PDX Portal

Model Details

Patient Information for Model: BCM-3561

Model Contact

Model: BCM-3561
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-3561

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
ABL1	chr9	130878561	130878561	C	T	c.1417C>T	Cga/Tga	p.R473*	0.4	55	1	Nonsense Mutation	Nonsense Mutation	HIGH	ENST00000318560.6		COSV59340385		.	55	1	ENST00000318560.6		COSV59340385	.
ABL2	chr1	179107929	179107929	C	T	c.3338G>A	gGa/gAa	p.G1113E	0.325	11	1	Missense Variant	Missense Variant	MODERATE	ENST00000502732.6				.	11	1	ENST00000502732.6			.
ACVR2A	chr2	147926116	147926117	TA	T	c.1310del	Aaa/aa	p.K437Rfs*5	0.994	8	2	Frameshift Mutation	Frameshift Mutation	HIGH	ENST00000241416.12		COSV54018504		rs764719749	8	2	ENST00000241416.12		COSV54018504	rs764719749
AKAP9	chr7	92079584	92079584	A	G	c.7451A>G	aAa/aGa	p.K2484R	0.538	115	14	Missense Variant	Missense Variant	MODERATE	ENST00000356239.8	Benign/Likely_benign		0.106317000000	rs35759833	115	14	ENST00000356239.8	Benign/Likely_benign		rs35759833
AKAP9	chr7	92085597	92085597	C	T	c.8935C>T	Cct/Tct	p.P2979S	0.981	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
AKT1	chr14	104780118	104780118	C	T	c.145G>A	Gag/Aag	p.E49K	0.423	15	1	Missense Variant	Missense Variant	MODERATE	ENST00000554581.5		COSV62573196		.	15	1	ENST00000554581.5		COSV62573196	.
ALK	chr2	29228923	29228927	CTCCA	C	c.2772_2775del	ggTGGA/gg	p.G927Afs*11	0.164	115	3	Frameshift Mutation	Frameshift Mutation	HIGH	ENST00000389048.8				rs1176720864	115	3	ENST00000389048.8			rs1176720864
ALK	chr2	29193706	29193706	T	C	c.4381A>G	Atc/Gtc	p.I1461V	0.994	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	0.442	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	0.592	115	80	Missense Variant	Missense Variant	MODERATE	ENST00000389048.8	Benign	COSV66569695	0.472160000000	rs1881421	115	80	ENST00000389048.8	Benign	COSV66569695	rs1881421
AMER1	chrX	64190105	64190105	G	A	c.3182C>T	tCt/tTt	p.S1061F	0.532	23	1	Missense Variant	Missense Variant	MODERATE	ENST00000374869.8				rs1930208989	23	1	ENST00000374869.8			rs1930208989
AMER1	chrX	64193059	64193060	TC	T	c.227del	gGa/ga	p.G76Dfs*24	0.462	23	1	Frameshift Mutation	Frameshift Mutation	HIGH	ENST00000374869.8		COSV57659636		.	23	1	ENST00000374869.8		COSV57659636	.
ANK1	chr8	41686157	41686157	G	A	c.4385C>T	gCa/gTa	p.A1462V	0.877	37	5	Missense Variant	Missense Variant	MODERATE	ENST00000289734.13	Benign/Likely_benign		0.022616200000	rs34664882	37	5	ENST00000289734.13	Benign/Likely_benign		rs34664882
ANK1	chr8	41686157	41686158	GC	AA	c.4384_4385delinsTT	GCa/TTa	p.A1462L	0.074	37	1	Missense Variant	Missense Variant	MODERATE	ENST00000289734.13				.	37	1	ENST00000289734.13			.
APC	chr5	112841059	112841059	T	A	c.5465T>A	gTc/gAc	p.V1822D	0.993	100	100	Missense Variant	Missense Variant	MODERATE	ENST00000257430.9	Benign	COSV57321643	0.794920000000	rs459552	100	100	ENST00000257430.9	Benign	COSV57321643	rs459552

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-3561

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	C188-9	6
Treatment	Docetaxel20	6
Treatment	Carboplatin	6
Control	Vehicle
Treatment	Carboplatin+C188-9	6

Treatment Results

Treatment Arm	Treatment Duration	Monitor Duration	Tumor volume over time (%)	Response Category
Docetaxel20+C188-9	28	98	-87	PR
C188-9	28	98	123	PD
Docetaxel20	28	98	-89	PR
Carboplatin	28	98	32	PD
Vehicle	28	98	361	PD
Carboplatin+C188-9	28	98	49	PD

Histology Information for Model: BCM-3561

There are no histology images for this model.

Metastasis Information for Model: BCM-3561

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-3561

Event Id	Treatment	Treatment Setting	Age at Start	Age at End	Duration	Clinical Response	Pathologic Response	Reason Stopped
10	Cyclophosphamide,Doxorubicin	Metastatic	56.16	56.46	110 days	Not Reported	Not Applicable	Treatment Completed
15	Anastrozole	Metastatic	56.51	59.31	1022 days	Disease Progression	Not Applicable	Disease Progression
30	Capecitabine	Metastatic	59.31	59.35	15 days	Not Reported	Not Applicable	Side Effects
35	Paclitaxel	Metastatic	59.38	59.47	33 days	Disease Progression	Not Applicable	Disease Progression
40	Paclitaxel	Metastatic	59.55	59.66	40 days	Disease Progression	Not Applicable	Disease Progression
45	Fulvestrant	Metastatic	59.66	60.05	142 days	Disease Progression	Not Applicable	Disease Progression
55	Capecitabine	Metastatic	60.05	60.14	33 days	Disease Progression	Not Applicable	Disease Progression