PDX Portal

Model Details

Patient Information for Model: BCM-3469

Model Contact

Model: BCM-3469
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-3469

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
AKAP9	chr7	92085597	92085597	C	T	c.8935C>T	Cct/Tct	p.P2979S	0.964	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	29275101	29275101	G	A	c.2039C>T	aCa/aTa	p.T680I	0.376	115	1	Missense Variant	Missense Variant; Splice Region Variant	MODERATE	ENST00000389048.8	Benign/Likely_benign	COSV66555766	0.016135300000	rs35228363	115	1	ENST00000389048.8	Benign/Likely_benign	COSV66555766	rs35228363
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
AMER1	chrX	64192553	64192553	G	T	c.734C>A	cCt/cAt	p.P245H	0.687	23	1	Missense Variant	Missense Variant	MODERATE	ENST00000374869.8			0.000012580000	rs1050642982	23	1	ENST00000374869.8			rs1050642982
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
AR	chrX	67545316	67545316	T	TGCAGCAGCAGCAGCA	c.225_239dup	ctg/ctGCAGCAGCAGCAGCAg	p.Q76_Q80dup	0.565	101	4	In-frame Insertion	In-frame Insertion	MODERATE	ENST00000374690.9		COSV65959057		.	101	4	ENST00000374690.9		COSV65959057	.
AR	chrX	67545316	67545316	T	TGCA	c.237_239dup	ctg/ctGCAg	p.Q80dup	0.384	101	14	In-frame Insertion	In-frame Insertion	MODERATE	ENST00000374690.9		COSV65952534		.	101	14	ENST00000374690.9		COSV65952534	.
ARHGEF12	chr11	120446508	120446508	G	A	c.1451G>A	cGg/cAg	p.R484Q	0.081	12	1	Missense Variant	Missense Variant; Splice Region Variant	MODERATE	ENST00000397843.7				rs1946051832	12	1	ENST00000397843.7			rs1946051832
ARID1A	chr1	26766265	26766265	C	G	c.2777C>G	aCt/aGt	p.T926S	0.517	48	1	Missense Variant	Missense Variant	MODERATE	ENST00000324856.13				.	48	1	ENST00000324856.13			.
ATP2B3	chrX	153580166	153580167	GT	CC	c.3531_3532delinsCC	ccGTcc/ccCCcc	p.S1178P	0.115	14	2	Missense Variant	Missense Variant	MODERATE	ENST00000263519.4		COSV105042211		.	14	2	ENST00000263519.4		COSV105042211	.
ATP2B3	chrX	153580173	153580174	AA	CC	c.3538_3539delinsCC	AAc/CCc	p.N1180P	0.089	14	1	Missense Variant	Missense Variant	MODERATE	ENST00000263519.4		COSV105042034		.	14	1	ENST00000263519.4		COSV105042034	.
ATRX	chrX	77682471	77682471	C	G	c.2785G>C	Gag/Cag	p.E929Q	0.979	91	73	Missense Variant	Missense Variant	MODERATE	ENST00000373344.10	Benign			rs3088074	91	73	ENST00000373344.10	Benign		rs3088074
ATRX	chrX	77682732	77682732	G	A	c.2524C>T	Cca/Tca	p.P842S	0.635	91	1	Missense Variant	Missense Variant	MODERATE	ENST00000373344.10	Benign		0.000193607000	rs782196312	91	1	ENST00000373344.10	Benign		rs782196312
BARD1	chr2	214780740	214780740	C	G	c.1134G>C	agG/agC	p.R378S	0.989	85	72	Missense Variant	Missense Variant	MODERATE	ENST00000260947.9	Benign	COSV53612030	0.542039000000	rs2229571	85	72	ENST00000260947.9	Benign	COSV53612030	rs2229571
BCL6	chr3	187728423	187728423	C	T	c.1477G>A	Gct/Act	p.A493T	0.53	39	34	Missense Variant	Missense Variant	MODERATE	ENST00000406870.7	not_provided	COSV51650064	0.141440000000	rs2229362	39	34	ENST00000406870.7	not_provided	COSV51650064	rs2229362

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-3469

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	AC	6
Treatment	Docetaxel20	6
Treatment	Carboplatin	6
Treatment	Carboplatin+C188-9	6
Control	Vehicle
Treatment	AC+C188-9	5

Treatment Results

Treatment Arm	Treatment Duration	Monitor Duration	Tumor volume over time (%)	Response Category
Docetaxel20+C188-9	28	235	36	PD
C188-9	28	235	409	PD
AC	28	235	121	PD
Docetaxel20	28	235	38	PD
Carboplatin	28	235	95	PD
Carboplatin+C188-9	28	235	-14	SD
Vehicle	28	235	299	PD
AC+C188-9	28	235	118	PD

Histology Information for Model: BCM-3469

There are no histology images for this model.

Metastasis Information for Model: BCM-3469

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-3469

Event Id	Treatment	Treatment Setting	Age at Start	Age at End	Duration	Clinical Response	Pathologic Response	Reason Stopped
15	Cyclophosphamide,Doxorubicin	Neoadjuvant	35.75	35.95	73 days	Partial Response	Partial Response	Treatment Completed
25	Docetaxel	Adjuvant	36.18	36.35	62 days	Not Reported	Not Applicable	Treatment Completed
30	Radiation Therapy	Adjuvant	36.68	36.76	29 days	Not Reported	Not Applicable	Treatment Completed
50	Cyclophosphamide,Docetaxel	Neoadjuvant	40.33	40.54	77 days	Partial Response	Partial Response	Treatment Completed
60	Oophorectomy	Prophylactic	40.72	40.72	1 day	Not Reported	Not Applicable	Treatment Completed
65	Radiation Therapy	Adjuvant	40.91	41.0	33 days	Not Reported	Not Applicable	Treatment Completed
70	Anastrozole	Adjuvant	41.16		Unknown	Not Reported	Not Applicable	Unknown