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
ALDH2	chr12	111789845	111789845	A	T	c.463A>T	Aag/Tag	p.K155*	0.805	2	1	Nonsense Mutation	Nonsense Mutation	HIGH	ENST00000261733.7					2	1	ENST00000261733.7
ATRX	chrX	77682471	77682471	C	G	c.2785G>C	Gag/Cag	p.E929Q	0.999	59	56	Missense Variant	Missense Variant	MODERATE	ENST00000373344.10	Benign			rs3088074	59	56	ENST00000373344.10	Benign		rs3088074
BAP1	chr3	52404500	52404500	A	C	c.1203T>G	taT/taG	p.Y401*	0.833	5	1	Nonsense Mutation	Nonsense Mutation	HIGH	ENST00000460680.6	Conflicting_interpretations_of_pathogenicity		0.000149294000	rs200156887	5	1	ENST00000460680.6	Conflicting_interpretations_of_pathogenicity		rs200156887
BAP1	chr3	52404502	52404502	A	C	c.1201T>G	Tat/Gat	p.Y401D	0.8	5	1	Missense Variant	Missense Variant	MODERATE	ENST00000460680.6	Uncertain_significance		0.000149312000	rs376563004	5	1	ENST00000460680.6	Uncertain_significance		rs376563004
BAZ1A	chr14	34792782	34792782	G	T	c.1503C>A	gaC/gaA	p.D501E	0.375	9	1	Missense Variant	Missense Variant	MODERATE	ENST00000360310.6					9	1	ENST00000360310.6
CIITA	chr16	10909070	10909070	A	G	c.2702A>G	cAg/cGg	p.Q901R	0.967	85	84	Missense Variant	Missense Variant	MODERATE	ENST00000618327.4	Benign		0.983235000000	rs7197779	85	84	ENST00000618327.4	Benign		rs7197779
COL2A1	chr12	47985759	47985759	C	A	c.1649G>T	cGt/cTt	p.R550L	0.42	9	1	Missense Variant	Missense Variant	MODERATE	ENST00000380518.8	Benign/Likely_benign		0.001235070000	rs186233557	9	1	ENST00000380518.8	Benign/Likely_benign		rs186233557
ERBB3	chr12	56101214	56101214	A	T	c.3355A>T	Agc/Tgc	p.S1119C	0.711	14	9	Missense Variant	Missense Variant	MODERATE	ENST00000267101.8	Benign	COSV57247854	0.088057000000	rs773123	14	9	ENST00000267101.8	Benign	COSV57247854	rs773123
ERCC2	chr19	45351661	45351661	T	G	c.2251A>C	Aag/Cag	p.K751Q	0.592	48	46	Missense Variant	Missense Variant	MODERATE	ENST00000391945.10	Benign/Likely_benign	COSV67266431	0.322955000000	rs13181	48	46	ENST00000391945.10	Benign/Likely_benign	COSV67266431	rs13181
FANCE	chr6	35457944	35457944	C	G	c.929C>G	cCa/cGa	p.P310R	0.134	4	1	Missense Variant	Missense Variant	MODERATE	ENST00000229769.3	Uncertain_significance		0.000147709000	rs139600847	4	1	ENST00000229769.3	Uncertain_significance		rs139600847
FH	chr1	241517259	241517259	T	C	c.190A>G	Aat/Gat	p.N64D	0.283	5	1	Missense Variant	Missense Variant	MODERATE	ENST00000366560.4	Uncertain_significance		0.000004221010	rs886046319	5	1	ENST00000366560.4	Uncertain_significance		rs886046319
KAT6B	chr10	75022147	75022150	GGAA	G	c.3310_3312del	GAA/-	p.E1104del	0.921	45	33	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000287239.10		COSV54741061			45	33	ENST00000287239.10		COSV54741061
KMT2A	chr11	118436670	118436670	C	T	c.158C>T	gCg/gTg	p.A53V	0.562	19	5	Missense Variant	Missense Variant	MODERATE	ENST00000534358.8	Benign/Likely_benign	COSV100630341	0.002430870000	rs9332747	19	5	ENST00000534358.8	Benign/Likely_benign	COSV100630341	rs9332747
MAML2	chr11	96092210	96092219	TTGCTGCTGC	T	c.1812_1820del	caGCAGCAGCAa/caa	p.Q619_Q621del	0.761	68	59	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000524717.6		COSV73262593			68	59	ENST00000524717.6		COSV73262593
MECOM	chr3	169116188	169116188	C	T	c.1684G>A	Gag/Aag	p.E562K	0.403	7	1	Missense Variant	Missense Variant	MODERATE	ENST00000651503.2		COSV52963475	0.000046565600	rs149928659	7	1	ENST00000651503.2		COSV52963475	rs149928659

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