PDX Portal

Model Details

Patient Information for Model: BCM-0132

Model Contact

Model: BCM-0132
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-0132

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	0.018	55	42	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000318560.6		COSV59324524		rs201725154	55	42	ENST00000318560.6		COSV59324524	rs201725154
AFF4	chr5	132897083	132897103	GTGTAGCTATTCCCAGTGCCC	G	c.1527_1546del	caGGGCACTGGGAATAGCTACAct/cact	p.Q509Hfs*2	0.535	20	1	Frameshift Mutation	Frameshift Mutation	HIGH	ENST00000265343.10				.	20	1	ENST00000265343.10			.
AKAP9	chr7	92085597	92085597	C	T	c.8935C>T	Cct/Tct	p.P2979S	0.971	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
ALK	chr2	29193706	29193706	T	C	c.4381A>G	Atc/Gtc	p.I1461V	0.037	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	0.969	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	TGCAGCAGCAGCA	c.228_239dup	ctg/ctGCAGCAGCAGCAg	p.Q77_Q80dup	0.923	101	8	In-frame Insertion	In-frame Insertion	MODERATE	ENST00000374690.9				.	101	8	ENST00000374690.9			.
AR	chrX	67546514	67546517	TGGC	T	c.1418_1420del	GGC/-	p.G473del	0.894	101	11	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000374690.9		COSV65958513		.	101	11	ENST00000374690.9		COSV65958513	.
ARID1A	chr1	26696761	26696761	C	T	c.358C>T	Ccg/Tcg	p.P120S	0.94	48	2	Missense Variant	Missense Variant	MODERATE	ENST00000324856.13	Conflicting_interpretations_of_pathogenicity	COSV61373973	0.000271628000	rs571264557	48	2	ENST00000324856.13	Conflicting_interpretations_of_pathogenicity	COSV61373973	rs571264557
ARID1B	chr6	157206530	157206534	CTGTT	C	c.5763_5766del	cTGTTt/ct	p.F1921Lfs*52	0.976	80	1	Frameshift Mutation	Frameshift Mutation	HIGH	ENST00000636930.2		COSV99269679		rs1554237269	80	1	ENST00000636930.2		COSV99269679	rs1554237269
ATR	chr3	142562770	142562770	A	G	c.632T>C	aTg/aCg	p.M211T	0.972	101	91	Missense Variant	Missense Variant	MODERATE	ENST00000350721.9	Benign/Likely_benign	COSV63383325	0.545488000000	rs2227928	101	91	ENST00000350721.9	Benign/Likely_benign	COSV63383325	rs2227928
BCL6	chr3	187728423	187728423	C	T	c.1477G>A	Gct/Act	p.A493T	0.606	39	34	Missense Variant	Missense Variant	MODERATE	ENST00000406870.7	not_provided	COSV51650064	0.141440000000	rs2229362	39	34	ENST00000406870.7	not_provided	COSV51650064	rs2229362
BCLAF1	chr6	136278255	136278255	G	C	c.626C>G	tCc/tGc	p.S209C	0.5	114	114	Missense Variant	Missense Variant	MODERATE	ENST00000531224.6		COSV62140211		rs6940018	114	114	ENST00000531224.6		COSV62140211	rs6940018
BCR	chr22	23285182	23285182	A	G	c.2387A>G	aAt/aGt	p.N796S	0.947	104	99	Missense Variant	Missense Variant	MODERATE	ENST00000305877.13	Benign	COSV59932309	0.812555000000	rs140504	104	99	ENST00000305877.13	Benign	COSV59932309	rs140504
BCR	chr22	23309463	23309463	A	G	c.3052A>G	Acc/Gcc	p.T1018A	0.069	104	19	Missense Variant	Missense Variant	MODERATE	ENST00000305877.13		COSV59933861	0.000222703000	rs746213513	104	19	ENST00000305877.13		COSV59933861	rs746213513
BIRC6	chr2	32488639	32488639	A	T	c.8020A>T	Act/Tct	p.T2674S	0.903	100	93	Missense Variant	Missense Variant	MODERATE	ENST00000421745.6	Benign	COSV70195673	0.588029000000	rs2366894	100	93	ENST00000421745.6	Benign	COSV70195673	rs2366894

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-0132

Patient

PDX

HER2

Metastasis Information for Model: BCM-0132

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-0132

Event Id	Treatment	Treatment Setting	Age at Start	Age at End	Duration	Clinical Response	Pathologic Response	Reason Stopped
20	Cyclophosphamide,Doxorubicin	Neoadjuvant	58.92	59.0	29 days	Partial Response	Not Reported	Treatment Completed
25	Carboplatin,Paclitaxel	Neoadjuvant	59.09	59.34	91 days	Complete Response	Partial Response	Treatment Completed
35	Docetaxel	Adjuvant	59.46	59.63	62 days	Not Reported	Not Applicable	Treatment Completed
40	Radiation Therapy	Adjuvant	59.76	59.84	29 days	Not Reported	Not Applicable	Treatment Completed
45	Capecitabine	Adjuvant	59.95	60.4	164 days	Stable Disease	Not Applicable	Treatment Completed