PDX Portal

Model Details

Patient Information for Model: BCM-0002

Model Contact

Model: BCM-0002
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-0002

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	92077721	92077721	C	T	c.6791C>T	gCc/gTc	p.A2264V	0.134	50	1	Missense Variant	Missense Variant	MODERATE	ENST00000356239.8					50	1	ENST00000356239.8
ALK	chr2	29193781	29193784	GCTC	G	c.4303_4305del	GAG/-	p.E1435del	0.346	10	2	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000389048.8				rs138827116	10	2	ENST00000389048.8			rs138827116
AR	chrX	67545316	67545331	TGCAGCAGCAGCAGCA	T	c.225_239del	ctGCAGCAGCAGCAGCAg/ctg	p.Q76_Q80del	0.706	48	1	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000374690.9		COSV104424802			48	1	ENST00000374690.9		COSV104424802
ARID1A	chr1	26775697	26775697	A	G	c.5114A>G	aAc/aGc	p.N1705S	0.339	19	2	Missense Variant	Missense Variant	MODERATE	ENST00000324856.13	Benign	COSV104411707	0.006846420000	rs61756316	19	2	ENST00000324856.13	Benign	COSV104411707	rs61756316
ARID1B	chr6	156778268	156778268	C	CCAG	c.609_611dup	-/CAG	p.Q214dup	0.871	37	2	In-frame Insertion	In-frame Insertion	MODERATE	ENST00000636930.2		COSV51651299			37	2	ENST00000636930.2		COSV51651299
BCL9	chr1	147619856	147619859	CATG	C	c.1704_1706del	ATG/-	p.M568del	0.315	11	2	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000234739.8				rs587603499	11	2	ENST00000234739.8			rs587603499
CASP9	chr1	15493953	15493953	G	T	c.1097C>A	aCc/aAc	p.T366N	0.215	13	7	Missense Variant	Missense Variant	MODERATE	ENST00000333868.10	Benign	COSV99049509	0.002324200000	rs61738967	13	7	ENST00000333868.10	Benign	COSV99049509	rs61738967
CDH11	chr16	64998805	64998805	C	T	c.280G>A	Ggg/Agg	p.G94R	0.493	6	1	Missense Variant	Missense Variant	MODERATE	ENST00000268603.9		COSV51769306			6	1	ENST00000268603.9		COSV51769306
CHD2	chr15	92949063	92949063	C	G	c.1489C>G	Cat/Gat	p.H497D	0.049	5	1	Missense Variant	Missense Variant	MODERATE	ENST00000394196.9					5	1	ENST00000394196.9
CIITA	chr16	10909070	10909070	A	G	c.2702A>G	cAg/cGg	p.Q901R	0.936	85	84	Missense Variant	Missense Variant	MODERATE	ENST00000618327.4	Benign		0.983235000000	rs7197779	85	84	ENST00000618327.4	Benign		rs7197779
CLTCL1	chr22	19226293	19226293	G	A	c.1873C>T	Caa/Taa	p.Q625*	0.977	19	1	Nonsense Mutation	Nonsense Mutation	HIGH	ENST00000427926.6			0.000038334100	rs372403893	19	1	ENST00000427926.6			rs372403893
CNTRL	chr9	121125866	121125866	G	T	c.1955G>T	aGa/aTa	p.R652I	0.305	10	1	Missense Variant	Missense Variant	MODERATE	ENST00000373855.5					10	1	ENST00000373855.5
CREB3L1	chr11	46320733	46320733	T	G	c.1547T>G	aTc/aGc	p.I516S	0.5	12	8	Missense Variant	Missense Variant	MODERATE	ENST00000621158.5	Benign		0.006321900000	rs73464035	12	8	ENST00000621158.5	Benign		rs73464035
CREB3L2	chr7	137928167	137928170	CTGG	C	c.299_301del	aCCAgt/agt	p.T100del	0.975	49	49	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000330387.11		COSV57791862		rs3217268	49	49	ENST00000330387.11		COSV57791862	rs3217268
CTNNA2	chr2	80393245	80393245	T	C	c.1091T>C	aTt/aCt	p.I364T	0.531	7	4	Missense Variant	Missense Variant	MODERATE	ENST00000402739.8	Benign	COSV99057397	0.003652210000	rs61754542	7	4	ENST00000402739.8	Benign	COSV99057397	rs61754542

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.

Histology Information for Model: BCM-0002

Patient

PDX

HER2

Metastasis Information for Model: BCM-0002

Patient

PDX

Abdomen

Adrenal gland

Bone

Bones

Brain

CTC

Chest

Chest wall

Contralateral Breast

Dura

Fallopian Tubes

Head

Kidney

Liver

Lung

Lymph node

Lymph nodes

Neck

Ovary

Pancreas

Pericardium

Peritoneal cavity

Peritoneum

Pleura

Pleural effusion

Shoulder

Skin

Spine

Spleen

Thoracic Spine

Thymus

Patient Treatment Information for Model: BCM-0002

Event Id	Treatment	Treatment Setting	Age at Start	Age at End	Duration	Clinical Response	Pathologic Response	Reason Stopped
10	Docetaxel,Doxorubicin	Neoadjuvant	43.62	44.12	183 days	Partial Response	Partial Response	Treatment Completed
15	Radiation Therapy	Adjuvant	43.7	43.87	62 days	Not Reported	Not Applicable	Treatment Completed
20	Docetaxel,Doxorubicin	Adjuvant	43.95	44.12	62 days	Not Reported	Not Applicable	Unknown
25	Docetaxel	Adjuvant	44.2	44.62	153 days	Not Reported	Not Applicable	Unknown
30	Tamoxifen	Adjuvant	45.62	50.45	1763 days	Not Reported	Not Applicable	Treatment Completed
35	Letrozole	Adjuvant	50.48	52.7	810 days	Not Reported	Not Applicable	Disease Progression
50	Carboplatin,Paclitaxel	Metastatic	52.77	54.13	496 days	Not Reported	Not Applicable	Unknown
55	Carboplatin	Metastatic	54.18	54.97	288 days	Not Reported	Not Applicable	Unknown
60	Anastrozole	Metastatic	55.62	56.08	168 days	Disease Progression	Not Applicable	Disease Progression
70	Radiation Therapy	Metastatic	56.0	56.1	37 days	Not Reported	Not Applicable	Treatment Completed
75	Capecitabine	Metastatic	56.08	57.0	336 days	Disease Progression	Not Applicable	Disease Progression
80	Gemcitabine	Metastatic	57.0	57.91	332 days	Disease Progression	Not Applicable	Disease Progression
90	Radiation Therapy	Metastatic	57.11	57.11	1	Not Reported	Not Applicable	Treatment Completed