PDX Portal

Model Details

Patient Information for Model: BCM-15046

Model Contact

Model: BCM-15046
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-15046

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	0.009452	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	0.072	115	73	Missense Variant	Missense Variant	MODERATE	ENST00000356239.8	Benign	COSV62345589	0.376835000000	rs6964587	115	73	ENST00000356239.8	Benign	COSV62345589	rs6964587
AKAP9	chr7	92097327	92097330	TAGA	T	c.10373_10375del	AGA/-	p.R3458del	0.291	115	3	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000356239.8				rs757087367	115	3	ENST00000356239.8			rs757087367
AKAP9	chr7	92085597	92085597	C	T	c.8935C>T	Cct/Tct	p.P2979S	0.994	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	0.04	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	0.068	115	73	In-frame Insertion	In-frame Insertion	MODERATE	ENST00000356239.8		COSV62337888		rs10644111	115	73	ENST00000356239.8		COSV62337888	rs10644111
ALK	chr2	29193706	29193706	T	C	c.4381A>G	Atc/Gtc	p.I1461V	0.998	115	115	Missense Variant	Missense Variant	MODERATE	ENST00000389048.8	Benign	COSV101201052	0.997594000000	rs1670283	115	115	ENST00000389048.8	Benign	COSV101201052	rs1670283
ANK1	chr8	41663737	41663737	A	C	c.5400T>G	aaT/aaG	p.N1800K	0.042	37	1	Missense Variant	Missense Variant	MODERATE	ENST00000289734.13				.	37	1	ENST00000289734.13			.
ANK1	chr8	41708920	41708920	C	T	c.1856G>A	cGt/cAt	p.R619H	0.086	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	0.997	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	0.44	101	17	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000374690.9		COSV65960938		.	101	17	ENST00000374690.9		COSV65960938	.
AR	chrX	67546514	67546514	T	TGGC	c.1418_1420dup	-/GGC	p.G473dup	0.889	101	18	In-frame Insertion	In-frame Insertion	MODERATE	ENST00000374690.9		COSV104687717		.	101	18	ENST00000374690.9		COSV104687717	.
AR	chrX	67545316	67545316	T	TGCAGCAGCA	c.231_239dup	ctg/ctGCAGCAGCAg	p.Q78_Q80dup	0.172	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	0.337	101	8	In-frame Insertion	In-frame Insertion	MODERATE	ENST00000374690.9				.	101	8	ENST00000374690.9			.
AR	chrX	67545316	67545331	TGCAGCAGCAGCAGCA	T	c.225_239del	ctGCAGCAGCAGCAGCAg/ctg	p.Q76_Q80del	0.042	101	16	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000374690.9		COSV104424802		.	101	16	ENST00000374690.9		COSV104424802	.

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-15046

Patient

PDX

H&E

HER2

Metastasis Information for Model: BCM-15046

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-15046

Event Id	Treatment	Treatment Setting	Age at Start	Age at End	Duration	Clinical Response	Pathologic Response	Reason Stopped
20	Cyclophosphamide,Doxorubicin	Neoadjuvant	33.95	34.07	44 days	Partial Response	Not Reported	Treatment Completed
25	Carboplatin,Paclitaxel	Neoadjuvant	34.11	34.32	77 days	Progressive Disease	Not Reported	Treatment Completed
40	Radiation Therapy	Neoadjuvant	34.37	34.5	47 days	Complete Response	Pathological Complete Response	Treatment Completed
45	Cisplatin	Neoadjuvant	34.38	34.45	26 days	Complete Response	Pathological Complete Response	Treatment Completed
55	Capecitabine	Metastatic	34.78	35.28	183 days	Not Reported	Not Applicable	Treatment Completed
70	Radiation Therapy	Metastatic	35.78	35.85	26 days	Not Reported	Not Applicable	Treatment Completed
75	Capecitabine	Metastatic	35.8	35.92	44 days	Not Reported	Not Applicable	Disease Progression
80	Eribulin	Metastatic	35.93	35.94	4 days	Not Reported	Not Applicable	Disease Progression