PDX Portal

Model Details

Patient Information for Model: BCM-15034

Model Contact

Model: BCM-15034
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-15034

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
AFDN	chr6	167918931	167918931	G	C	c.2762G>C	aGa/aCa	p.R921T	0.035	50	1	Missense Variant	Missense Variant; Splice Region Variant	MODERATE	ENST00000366806.6				.	50	1	ENST00000366806.6			.
AFF4	chr5	132897131	132897131	T	G	c.1499A>C	cAa/cCa	p.Q500P	0.021	20	2	Missense Variant	Missense Variant	MODERATE	ENST00000265343.10				.	20	2	ENST00000265343.10			.
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	92097327	92097330	TAGA	T	c.10373_10375del	AGA/-	p.R3458del	0.074	115	3	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000356239.8				rs757087367	115	3	ENST00000356239.8			rs757087367
ALK	chr2	29193500	29193500	G	C	c.4587C>G	gaC/gaG	p.D1529E	0.419	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	0.998	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	0.993	100	100	Missense Variant	Missense Variant	MODERATE	ENST00000257430.9	Benign	COSV57321643	0.794920000000	rs459552	100	100	ENST00000257430.9	Benign	COSV57321643	rs459552
AR	chrX	67545316	67545319	TGCA	T	c.237_239del	ctGCAg/ctg	p.Q80del	0.372	101	35	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000374690.9		COSV65954886		.	101	35	ENST00000374690.9		COSV65954886	.
AR	chrX	67546514	67546514	T	TGGC	c.1418_1420dup	-/GGC	p.G473dup	0.892	101	18	In-frame Insertion	In-frame Insertion	MODERATE	ENST00000374690.9		COSV104687717		.	101	18	ENST00000374690.9		COSV104687717	.
AR	chrX	67545316	67545322	TGCAGCA	T	c.234_239del	ctGCAGCAg/ctg	p.Q79_Q80del	0.075	101	24	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000374690.9		COSV65952724		.	101	24	ENST00000374690.9		COSV65952724	.
AR	chrX	67545316	67545316	T	TGCA	c.237_239dup	ctg/ctGCAg	p.Q80dup	0.448	101	14	In-frame Insertion	In-frame Insertion	MODERATE	ENST00000374690.9		COSV65952534		.	101	14	ENST00000374690.9		COSV65952534	.
ARID1A	chr1	26696849	26696849	G	A	c.446G>A	gGc/gAc	p.G149D	0.104	48	3	Missense Variant	Missense Variant	MODERATE	ENST00000324856.13	Uncertain_significance	COSV61376273		rs2080267760	48	3	ENST00000324856.13	Uncertain_significance	COSV61376273	rs2080267760
ARID1B	chr6	156778847	156778850	GGGC	G	c.1191_1193del	GGC/-	p.G402del	0.038	80	15	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000636930.2		COSV51674296		.	80	15	ENST00000636930.2		COSV51674296	.
ARID1B	chr6	157201331	157201331	G	T	c.5106G>T	aaG/aaT	p.K1702N	0.034	80	1	Missense Variant	Missense Variant	MODERATE	ENST00000636930.2				.	80	1	ENST00000636930.2			.
ARID1B	chr6	156778889	156778892	CGGA	C	c.1232_1234del	GGA/-	p.G411del	0.037	80	16	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000636930.2		COSV51648106		.	80	16	ENST00000636930.2		COSV51648106	.

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-15034

Patient

PDX

HER2

Metastasis Information for Model: BCM-15034

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-15034

Event Id	Treatment	Treatment Setting	Age at Start	Age at End	Duration	Clinical Response	Pathologic Response	Reason Stopped
15	Letrozole	Adjuvant	62.95	63.0	18 days	Not Reported	Not Applicable	Side Effects
25	Anastrozole,Palbociclib	Metastatic	63.0	63.54	197 days	Disease Progression	Not Applicable	Disease Progression
35	Paclitaxel	Metastatic	63.62	64.05	157 days	Disease Progression	Not Applicable	Disease Progression
45	Everolimus,Exemestane	Metastatic	64.11	64.29	66 days	Disease Progression	Not Applicable	Disease Progression
50	Capecitabine	Metastatic	64.29	64.37	29 days	Disease Progression	Not Applicable	Disease Progression
55	Eribulin	Metastatic	64.39	64.54	55 days	Disease Progression	Not Applicable	Disease Progression
70	Docetaxel,Pertuzumab,Trastuzumab	Metastatic	64.62	64.84	80 days	Disease Progression	Not Applicable	Disease Progression
75	Pertuzumab,Trastuzumab	Metastatic	65.2	65.54	124 days	Disease Progression	Not Applicable	Disease Progression