PDX Portal

Model Details

Patient Information for Model: BCM-15008

Model Contact

Model: BCM-15008
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-15008

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
ABL2	chr1	179108478	179108478	T	C	c.2789A>G	aAa/aGa	p.K930R	0.481	11	4	Missense Variant	Missense Variant	MODERATE	ENST00000502732.6	Benign	COSV99048946	0.008745050000	rs17277288	11	4	ENST00000502732.6	Benign	COSV99048946	rs17277288
AKAP9	chr7	92079584	92079584	A	G	c.7451A>G	aAa/aGa	p.K2484R	0.502	115	14	Missense Variant	Missense Variant	MODERATE	ENST00000356239.8	Benign/Likely_benign		0.106317000000	rs35759833	115	14	ENST00000356239.8	Benign/Likely_benign		rs35759833
AKAP9	chr7	92085597	92085597	C	T	c.8935C>T	Cct/Tct	p.P2979S	0.989	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	0.979	115	115	Missense Variant	Missense Variant	MODERATE	ENST00000389048.8	Benign	COSV101201052	0.997594000000	rs1670283	115	115	ENST00000389048.8	Benign	COSV101201052	rs1670283
ARAF	chrX	47569034	47569038	GTATC	G	c.1300+7_1300+10del			0.857	4	1	Splice Donor Variant	Splice Donor Variant; Intronic Variant	HIGH	ENST00000377045.9		COSV51691850		.	4	1	ENST00000377045.9		COSV51691850	.
ARHGEF10	chr8	1885635	1885635	G	C	c.1110G>C	ttG/ttC	p.L370F	0.937	43	21	Missense Variant	Missense Variant	MODERATE	ENST00000349830.8	Benign	COSV50643418	0.160503000000	rs9657362	43	21	ENST00000349830.8	Benign	COSV50643418	rs9657362
ARID2	chr12	45730136	45730136	A	G	c.185A>G	aAg/aGg	p.K62R	0.222	20	1	Missense Variant	Missense Variant; Splice Region Variant	MODERATE	ENST00000334344.11				.	20	1	ENST00000334344.11			.
ATIC	chr2	215325297	215325297	C	G	c.347C>G	aCt/aGt	p.T116S	0.917	52	43	Missense Variant	Missense Variant	MODERATE	ENST00000236959.14	Benign	COSV52691660	0.326476000000	rs2372536	52	43	ENST00000236959.14	Benign	COSV52691660	rs2372536
ATM	chr11	108304735	108304735	G	A	c.5557G>A	Gat/Aat	p.D1853N	0.942	51	17	Missense Variant	Missense Variant	MODERATE	ENST00000278616.8	Benign	COSV53728020	0.113458000000	rs1801516	51	17	ENST00000278616.8	Benign	COSV53728020	rs1801516
ATM	chr11	108353828	108353828	A	G	c.8734A>G	Aga/Gga	p.R2912G	0.5	51	1	Missense Variant	Missense Variant	MODERATE	ENST00000278616.8	Uncertain_significance		0.000215270000	rs376676328	51	1	ENST00000278616.8	Uncertain_significance		rs376676328
ATR	chr3	142562770	142562770	A	G	c.632T>C	aTg/aCg	p.M211T	0.833	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
ATRX	chrX	77682471	77682471	C	G	c.2785G>C	Gag/Cag	p.E929Q	0.912	91	73	Missense Variant	Missense Variant	MODERATE	ENST00000373344.10	Benign			rs3088074	91	73	ENST00000373344.10	Benign		rs3088074
AXIN2	chr17	65538227	65538227	C	G	c.1176G>C	gaG/gaC	p.E392D	0.251	75	1	Missense Variant	Missense Variant	MODERATE	ENST00000307078.10				.	75	1	ENST00000307078.10			.
BARD1	chr2	214809500	214809500	G	A	c.70C>T	Ccc/Tcc	p.P24S	0.889	85	52	Missense Variant	Missense Variant	MODERATE	ENST00000260947.9	Benign	COSV53608734	0.384797000000	rs1048108	85	52	ENST00000260947.9	Benign	COSV53608734	rs1048108
BARD1	chr2	214780740	214780740	C	G	c.1134G>C	agG/agC	p.R378S	0.966	85	72	Missense Variant	Missense Variant	MODERATE	ENST00000260947.9	Benign	COSV53612030	0.542039000000	rs2229571	85	72	ENST00000260947.9	Benign	COSV53612030	rs2229571

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-15008

Patient

PDX

HER2

Metastasis Information for Model: BCM-15008

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-15008

Event Id	Treatment	Treatment Setting	Age at Start	Age at End	Duration	Clinical Response	Pathologic Response	Reason Stopped
15	Cyclophosphamide,Doxorubicin	Adjuvant	64.06	64.06	1	Not Reported	Not Applicable	Side Effects
20	Cyclophosphamide,Docetaxel	Adjuvant	64.07	64.4	120 days	Disease Progression	Not Applicable	Disease Progression
35	Cisplatin,Gemcitabine	Metastatic	64.5	64.5	1	Disease Progression	Not Applicable	Disease Progression
45	Radiation Therapy	Metastatic	64.55	64.6	18 days	Disease Progression	Not Applicable	Disease Progression