PDX Portal

Model Details

Patient Information for Model: BCM-15006

Model Contact

Model: BCM-15006
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-15006

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
ACVR1	chr2	157765946	157765949	ATTC	A	c.1038_1040del	aaGAAt/aat	p.K346del	0.259	7	1	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000434821.7				.	7	1	ENST00000434821.7			.
AKAP9	chr7	92085597	92085597	C	T	c.8935C>T	Cct/Tct	p.P2979S	0.963	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	92097327	92097330	TAGA	T	c.10373_10375del	AGA/-	p.R3458del	0.199	115	3	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000356239.8				rs757087367	115	3	ENST00000356239.8			rs757087367
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	0.971	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	0.658	101	17	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000374690.9		COSV65960938		.	101	17	ENST00000374690.9		COSV65960938	.
ARID1A	chr1	26696849	26696849	G	A	c.446G>A	gGc/gAc	p.G149D	0.881	48	3	Missense Variant	Missense Variant	MODERATE	ENST00000324856.13	Uncertain_significance	COSV61376273		rs2080267760	48	3	ENST00000324856.13	Uncertain_significance	COSV61376273	rs2080267760
ATM	chr11	108304735	108304735	G	A	c.5557G>A	Gat/Aat	p.D1853N	0.964	51	17	Missense Variant	Missense Variant	MODERATE	ENST00000278616.8	Benign	COSV53728020	0.113458000000	rs1801516	51	17	ENST00000278616.8	Benign	COSV53728020	rs1801516
ATRX	chrX	77682471	77682471	C	G	c.2785G>C	Gag/Cag	p.E929Q	0.241	91	73	Missense Variant	Missense Variant	MODERATE	ENST00000373344.10	Benign			rs3088074	91	73	ENST00000373344.10	Benign		rs3088074
AXIN2	chr17	65558473	65558473	G	A	c.148C>T	Cct/Tct	p.P50S	0.944	75	60	Missense Variant	Missense Variant	MODERATE	ENST00000307078.10	Benign	COSV61057354	0.474888000000	rs2240308	75	60	ENST00000307078.10	Benign	COSV61057354	rs2240308
BARD1	chr2	214752454	214752454	C	G	c.1670G>C	tGc/tCc	p.C557S	0.542	85	5	Missense Variant	Missense Variant	MODERATE	ENST00000260947.9	Benign	COSV104530488	0.014751500000	rs28997576	85	5	ENST00000260947.9	Benign	COSV104530488	rs28997576
BARD1	chr2	214780740	214780740	C	G	c.1134G>C	agG/agC	p.R378S	0.439	85	72	Missense Variant	Missense Variant	MODERATE	ENST00000260947.9	Benign	COSV53612030	0.542039000000	rs2229571	85	72	ENST00000260947.9	Benign	COSV53612030	rs2229571
BARD1	chr2	214767531	214767532	CA	TG	c.1518_1519inv	caTGtg/caCAtg	p.V507M	0.5	85	57	Missense Variant	Missense Variant	MODERATE	ENST00000260947.9		COSV105837301		rs386654966	85	57	ENST00000260947.9		COSV105837301	rs386654966
BCLAF1	chr6	136278255	136278255	G	C	c.626C>G	tCc/tGc	p.S209C	0.326	114	114	Missense Variant	Missense Variant	MODERATE	ENST00000531224.6		COSV62140211		rs6940018	114	114	ENST00000531224.6		COSV62140211	rs6940018
BCR	chr22	23314599	23314599	C	G	c.3611C>G	gCc/gGc	p.A1204G	0.19	104	3	Missense Variant	Missense Variant	MODERATE	ENST00000305877.13		COSV59925974	0.000060068300	rs56265970	104	3	ENST00000305877.13		COSV59925974	rs56265970

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-15006

Patient

PDX

H&E

HER2

Metastasis Information for Model: BCM-15006

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-15006

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