 / 0.52±0.20 / 0.38±0.81
P-value / 9.97E-05 / 2.77E-02 / 3.01E-03 / 4.51E-02
Luminal B / n=21 / MBCBL / 0.45±0.21 / 0.94±1.76 / 0.38±0.21 / 1.35±2.80
MBC1C / 0.55±0.22 / 0.34±0.67 / 0.39±0.16 / 0.55±1.18
P-value / 3.27E-02 / 0.06 / 0.82 / 0.11
HER2 / n=17 / MBCBL / 0.56±0.21 / 0.74±1.76 / 0.51±0.20 / 1.11±2.80
MBC1C / 0.63±0.20 / 0.24±0.30 / 0.54±0.20 / 0.32±0.43
P-value / 0.26 / 0.23 / 0.49 / 0.24
Triple Negative / n=42 / MBCBL / 0.49±0.21 / 0.35±0.52 / 0.44±0.20 / 0.40±0.60
MBC1C / 0.58±0.19 / 0.31±0.47 / 0.49±0.21 / 0.57±1.24
P-value / 4.10E-03 / 0.54 / 5.58E-02 / 0.22

conc: concentration

Supplemental Table2: Mean±SD of cfDNA concentration (cfDNA conc) and cfDNA integrity (cfDI) in different metastasis groups from ALU and LINE1 targets, and P-values of one-way ANOVA were used to compare difference between the three groups. Statistically significant P < 0.05 is highlighted in bold.

Value / P value
Patients / Markers / Non-visceral
metastasis
(n=53) / Liver
metastasis
(n=101) / Non-liver
metastasis
(n=113) / Non-visceral vs
Liver metastasis / Non-visceral vs
non-liver visceral metastasis / Liver metastasis vs
non-liver visceral metastasis
MBCBL / ALU / cfDNA conc (ng/ul) / 0.32±0.50 / 0.67±1.25 / 0.41±1.47 / 0.101 / 0.669 / 0.131
cfDI / 0.63±0.21 / 0.48±0.18 / 0.54±0.21 / 4.80E-05 / 0.013 / 0.039
LINE1 / cfDNA conc (ng/ul) / 0.43±0.81 / 0.92±1.99 / 0.55±2.52 / 0.168 / 0.728 / 0.199
cfDI / 0.57±0.20 / 0.42±0.20 / 0.48±0.20 / 6.17E-06 / 0.0064 / 0.018
MBC1C / ALU / cfDNA conc (ng/ul) / 0.21±0.28 / 0.33±0.56 / 0.28±0.52 / 0.152 / 0.425 / 0.42
cfDI / 0.66±0.17 / 0.58±0.21 / 0.61±0.20 / 0.028 / 0.134 / 0.367
LINE1 / cfDNA conc (ng/ul) / 0.32±0.64 / 0.52±1.08 / 0.38±0.85 / 0.201 / 0.713 / 0.256
cfDI / 0.57±0.19 / 0.46±0.20 / 0.52±0.21 / 0.0014 / 0.159 / 0.023

conc: concentration

Supplemental Table 3: cell-free DNA concentration (cfDNA conc) and cell-free DNA integrity (cfDI) change according to specific therapy. Statistically significant P < 0.05 is highlighted in bold.

Treatment / Number / Group / ALU / LINE1
cfDI / cfDNA conc (ng/uL) / cfDI / cfDNA conc (ng/uL)
Mean±SD / Mean±SD / Mean±SD / Mean±SD
Chemo
therapy / n=236 / MBCBL / 0.53±0.20 / 0.50±1.29 / 0.47±0.20 / 0.68±2.15
MBC1C / 0.61±0.20 / 0.28±0.47 / 0.51±0.20 / 0.39±0.78
P-value / 7.82E-08 / 1.85E-03 / 4.21E-05 / 1.03E-02
Radio
therapy / n=85 / MBCBL / 0.55±0.21 / 0.55±1.68 / 0.51±0.20 / 0.84±2.94
MBC1C / 0.64±0.20 / 0.34±0.64 / 0.55±0.20 / 0.51±1.05
P-value / 5.66E-04 / 0.102 / 0.046 / 0.144
Endocrine
therapy / n=131 / MBCBL / 0.56±0.20 / 0.42±1.40 / 0.50±0.22 / 0.61±2.43
MBC1C / 0.65±0.20 / 0.25±0.52 / 0.54±0.21 / 0.37±0.93
P-value / 5.50E-07 / 0.039 / 0.011 / 0.106
Anti-HER2
therapy / n=51 / MBCBL / 0.52±0.19 / 0.54±1.36 / 0.46±0.21 / 0.76±2.15
MBC1C / 0.59±0.20 / 0.20±0.19 / 0.47±0.17 / 0.27±0.28
P-value / 0.0415 / 0.064 / 0.663 / 0.09

conc: concentration