PDX Portal

Model Details

Patient Information for Model: BCM-15051

Model Contact

Model: BCM-15051
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-15051

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	92022864	92022864	A	AAAC	c.4004_4006dup	aaa/aAACaa	p.K1335_L1336insQ	0.976	50	35	In-frame Insertion	In-frame Insertion	MODERATE	ENST00000356239.8		COSV62337888		rs10644111	50	35	ENST00000356239.8		COSV62337888	rs10644111
AR	chrX	67546514	67546514	T	TGGC	c.1418_1420dup	-/GGC	p.G473dup	0.832	48	8	In-frame Insertion	In-frame Insertion	MODERATE	ENST00000374690.9		COSV104687717			48	8	ENST00000374690.9		COSV104687717
ARNT	chr1	150817408	150817408	C	T	c.1531G>A	Gac/Aac	p.D511N	0.394	5	2	Missense Variant	Missense Variant	MODERATE	ENST00000358595.10	Benign		0.005402390000	rs1805133	5	2	ENST00000358595.10	Benign		rs1805133
ATRX	chrX	77682471	77682471	C	G	c.2785G>C	Gag/Cag	p.E929Q	0.364	59	56	Missense Variant	Missense Variant	MODERATE	ENST00000373344.10	Benign			rs3088074	59	56	ENST00000373344.10	Benign		rs3088074
BAZ1A	chr14	34800248	34800248	C	G	c.1104G>C	gaG/gaC	p.E368D	0.98	9	2	Missense Variant	Missense Variant	MODERATE	ENST00000360310.6				rs1773618060	9	2	ENST00000360310.6			rs1773618060
BCR	chr22	23182000	23182000	C	T	c.1040C>T	tCt/tTt	p.S347F	0.978	7	2	Missense Variant	Missense Variant	MODERATE	ENST00000305877.13					7	2	ENST00000305877.13
CIITA	chr16	10907834	10907834	C	T	c.2345C>T	tCg/tTg	p.S782L	0.992	85	2	Missense Variant	Missense Variant	MODERATE	ENST00000618327.4	Benign	COSV60855363	0.062111600000	rs13330686	85	2	ENST00000618327.4	Benign	COSV60855363	rs13330686
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
CIITA	chr16	10907837	10907837	T	C	c.2348T>C	gTg/gCg	p.V783A	0.981	85	2	Missense Variant	Missense Variant	MODERATE	ENST00000618327.4	Benign	COSV60855512	0.062202200000	rs13336804	85	2	ENST00000618327.4	Benign	COSV60855512	rs13336804
CREB3L2	chr7	137928167	137928170	CTGG	C	c.299_301del	aCCAgt/agt	p.T100del	0.375	49	49	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000330387.11		COSV57791862		rs3217268	49	49	ENST00000330387.11		COSV57791862	rs3217268
ERCC2	chr19	45351661	45351661	T	G	c.2251A>C	Aag/Cag	p.K751Q	0.368	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
EZH2	chr7	148828812	148828812	C	G	c.553G>C	Gac/Cac	p.D185H	0.286	13	12	Missense Variant	Missense Variant	MODERATE	ENST00000320356.7	Benign	COSV57449162	0.078149200000	rs2302427	13	12	ENST00000320356.7	Benign	COSV57449162	rs2302427
FAM47C	chrX	37009783	37009783	G	T	c.1373G>T	cGg/cTg	p.R458L	0.035	14	7	Missense Variant	Missense Variant	MODERATE	ENST00000358047.5			0.000123073000	rs200849623	14	7	ENST00000358047.5			rs200849623
FANCF	chr11	22624823	22624823	C	T	c.988G>A	Gag/Aag	p.E330K	0.446	4	2	Missense Variant	Missense Variant	MODERATE	ENST00000327470.6					4	2	ENST00000327470.6
GNAS	chr20	58855157	58855157	C	T	c.1892C>T	tCg/tTg	p.S631L	0.409	15	2	Missense Variant	Missense Variant	MODERATE	ENST00000371100.8					15	2	ENST00000371100.8

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-15051

Patient

PDX

H&E

HER2

Metastasis Information for Model: BCM-15051

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-15051

Event Id	Treatment	Treatment Setting	Age at Start	Age at End	Duration	Clinical Response	Pathologic Response	Reason Stopped
10	Carboplatin,Paclitaxel	Neoadjuvant	59.45	59.69	88 days	Not Reported	No Response	Treatment Completed
20	Cyclophosphamide,Doxorubicin	Neoadjuvant	59.76	59.8	15 days	Progressive Disease	Not Applicable	Disease Progression
35	Radiation Therapy	Adjuvant	59.96	60.08	44 days	Not Reported	Not Applicable	Treatment Completed
40	Capecitabine	Adjuvant	60.08	60.56	175 days	Not Reported	Not Applicable	Treatment Completed