PDX Portal

Model Details

Patient Information for Model: BCM-5998

Model Contact

Model: BCM-5998
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-5998

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	0.722	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	0.733	115	73	Missense Variant	Missense Variant	MODERATE	ENST00000356239.8	Benign	COSV62345589	0.376835000000	rs6964587	115	73	ENST00000356239.8	Benign	COSV62345589	rs6964587
AKAP9	chr7	92085597	92085597	C	T	c.8935C>T	Cct/Tct	p.P2979S	0.991	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	0.71	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
AKAP9	chr7	92079753	92079753	T	G	c.7620T>G	atT/atG	p.I2540M	0.252	115	1	Missense Variant	Missense Variant	MODERATE	ENST00000356239.8				.	115	1	ENST00000356239.8			.
ALK	chr2	29193706	29193706	T	C	c.4381A>G	Atc/Gtc	p.I1461V	0.992	115	115	Missense Variant	Missense Variant	MODERATE	ENST00000389048.8	Benign	COSV101201052	0.997594000000	rs1670283	115	115	ENST00000389048.8	Benign	COSV101201052	rs1670283
APC	chr5	112841059	112841059	T	A	c.5465T>A	gTc/gAc	p.V1822D	0.994	100	100	Missense Variant	Missense Variant	MODERATE	ENST00000257430.9	Benign	COSV57321643	0.794920000000	rs459552	100	100	ENST00000257430.9	Benign	COSV57321643	rs459552
AR	chrX	67545316	67545322	TGCAGCA	T	c.234_239del	ctGCAGCAg/ctg	p.Q79_Q80del	0.334	101	24	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000374690.9		COSV65952724		.	101	24	ENST00000374690.9		COSV65952724	.
AR	chrX	67545316	67545316	T	TGCAGCAGCAGCAGCA	c.225_239dup	ctg/ctGCAGCAGCAGCAGCAg	p.Q76_Q80dup	0.63	101	4	In-frame Insertion	In-frame Insertion	MODERATE	ENST00000374690.9		COSV65959057		.	101	4	ENST00000374690.9		COSV65959057	.
ARHGEF10	chr8	1929314	1929314	T	G	c.2950T>G	Tcc/Gcc	p.S984A	0.976	43	10	Missense Variant	Missense Variant	MODERATE	ENST00000349830.8	Benign	COSV50664117	0.053800200000	rs17683288	43	10	ENST00000349830.8	Benign	COSV50664117	rs17683288
ARHGEF12	chr11	120465352	120465352	C	G	c.2729C>G	aCt/aGt	p.T910S	0.967	12	1	Missense Variant	Missense Variant	MODERATE	ENST00000397843.7				.	12	1	ENST00000397843.7			.
ATIC	chr2	215325297	215325297	C	G	c.347C>G	aCt/aGt	p.T116S	0.597	52	43	Missense Variant	Missense Variant	MODERATE	ENST00000236959.14	Benign	COSV52691660	0.326476000000	rs2372536	52	43	ENST00000236959.14	Benign	COSV52691660	rs2372536
ATR	chr3	142459302	142459302	C	T	c.7274G>A	cGa/cAa	p.R2425Q	0.146	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	0.529	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
ATRX	chrX	77682471	77682471	C	G	c.2785G>C	Gag/Cag	p.E929Q	0.993	91	73	Missense Variant	Missense Variant	MODERATE	ENST00000373344.10	Benign			rs3088074	91	73	ENST00000373344.10	Benign		rs3088074

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-5998

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
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	102	81	PD
C188-9	28	102	144	PD
AC	28	102	82	PD
Docetaxel20	28	102	51	PD
Carboplatin	28	102	162	PD
Vehicle	28	102	221	PD
Carboplatin+C188-9	28	102	134	PD
AC+C188-9	28	102	48	PD

Histology Information for Model: BCM-5998

There are no histology images for this model.

Metastasis Information for Model: BCM-5998

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-5998

Event Id	Treatment	Treatment Setting	Age at Start	Age at End	Duration	Clinical Response	Pathologic Response	Reason Stopped
15	Cyclophosphamide,Doxorubicin	Adjuvant	47.79	47.91	44 days	Not Reported	Not Applicable	Treatment Completed
20	Paclitaxel	Adjuvant	47.95	48.06	40 days	Progressive Disease	No Response	Disease Progression
35	Radiation Therapy	Adjuvant	48.26	48.27	4 days	Not Reported	Not Applicable	Disease Progression
50	Radiation Therapy	Metastatic	48.44	48.5	22 days	Not Reported	Not Applicable	Treatment Completed
55	Tamoxifen	Metastatic	48.51	49.16	237 days	Disease Progression	Not Applicable	Disease Progression
75	Carboplatin,Gemcitabine	Metastatic	49.25	49.58	120 days	Not Reported	Not Applicable	Side Effects
80	Radiation Therapy	Metastatic	49.73	49.82	33 days	Not Reported	Not Applicable	Treatment Completed
90	Anastrozole	Metastatic	49.91	50.09	66 days	Disease Progression	Not Applicable	Disease Progression
95	Capecitabine	Metastatic	50.12	50.46	124 days	Disease Progression	Not Applicable	Disease Progression
110	Everolimus,Exemestane	Metastatic	51.51	52.0	179 days	Disease Progression	Not Applicable	Disease Progression