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
AFF4	chr5	132897083	132897103	GTGTAGCTATTCCCAGTGCCC	G	c.1527_1546del	caGGGCACTGGGAATAGCTACAct/cact	p.Q509Hfs*2	0.523	7	1	Frameshift Mutation	Frameshift Mutation	HIGH	ENST00000265343.10					7	1	ENST00000265343.10
AR	chrX	67546514	67546517	TGGC	T	c.1418_1420del	GGC/-	p.G473del	0.858	48	3	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000374690.9		COSV65958513			48	3	ENST00000374690.9		COSV65958513
ARID1A	chr1	26696761	26696761	C	T	c.358C>T	Ccg/Tcg	p.P120S	0.952	19	2	Missense Variant	Missense Variant	MODERATE	ENST00000324856.13	Conflicting_interpretations_of_pathogenicity	COSV61373973	0.000271628000	rs571264557	19	2	ENST00000324856.13	Conflicting_interpretations_of_pathogenicity	COSV61373973	rs571264557
ARID1B	chr6	157206530	157206534	CTGTT	C	c.5763_5766del	cTGTTt/ct	p.F1921Lfs*52	0.937	37	1	Frameshift Mutation	Frameshift Mutation	HIGH	ENST00000636930.2		COSV99269679		rs1554237269	37	1	ENST00000636930.2		COSV99269679	rs1554237269
BIRC6	chr2	32529771	32529771	C	T	c.12041C>T	aCa/aTa	p.T4014I	1.0	15	1	Missense Variant	Missense Variant	MODERATE	ENST00000421745.6			0.000038112000	rs141336419	15	1	ENST00000421745.6			rs141336419
BRCA2	chr13	32340575	32340575	C	A	c.6220C>A	Cac/Aac	p.H2074N	0.985	21	2	Missense Variant	Missense Variant	MODERATE	ENST00000380152.7	Benign		0.000727523000	rs34309943	21	2	ENST00000380152.7	Benign		rs34309943
BUB1B	chr15	40196656	40196656	G	C	c.1170G>C	gaG/gaC	p.E390D	0.985	5	3	Missense Variant	Missense Variant	MODERATE	ENST00000287598.11	Benign	COSV55010791	0.008655650000	rs1017842	5	3	ENST00000287598.11	Benign	COSV55010791	rs1017842
CIITA	chr16	10909070	10909070	A	G	c.2702A>G	cAg/cGg	p.Q901R	0.386	85	84	Missense Variant	Missense Variant	MODERATE	ENST00000618327.4	Benign		0.983235000000	rs7197779	85	84	ENST00000618327.4	Benign		rs7197779
CLTCL1	chr22	19219970	19219970	C	T	c.2834G>A	cGc/cAc	p.R945H	0.444	19	3	Missense Variant	Missense Variant	MODERATE	ENST00000427926.6	Benign	COSV99067208	0.003138280000	rs36077768	19	3	ENST00000427926.6	Benign	COSV99067208	rs36077768
COL1A1	chr17	50188134	50188134	C	T	c.3223G>A	Gcc/Acc	p.A1075T	0.996	11	3	Missense Variant	Missense Variant	MODERATE	ENST00000225964.10	Benign			rs1800215	11	3	ENST00000225964.10	Benign		rs1800215
ELK4	chr1	205620109	205620109	C	T	c.937G>A	Gta/Ata	p.V313I	0.483	3	1	Missense Variant	Missense Variant	MODERATE	ENST00000357992.9			0.000244833000	rs34515238	3	1	ENST00000357992.9			rs34515238
EPHA3	chr3	89210224	89210224	C	G	c.518C>G	cCt/cGt	p.P173R	0.528	5	1	Missense Variant	Missense Variant	MODERATE	ENST00000336596.7					5	1	ENST00000336596.7
ERCC5	chr13	102854340	102854340	G	A	c.433G>A	Gtt/Att	p.V145I	0.962	14	1	Missense Variant	Missense Variant	MODERATE	ENST00000652225.2	Benign/Likely_benign	COSV104673176	0.001582750000	rs4987063	14	1	ENST00000652225.2	Benign/Likely_benign	COSV104673176	rs4987063
ESR1	chr6	151808321	151808321	A	G	c.409A>G	Agc/Ggc	p.S137G	0.976	10	3	Missense Variant	Missense Variant	MODERATE	ENST00000440973.5	Benign		0.000500829000	rs185717042	10	3	ENST00000440973.5	Benign		rs185717042
ETV5	chr3	186080022	186080022	G	C	c.445C>G	Cta/Gta	p.L149V	0.562	4	1	Missense Variant	Missense Variant	MODERATE	ENST00000306376.10	Benign		0.002721030000	rs78506201	4	1	ENST00000306376.10	Benign		rs78506201

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