PDX Portal

Model Details

Patient Information for Model: BCM-3936

Model Contact

Model: BCM-3936
Model Contact: Michael Lewis
Institution: BCM Breast PDX Program
Email: mtlewis@bcm.edu

Patient Information

Clinical Timeline

Color Keys:

Positive

Negative

N/A

Clinical Information at Collection

Clinical Biomarkers/Mutations at Collection

Pathology Information at Collection

Model Information for Model: BCM-3936

Model Details - Initial Implantation of Patient Tissue

Biomarkers & Mutations

Model Details - Acceptable Conditions for Passaging

Mutations (Cancer Gene Census List)

GeneFilter by Gene	ChrFilter by Chr	Start	End	Ref	Alt	cDNA Change	Codon Change	Protein Change	TVAF	Gene Mutation Freq.	Site Mutation Freq.	Most Severe Effect	All Effects	Mutation Impact	Transcript ID	ClinVar Clinical Significance	COSMIC ID	gnomAD Non-Cancer AF	dbSNP ID	Gene Mutation Freq.	Site Mutation Freq.	Transcript ID	ClinVar Clinical Significance	COSMIC ID	dbSNP ID
AFF1	chr4	87131211	87131211	T	G	c.3093T>G	gaT/gaG	p.D1031E	0.667	12	1	Missense Variant	Missense Variant	MODERATE	ENST00000395146.8				.	12	1	ENST00000395146.8			.
AKAP9	chr7	92085597	92085597	C	T	c.8935C>T	Cct/Tct	p.P2979S	0.979	115	115	Missense Variant	Missense Variant	MODERATE	ENST00000356239.8	Benign/Likely_benign	COSV104663065	0.996325000000	rs1063242	115	115	ENST00000356239.8	Benign/Likely_benign	COSV104663065	rs1063242
ALK	chr2	29193706	29193706	T	C	c.4381A>G	Atc/Gtc	p.I1461V	0.99	115	115	Missense Variant	Missense Variant	MODERATE	ENST00000389048.8	Benign	COSV101201052	0.997594000000	rs1670283	115	115	ENST00000389048.8	Benign	COSV101201052	rs1670283
ALK	chr2	29193615	29193615	T	C	c.4472A>G	aAg/aGg	p.K1491R	0.626	115	51	Missense Variant	Missense Variant	MODERATE	ENST00000389048.8	Benign	COSV66555753	0.349007000000	rs1881420	115	51	ENST00000389048.8	Benign	COSV66555753	rs1881420
ALK	chr2	29193500	29193500	G	C	c.4587C>G	gaC/gaG	p.D1529E	0.685	115	80	Missense Variant	Missense Variant	MODERATE	ENST00000389048.8	Benign	COSV66569695	0.472160000000	rs1881421	115	80	ENST00000389048.8	Benign	COSV66569695	rs1881421
ALK	chr2	29320870	29320870	A	G	c.1427T>C	gTg/gCg	p.V476A	0.305	115	8	Missense Variant	Missense Variant	MODERATE	ENST00000389048.8	Benign	COSV66568530	0.028229100000	rs35093491	115	8	ENST00000389048.8	Benign	COSV66568530	rs35093491
AMER1	chrX	64190069	64190069	G	A	c.3218C>T	cCa/cTa	p.P1073L	0.493	23	1	Missense Variant	Missense Variant	MODERATE	ENST00000374869.8				.	23	1	ENST00000374869.8			.
ANK1	chr8	41690309	41690309	G	T	c.4022C>A	tCg/tAg	p.S1341*	0.938	37	1	Nonsense Mutation	Nonsense Mutation	HIGH	ENST00000289734.13				.	37	1	ENST00000289734.13			.
ANK1	chr8	41723629	41723629	C	T	c.716G>A	gGc/gAc	p.G239D	0.068	37	1	Missense Variant	Missense Variant	MODERATE	ENST00000289734.13		COSV55881818		rs867799041	37	1	ENST00000289734.13		COSV55881818	rs867799041
ATR	chr3	142459302	142459302	C	T	c.7274G>A	cGa/cAa	p.R2425Q	0.18	101	24	Missense Variant	Missense Variant	MODERATE	ENST00000350721.9	Benign	COSV63383988	0.130080000000	rs2229032	101	24	ENST00000350721.9	Benign	COSV63383988	rs2229032
ATR	chr3	142562770	142562770	A	G	c.632T>C	aTg/aCg	p.M211T	0.97	101	91	Missense Variant	Missense Variant	MODERATE	ENST00000350721.9	Benign/Likely_benign	COSV63383325	0.545488000000	rs2227928	101	91	ENST00000350721.9	Benign/Likely_benign	COSV63383325	rs2227928
ATR	chr3	142558717	142558717	A	T	c.1792T>A	Tgg/Agg	p.W598R	0.112	101	1	Missense Variant	Missense Variant	MODERATE	ENST00000350721.9				.	101	1	ENST00000350721.9			.
ATRX	chrX	77682471	77682471	C	G	c.2785G>C	Gag/Cag	p.E929Q	0.512	91	73	Missense Variant	Missense Variant	MODERATE	ENST00000373344.10	Benign			rs3088074	91	73	ENST00000373344.10	Benign		rs3088074
AXIN2	chr17	65558473	65558473	G	A	c.148C>T	Cct/Tct	p.P50S	0.987	75	60	Missense Variant	Missense Variant	MODERATE	ENST00000307078.10	Benign	COSV61057354	0.474888000000	rs2240308	75	60	ENST00000307078.10	Benign	COSV61057354	rs2240308
BARD1	chr2	214809500	214809500	G	A	c.70C>T	Ccc/Tcc	p.P24S	0.5	85	52	Missense Variant	Missense Variant	MODERATE	ENST00000260947.9	Benign	COSV53608734	0.384797000000	rs1048108	85	52	ENST00000260947.9	Benign	COSV53608734	rs1048108

CNV

PDX Validation

In order to validate the identity of Baylor College of Medicine patient-derived xenograft (PDX) models, short tandem repeat (STR) testing is performed at the Cytogenetics and Cell Authentication core facility at MDACC. STR testing is performed on tissue from the initial tumor grown in the mouse (transplant generation 1 - TG1) and from a patient sample when possible. Thereafter, STR testing is performed every five transplant generations (TG5, TG10, TG15, and TG20). In the case that a PDX model is transplanted from viably frozen tissue to restart the model, the PDX Core will test the first outgrowth to confirm identity and every five transplant generations thereafter. In addition to STR, we assess clinical biomarkers and histology every 5th transplant generation. Finally, RNAseq gene expression profiles are evaluated periodically to ensure consistency with previous results and to evaluate phenotypic drift. If a significant change in PDX biology is noted, we identify the last known stable stock and re-start the model.

Drug Studies for Model: BCM-3936

Treatment Response Across All Studies

CR <=-95% to -100% PR <-30% to >-95% SD >=-30% to +20% PD >=+20% NA

Drug Study: VFoundation

Study Metadata

Study ID: VFoundation
Study Type: Efficacy
Study Description:
Dosing Initiation Timepoint: Randomization and treatment began after average tumor size in cohort reached 150 mm³
Number of Arms: 10
Mouse Strain:

PI: Mike Lewis
Study Title: VFoundation Study
Treatments: AC, AC+C188-9, C188-9, Carbo, Carbo+C188-9, Doc20, Doc20+C188-9, Pac, Pac+C188-9
Study Duration:
Transplant Site
Transplant Material:

Study Design

Arm Type	Treatment Arms	Number of Mice
Treatment	Docetaxel20+C188-9	6
Treatment	AC	6
Treatment	C188-9	6
Treatment	Docetaxel20	6
Treatment	Carboplatin	6
Control	Vehicle
Treatment	Carboplatin+C188-9	6
Treatment	AC+C188-9	5

Treatment Results

Treatment Arm	Treatment Duration	Monitor Duration	Tumor volume over time (%)	Response Category
Docetaxel20+C188-9	28	28	-42	PR
AC	28	28	152	PD
C188-9	28	28	322	PD
Docetaxel20	28	28	-59	PR
Carboplatin	28	28	182	PD
Vehicle	28	28	327	PD
Carboplatin+C188-9	28	28	258	PD
AC+C188-9	28	28	162	PD

Histology Information for Model: BCM-3936

There are no histology images for this model.

Metastasis Information for Model: BCM-3936

Patient

PDX

Abdomen

Adrenal gland

Bone

Bone (de novo)

Bones

Brain

CTC

Chest

Chest wall

Contralateral Breast

Dura

Fallopian Tubes

Head

Kidney

LMD

Liver

Lung

Lymph node

Lymph nodes

Neck

None

Ovary

Pancreas

Pericardium

Peritoneal cavity

Peritoneum

Pleura

Pleural effusion

Shoulder

Skin

Spine

Spleen

Thoracic Spine

Thymus

medistinal and right hilar

Patient Treatment Information for Model: BCM-3936

Event Id	Treatment	Treatment Setting	Age at Start	Age at End	Duration	Clinical Response	Pathologic Response	Reason Stopped
15	Cyclophosphamide,Doxorubicin	Neoadjuvant	44.21	44.38	62 days	Partial Response	Partial Response	Treatment Completed
25	Docetaxel	Adjuvant	44.61	44.79	66 days	Not Reported	Not Applicable	Treatment Completed
35	Radiation Therapy	Adjuvant	44.88	44.96	29 days	Not Reported	Not Applicable	Treatment Completed