PDX Portal

Model Details

Patient Information for Model: BCM-15003

Model Contact

Model: BCM-15003
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-15003

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	130878451	130878451	G	T	c.1307G>T	gGc/gTc	p.G436V	0.225	55	1	Missense Variant	Missense Variant	MODERATE	ENST00000318560.6				.	55	1	ENST00000318560.6			.
AFF3	chr2	100104432	100104432	A	G	c.23T>C	cTg/cCg	p.L8P	0.5	56	1	Missense Variant	Missense Variant	MODERATE	ENST00000409579.5				.	56	1	ENST00000409579.5			.
AKAP9	chr7	92001306	92001306	G	T	c.1389G>T	atG/atT	p.M463I	0.653	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	0.987	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	0.586	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	92022864	92022864	A	AAAC	c.4004_4006dup	aaa/aAACaa	p.K1335_L1336insQ	0.51	115	73	In-frame Insertion	In-frame Insertion	MODERATE	ENST00000356239.8		COSV62337888		rs10644111	115	73	ENST00000356239.8		COSV62337888	rs10644111
ALK	chr2	29193500	29193500	G	C	c.4587C>G	gaC/gaG	p.D1529E	0.352	115	80	Missense Variant	Missense Variant	MODERATE	ENST00000389048.8	Benign	COSV66569695	0.472160000000	rs1881421	115	80	ENST00000389048.8	Benign	COSV66569695	rs1881421
ALK	chr2	29193706	29193706	T	C	c.4381A>G	Atc/Gtc	p.I1461V	0.995	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	0.353	115	51	Missense Variant	Missense Variant	MODERATE	ENST00000389048.8	Benign	COSV66555753	0.349007000000	rs1881420	115	51	ENST00000389048.8	Benign	COSV66555753	rs1881420
APC	chr5	112841059	112841059	T	A	c.5465T>A	gTc/gAc	p.V1822D	0.984	100	100	Missense Variant	Missense Variant	MODERATE	ENST00000257430.9	Benign	COSV57321643	0.794920000000	rs459552	100	100	ENST00000257430.9	Benign	COSV57321643	rs459552
AR	chrX	67545316	67545328	TGCAGCAGCAGCA	T	c.228_239del	ctGCAGCAGCAGCAg/ctg	p.Q77_Q80del	0.822	101	17	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000374690.9		COSV65960938		.	101	17	ENST00000374690.9		COSV65960938	.
ARHGEF10	chr8	1885635	1885635	G	C	c.1110G>C	ttG/ttC	p.L370F	0.987	43	21	Missense Variant	Missense Variant	MODERATE	ENST00000349830.8	Benign	COSV50643418	0.160503000000	rs9657362	43	21	ENST00000349830.8	Benign	COSV50643418	rs9657362
ARID1B	chr6	156778889	156778892	CGGA	C	c.1232_1234del	GGA/-	p.G411del	0.161	80	16	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000636930.2		COSV51648106		.	80	16	ENST00000636930.2		COSV51648106	.
ATIC	chr2	215325297	215325297	C	G	c.347C>G	aCt/aGt	p.T116S	0.725	52	43	Missense Variant	Missense Variant	MODERATE	ENST00000236959.14	Benign	COSV52691660	0.326476000000	rs2372536	52	43	ENST00000236959.14	Benign	COSV52691660	rs2372536
ATR	chr3	142449479	142449479	C	A	c.7885G>T	Gat/Tat	p.D2629Y	0.128	101	1	Missense Variant	Missense Variant	MODERATE	ENST00000350721.9				.	101	1	ENST00000350721.9			.

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-15003

Patient

PDX

H&E

HER2

Metastasis Information for Model: BCM-15003

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-15003

Event Id	Treatment	Treatment Setting	Age at Start	Age at End	Duration	Clinical Response	Pathologic Response	Reason Stopped
15	Cyclophosphamide,Docetaxel	Adjuvant	66.61	66.81	73 days	Not Reported	Not Applicable	Treatment Completed
20	Radiation Therapy	Adjuvant	66.87	66.94	26 days	Not Reported	Not Applicable	Treatment Completed