PDX Portal

Model Details

Patient Information for Model: BCM-15051

Model Contact

Model: BCM-15051
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-15051

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	0.014	55	42	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000318560.6		COSV59324524		rs201725154	55	42	ENST00000318560.6		COSV59324524	rs201725154
AKAP9	chr7	92001306	92001306	G	T	c.1389G>T	atG/atT	p.M463I	0.996	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	0.993	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	0.996	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	0.994	115	73	In-frame Insertion	In-frame Insertion	MODERATE	ENST00000356239.8		COSV62337888		rs10644111	115	73	ENST00000356239.8		COSV62337888	rs10644111
ALK	chr2	29920262	29920262	C	T	c.398G>A	cGc/cAc	p.R133H	0.007841	115	1	Missense Variant	Missense Variant	MODERATE	ENST00000389048.8	Uncertain_significance		0.000024843000	rs768229646	115	1	ENST00000389048.8	Uncertain_significance		rs768229646
ALK	chr2	29193706	29193706	T	C	c.4381A>G	Atc/Gtc	p.I1461V	0.999	115	115	Missense Variant	Missense Variant	MODERATE	ENST00000389048.8	Benign	COSV101201052	0.997594000000	rs1670283	115	115	ENST00000389048.8	Benign	COSV101201052	rs1670283
ANK1	chr8	41708920	41708920	C	T	c.1856G>A	cGt/cAt	p.R619H	0.991	37	11	Missense Variant	Missense Variant	MODERATE	ENST00000289734.13	Benign/Likely_benign	COSV55882618	0.044445800000	rs2304877	37	11	ENST00000289734.13	Benign/Likely_benign	COSV55882618	rs2304877
APC	chr5	112841059	112841059	T	A	c.5465T>A	gTc/gAc	p.V1822D	0.99	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	TGCAGCA	c.234_239dup	ctg/ctGCAGCAg	p.Q79_Q80dup	0.086	101	15	In-frame Insertion	In-frame Insertion	MODERATE	ENST00000374690.9		COSV65953707		.	101	15	ENST00000374690.9		COSV65953707	.
AR	chrX	67546514	67546514	T	TGGC	c.1418_1420dup	-/GGC	p.G473dup	0.937	101	18	In-frame Insertion	In-frame Insertion	MODERATE	ENST00000374690.9		COSV104687717		.	101	18	ENST00000374690.9		COSV104687717	.
AR	chrX	67545400	67545403	GGCA	G	c.271_273del	agGCAg/agg	p.Q91del	0.014	101	24	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000374690.9		COSV65954891		rs753526329	101	24	ENST00000374690.9		COSV65954891	rs753526329
AR	chrX	67545316	67545316	T	TGCAGCAGCA	c.231_239dup	ctg/ctGCAGCAGCAg	p.Q78_Q80dup	0.609	101	15	In-frame Insertion	In-frame Insertion	MODERATE	ENST00000374690.9		COSV105309998		.	101	15	ENST00000374690.9		COSV105309998	.
AR	chrX	67545316	67545316	T	TGCAGCAGCAGCA	c.228_239dup	ctg/ctGCAGCAGCAGCAg	p.Q77_Q80dup	0.293	101	8	In-frame Insertion	In-frame Insertion	MODERATE	ENST00000374690.9				.	101	8	ENST00000374690.9			.
ARHGAP5	chr14	32092134	32092134	G	A	c.1465G>A	Gag/Aag	p.E489K	0.044	13	4	Missense Variant	Missense Variant	MODERATE	ENST00000345122.8		COSV61533654		rs78337553	13	4	ENST00000345122.8		COSV61533654	rs78337553

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-15051

Patient

PDX

H&E

HER2

Metastasis Information for Model: BCM-15051

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-15051

Event Id	Treatment	Treatment Setting	Age at Start	Age at End	Duration	Clinical Response	Pathologic Response	Reason Stopped
10	Carboplatin,Paclitaxel	Neoadjuvant	59.45	59.69	88 days	Not Reported	No Response	Treatment Completed
20	Cyclophosphamide,Doxorubicin	Neoadjuvant	59.76	59.8	15 days	Progressive Disease	Not Applicable	Disease Progression
35	Radiation Therapy	Adjuvant	59.96	60.08	44 days	Not Reported	Not Applicable	Treatment Completed
40	Capecitabine	Adjuvant	60.08	60.56	175 days	Not Reported	Not Applicable	Treatment Completed