PDX Portal

Model Details

Patient Information for Model: BCM-3887

Model Contact

Model: BCM-3887
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-3887

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	92022864	92022864	A	AAAC	c.4004_4006dup	aaa/aAACaa	p.K1335_L1336insQ	0.342	115	73	In-frame Insertion	In-frame Insertion	MODERATE	ENST00000356239.8		COSV62337888		rs10644111	115	73	ENST00000356239.8		COSV62337888	rs10644111
AKAP9	chr7	92001306	92001306	G	T	c.1389G>T	atG/atT	p.M463I	0.386	115	73	Missense Variant	Missense Variant	MODERATE	ENST00000356239.8	Benign	COSV62345589	0.376835000000	rs6964587	115	73	ENST00000356239.8	Benign	COSV62345589	rs6964587
AKAP9	chr7	92086295	92086295	A	G	c.9092A>G	cAa/cGa	p.Q3031R	0.395	115	1	Missense Variant	Missense Variant	MODERATE	ENST00000356239.8	Benign		0.001313080000	rs61757673	115	1	ENST00000356239.8	Benign		rs61757673
AKAP9	chr7	92085597	92085597	C	T	c.8935C>T	Cct/Tct	p.P2979S	0.98	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
AKAP9	chr7	92083384	92083384	A	G	c.8375A>G	aAt/aGt	p.N2792S	0.561	115	62	Missense Variant	Missense Variant	MODERATE	ENST00000356239.8	Benign/Likely_benign	COSV62339152	0.357813000000	rs6960867	115	62	ENST00000356239.8	Benign/Likely_benign	COSV62339152	rs6960867
ALK	chr2	29193706	29193706	T	C	c.4381A>G	Atc/Gtc	p.I1461V	0.993	115	115	Missense Variant	Missense Variant	MODERATE	ENST00000389048.8	Benign	COSV101201052	0.997594000000	rs1670283	115	115	ENST00000389048.8	Benign	COSV101201052	rs1670283
ANK1	chr8	41694695	41694695	G	A	c.3224C>T	aCc/aTc	p.T1075I	0.455	37	4	Missense Variant	Missense Variant	MODERATE	ENST00000289734.13	Benign/Likely_benign		0.003478170000	rs35213384	37	4	ENST00000289734.13	Benign/Likely_benign		rs35213384
APC	chr5	112841059	112841059	T	A	c.5465T>A	gTc/gAc	p.V1822D	0.978	100	100	Missense Variant	Missense Variant	MODERATE	ENST00000257430.9	Benign	COSV57321643	0.794920000000	rs459552	100	100	ENST00000257430.9	Benign	COSV57321643	rs459552
APOBEC3B	chr22	38989458	38989458	T	C	c.571T>C	Tac/Cac	p.Y191H	0.346	15	1	Missense Variant	Missense Variant; Splice Region Variant	MODERATE	ENST00000333467.4			0.000670265000	rs61730556	15	1	ENST00000333467.4			rs61730556
AR	chrX	67545316	67545334	TGCAGCAGCAGCAGCAGCA	T	c.222_239del	ctGCAGCAGCAGCAGCAGCAg/ctg	p.Q75_Q80del	0.636	101	4	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000374690.9		COSV65961770		.	101	4	ENST00000374690.9		COSV65961770	.
AR	chrX	67546514	67546523	TGGCGGCGGC	T	c.1412_1420del	GGCGGCGGC/-	p.G471_G473del	0.898	101	7	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000374690.9		COSV65963320		.	101	7	ENST00000374690.9		COSV65963320	.
ARHGEF10	chr8	1909318	1909318	T	C	c.1991T>C	aTg/aCg	p.M664T	0.917	43	1	Missense Variant	Missense Variant	MODERATE	ENST00000349830.8	Benign		0.001823120000	rs34319003	43	1	ENST00000349830.8	Benign		rs34319003
ARID1B	chr6	156778052	156778061	CGCGGCGGCA	C	c.382_390del	GCGGCGGCA/-	p.A128_A130del	0.453	80	2	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000636930.2		COSV51671259		rs769480864	80	2	ENST00000636930.2		COSV51671259	rs769480864
ARID1B	chr6	157201089	157201089	A	T	c.4864A>T	Atg/Ttg	p.M1622L	0.417	80	4	Missense Variant	Missense Variant	MODERATE	ENST00000636930.2	Benign	COSV51656866	0.003566940000	rs34870395	80	4	ENST00000636930.2	Benign	COSV51656866	rs34870395
ARID1B	chr6	157174847	157174847	G	C	c.3346G>C	Gat/Cat	p.D1116H	0.187	80	1	Missense Variant	Missense Variant; Splice Region Variant	MODERATE	ENST00000636930.2				.	80	1	ENST00000636930.2			.

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-3887

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

Treatment Results

Treatment Arm	Treatment Duration	Monitor Duration	Tumor volume over time (%)	Response Category
Docetaxel20+C188-9	28	329	-100	CR
C188-9	28	329	505	PD
Docetaxel20	28	329	-99	CR
Paclitaxel	28	329	283	PD
Carboplatin	28	329	-96	CR
Vehicle	28	329	475	PD
Carboplatin+C188-9	28	329	-95	CR
Paclitaxel+C188-9	28	329	323	PD

Histology Information for Model: BCM-3887

There are no histology images for this model.

Metastasis Information for Model: BCM-3887

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-3887

Event Id	Treatment	Treatment Setting	Age at Start	Age at End	Duration	Clinical Response	Pathologic Response	Reason Stopped
25	Oophorectomy	Prophylactic	53.21	53.21	1 day	Not Reported	Not Applicable	Treatment Completed
30	Radiation	Metastatic	53.73	53.82	33 days	Not Reported	Not Applicable	Treatment Completed
40	Capecitabine	Metastatic	53.89		Unknown	Not Reported	Not Applicable	Unknown