1. Supplementary Table S1 Pre-chemo Post-chemo No ultrasound Ultrasound
Pre-chemo
Post-chemo
No ultrasound
Ultrasound
Not-evaluable
18.2% (n=6)
1.4% (n=2)
5.4% (n=3)
No tumor cells
24.2% (n=8)
12.2% (n=17)
32.1% (n=18)
<50% tumor content
27.3% (n=9)
47.5% (n=66)
33.9% (n=19)
≥50% tumor content
30.3% (n=10)
38.9% (n=54)
28.6% (n=16)
Supplementary Table S1
Tumor cellularity in biopsies collected with and without ultrasound guidance

2. Supplementary Figure S1.
Q-CROC-03 study: patients eligible to participate in the study were triple negative breast cancer patients with
primary tumors ≥2cm and eligible to receive neoadjuvant chemotherapy. Biopsy samples were collected before
initiation of treatment and/or after treatment. Surgical specimens were collected at the time of surgery.

3. RNAlater and Snap Frozen Shipped on dry ice
4 core biopsies
from primary
breast tumor
And
4 pieces of
tissue collected
at the time of surgery
Snap Frozen
Formalin
RNAlater and Snap Frozen
Shipped on dry ice
Shipped at 4°C
Standard operating procedure
14-16 Gauge
JGH
Central
Lab
Standard operating procedure
Supplementary Figure S2. At the time of biopsy or surgery, two samples are immediately snap frozen in liquid nitrogen, one sample is put in 1ml RNAlater and snap frozen and one sample is put in formalin. Samples are then shipped to the Central Laboratory for further processing. Established standard operating procedures were followed.

4. Macrodissected area containing tumor is used for DNA/RNA isolation
Supplementary Figure S3
Top panel shows a frozen block of a breast biopsy specimen embedded in optimal cutting temperature medium. The pathologists circles the area where ≥50% tumor cellularity is observed to facilitate macrodissection. Bottom panel shows the frozen block macrodissected following an established standard operating procedure, only the portion with tumor is retrieved from the tissue block and used for nucleic acid extraction.
SOP
Macrodissected area containing tumor is
used for DNA/RNA isolation