PDX Portal

Model Details

Patient Information for Model: BCM-0046

Model Contact

Model: BCM-0046
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-0046

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
AKAP9	chr7	92085597	92085597	C	T	c.8935C>T	Cct/Tct	p.P2979S	0.967	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
ALDH2	chr12	111789845	111789845	A	T	c.463A>T	Aag/Tag	p.K155*	0.813	4	1	Nonsense Mutation	Nonsense Mutation	HIGH	ENST00000261733.7				.	4	1	ENST00000261733.7			.
ALK	chr2	29193500	29193500	G	C	c.4587C>G	gaC/gaG	p.D1529E	0.992	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	0.993	115	115	Missense Variant	Missense Variant	MODERATE	ENST00000389048.8	Benign	COSV101201052	0.997594000000	rs1670283	115	115	ENST00000389048.8	Benign	COSV101201052	rs1670283
ALK	chr2	29193615	29193615	T	C	c.4472A>G	aAg/aGg	p.K1491R	0.992	115	51	Missense Variant	Missense Variant	MODERATE	ENST00000389048.8	Benign	COSV66555753	0.349007000000	rs1881420	115	51	ENST00000389048.8	Benign	COSV66555753	rs1881420
ASXL1	chr20	32436404	32436404	C	T	c.3692C>T	tCc/tTc	p.S1231F	0.317	40	5	Missense Variant	Missense Variant	MODERATE	ENST00000375687.10	Benign	COSV105900478	0.021269300000	rs74638057	40	5	ENST00000375687.10	Benign	COSV105900478	rs74638057
ATRX	chrX	77682471	77682471	C	G	c.2785G>C	Gag/Cag	p.E929Q	0.923	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	0.994	75	60	Missense Variant	Missense Variant	MODERATE	ENST00000307078.10	Benign	COSV61057354	0.474888000000	rs2240308	75	60	ENST00000307078.10	Benign	COSV61057354	rs2240308
BAP1	chr3	52404500	52404500	A	C	c.1203T>G	taT/taG	p.Y401*	0.942	8	1	Nonsense Mutation	Nonsense Mutation	HIGH	ENST00000460680.6	Conflicting_interpretations_of_pathogenicity		0.000149294000	rs200156887	8	1	ENST00000460680.6	Conflicting_interpretations_of_pathogenicity		rs200156887
BAP1	chr3	52404502	52404502	A	C	c.1201T>G	Tat/Gat	p.Y401D	0.943	8	1	Missense Variant	Missense Variant	MODERATE	ENST00000460680.6	Uncertain_significance		0.000149312000	rs376563004	8	1	ENST00000460680.6	Uncertain_significance		rs376563004
BARD1	chr2	214809500	214809500	G	A	c.70C>T	Ccc/Tcc	p.P24S	0.969	85	52	Missense Variant	Missense Variant	MODERATE	ENST00000260947.9	Benign	COSV53608734	0.384797000000	rs1048108	85	52	ENST00000260947.9	Benign	COSV53608734	rs1048108
BAZ1A	chr14	34792782	34792782	G	T	c.1503C>A	gaC/gaA	p.D501E	0.382	15	1	Missense Variant	Missense Variant	MODERATE	ENST00000360310.6				.	15	1	ENST00000360310.6			.
BCLAF1	chr6	136278255	136278255	G	C	c.626C>G	tCc/tGc	p.S209C	0.234	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	0.901	104	99	Missense Variant	Missense Variant	MODERATE	ENST00000305877.13	Benign	COSV59932309	0.812555000000	rs140504	104	99	ENST00000305877.13	Benign	COSV59932309	rs140504
BIRC6	chr2	32488639	32488639	A	T	c.8020A>T	Act/Tct	p.T2674S	0.941	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-0046

Patient

PDX

H&E

HER2

Metastasis Information for Model: BCM-0046

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-0046

Event Id	Treatment	Treatment Setting	Age at Start	Age at End	Duration	Clinical Response	Pathologic Response	Reason Stopped
15	Cyclophosphamide,Epirubicin	Neoadjuvant	53.58	53.76	66 days	Partial Response	Not Applicable	Treatment Completed
20	Docetaxel	Neoadjuvant	53.81	53.99	66 days	Stable Disease	Partial Response	Treatment Completed
30	Radiation Therapy	Adjuvant	54.2	54.33	47 days	Not Reported	Not Applicable	Treatment Completed