PDX Portal

Model Details

Patient Information for Model: BCM-15057

Model Contact

Model: BCM-15057
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-15057

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
A1CF	chr10	50809906	50809909	TAGC	T	c.1594_1596del	GCT/-	p.A532del	0.044	20	11	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000373997.8		COSV50964203		rs747104061	20	11	ENST00000373997.8		COSV50964203	rs747104061
ABL1	chr9	130884102	130884105	CAAG	C	c.1826_1828del	AAG/-	p.K609del	0.051	55	42	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000318560.6		COSV59324524		rs201725154	55	42	ENST00000318560.6		COSV59324524	rs201725154
ACSL3	chr2	222908920	222908920	G	A	c.148G>A	Gaa/Aaa	p.E50K	0.549	6	1	Missense Variant	Missense Variant	MODERATE	ENST00000357430.8				.	6	1	ENST00000357430.8			.
ACVR1	chr2	157780592	157780592	G	A	c.76C>T	Ccc/Tcc	p.P26S	0.461	7	1	Missense Variant	Missense Variant	MODERATE	ENST00000434821.7			0.000012695100	rs377197386	7	1	ENST00000434821.7			rs377197386
AFF3	chr2	99601548	99601551	CGCT	C	c.1330_1332del	AGC/-	p.S444del	0.055	56	43	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000409579.5		COSV57843239		.	56	43	ENST00000409579.5		COSV57843239	.
AKAP9	chr7	92001306	92001306	G	T	c.1389G>T	atG/atT	p.M463I	0.988	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	0.981	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	0.988	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	0.982	115	73	In-frame Insertion	In-frame Insertion	MODERATE	ENST00000356239.8		COSV62337888		rs10644111	115	73	ENST00000356239.8		COSV62337888	rs10644111
AKT1	chr14	104775735	104775738	TCTC	T	c.349_351del	GAG/-	p.E117del	0.062	15	8	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000554581.5		COSV62573212		rs768025881	15	8	ENST00000554581.5		COSV62573212	rs768025881
ALK	chr2	29193500	29193500	G	C	c.4587C>G	gaC/gaG	p.D1529E	0.452	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	0.987	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	0.624	100	100	Missense Variant	Missense Variant	MODERATE	ENST00000257430.9	Benign	COSV57321643	0.794920000000	rs459552	100	100	ENST00000257430.9	Benign	COSV57321643	rs459552
APC	chr5	112842738	112842738	A	G	c.7144A>G	Aca/Gca	p.T2382A	0.094	100	1	Missense Variant	Missense Variant	MODERATE	ENST00000257430.9			0.000004239980	rs1243977560	100	1	ENST00000257430.9			rs1243977560
AR	chrX	67545316	67545319	TGCA	T	c.237_239del	ctGCAg/ctg	p.Q80del	0.427	101	35	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000374690.9		COSV65954886		.	101	35	ENST00000374690.9		COSV65954886	.

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-15057

Patient

PDX

H&E

HER2

Metastasis Information for Model: BCM-15057

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-15057

Event Id	Treatment	Treatment Setting	Age at Start	Age at End	Duration	Clinical Response	Pathologic Response	Reason Stopped
10	Anastrozole	Neoadjuvant	80.11	81.09	358 days	Not Reported	Not Reported	Treatment Completed
25	Paclitaxel	Adjuvant	81.2	81.46	95 days	Not Reported	Not Applicable	Treatment Completed
30	Radiation Therapy	Adjuvant	81.49	81.62	47 days	Not Reported	Not Applicable	Treatment Completed
35	Exemestane	Adjuvant	81.64	82.52	321 days	Not Reported	Not Applicable	Disease Progression