PDX Portal

Model Details

Patient Information for Model: BCM-4195

Model Contact

Model: BCM-4195
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-4195

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	130884102	130884105	CAAG	C	c.1826_1828del	AAG/-	p.K609del	0.01	55	42	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000318560.6		COSV59324524		rs201725154	55	42	ENST00000318560.6		COSV59324524	rs201725154
ABL2	chr1	179108917	179108917	T	A	c.2350A>T	Aca/Tca	p.T784S	0.257	11	1	Missense Variant	Missense Variant	MODERATE	ENST00000502732.6	Likely_benign	COSV105243257	0.003241380000	rs55892721	11	1	ENST00000502732.6	Likely_benign	COSV105243257	rs55892721
AKAP9	chr7	92085597	92085597	C	T	c.8935C>T	Cct/Tct	p.P2979S	0.941	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	92001306	92001306	G	T	c.1389G>T	atG/atT	p.M463I	0.107	115	73	Missense Variant	Missense Variant	MODERATE	ENST00000356239.8	Benign	COSV62345589	0.376835000000	rs6964587	115	73	ENST00000356239.8	Benign	COSV62345589	rs6964587
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	0.579	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	0.994	115	80	Missense Variant	Missense Variant	MODERATE	ENST00000389048.8	Benign	COSV66569695	0.472160000000	rs1881421	115	80	ENST00000389048.8	Benign	COSV66569695	rs1881421
APC	chr5	112841059	112841059	T	A	c.5465T>A	gTc/gAc	p.V1822D	0.948	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	TGCA	c.237_239dup	ctg/ctGCAg	p.Q80dup	0.836	101	14	In-frame Insertion	In-frame Insertion	MODERATE	ENST00000374690.9		COSV65952534		.	101	14	ENST00000374690.9		COSV65952534	.
ATIC	chr2	215325297	215325297	C	G	c.347C>G	aCt/aGt	p.T116S	0.98	52	43	Missense Variant	Missense Variant	MODERATE	ENST00000236959.14	Benign	COSV52691660	0.326476000000	rs2372536	52	43	ENST00000236959.14	Benign	COSV52691660	rs2372536
ATM	chr11	108304735	108304735	G	A	c.5557G>A	Gat/Aat	p.D1853N	0.913	51	17	Missense Variant	Missense Variant	MODERATE	ENST00000278616.8	Benign	COSV53728020	0.113458000000	rs1801516	51	17	ENST00000278616.8	Benign	COSV53728020	rs1801516
ATRX	chrX	77682471	77682471	C	G	c.2785G>C	Gag/Cag	p.E929Q	0.906	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	0.988	75	60	Missense Variant	Missense Variant	MODERATE	ENST00000307078.10	Benign	COSV61057354	0.474888000000	rs2240308	75	60	ENST00000307078.10	Benign	COSV61057354	rs2240308
BCL11B	chr14	99175206	99175209	GCTC	G	c.1627_1629del	GAG/-	p.E543del	0.067	55	45	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000357195.8		COSV61733777		.	55	45	ENST00000357195.8		COSV61733777	.
BCLAF1	chr6	136278255	136278255	G	C	c.626C>G	tCc/tGc	p.S209C	0.137	114	114	Missense Variant	Missense Variant	MODERATE	ENST00000531224.6		COSV62140211		rs6940018	114	114	ENST00000531224.6		COSV62140211	rs6940018

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-4195

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
Treatment	Paclitaxel
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	196	-10	SD
C188-9	28	196	627	PD
Docetaxel20	28	196	-38	PR
Carboplatin	28	196	-100	CR
Paclitaxel	28	196	807	PD
Vehicle	28	196	610	PD
Carboplatin+C188-9	28	196	-100	CR
Paclitaxel+C188-9	28	196	685	PD

Histology Information for Model: BCM-4195

There are no histology images for this model.

Metastasis Information for Model: BCM-4195

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-4195

Event Id	Treatment	Treatment Setting	Age at Start	Age at End	Duration	Clinical Response	Pathologic Response	Reason Stopped
10	Other	Neoadjuvant	51.99	52.06	26 days	Stable Disease	Not Reported	Treatment Completed
15	Docetaxel	Neoadjuvant	52.07	52.24	62 days	Stable Disease	No Response	Treatment Completed
25	Cyclophosphamide,Doxorubicin	Adjuvant	52.42	52.6	66 days	Not Reported	Not Applicable	Treatment Completed
30	Radiation Therapy	Adjuvant	52.7	52.83	47 days	Not Reported	Not Applicable	Treatment Completed