PDX Portal

Model Details

Patient Information for Model: BCM-0104

Model Contact

Model: BCM-0104
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-0104

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
ABL1	chr9	130885205	130885205	C	T	c.2915C>T	tCg/tTg	p.S972L	0.994	55	2	Missense Variant	Missense Variant	MODERATE	ENST00000318560.6	not_provided	COSV104403997	0.020952300000	rs2229067	55	2	ENST00000318560.6	not_provided	COSV104403997	rs2229067
AFF3	chr2	100007213	100007213	C	T	c.497G>A	aGt/aAt	p.S166N	0.683	56	1	Missense Variant	Missense Variant	MODERATE	ENST00000409579.5			0.000004220760	rs151087811	56	1	ENST00000409579.5			rs151087811
AKAP9	chr7	92079584	92079584	A	G	c.7451A>G	aAa/aGa	p.K2484R	0.965	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	0.947	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	29193500	29193500	G	C	c.4587C>G	gaC/gaG	p.D1529E	0.991	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	0.992	115	115	Missense Variant	Missense Variant	MODERATE	ENST00000389048.8	Benign	COSV101201052	0.997594000000	rs1670283	115	115	ENST00000389048.8	Benign	COSV101201052	rs1670283
APC	chr5	112841059	112841059	T	A	c.5465T>A	gTc/gAc	p.V1822D	0.96	100	100	Missense Variant	Missense Variant	MODERATE	ENST00000257430.9	Benign	COSV57321643	0.794920000000	rs459552	100	100	ENST00000257430.9	Benign	COSV57321643	rs459552
AR	chrX	67545316	67545319	TGCA	T	c.237_239del	ctGCAg/ctg	p.Q80del	0.948	101	35	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000374690.9		COSV65954886		.	101	35	ENST00000374690.9		COSV65954886	.
ARHGAP26	chr5	143214082	143214082	G	A	c.2185G>A	Gat/Aat	p.D729N	0.893	8	1	Missense Variant	Missense Variant	MODERATE	ENST00000645722.2	not_provided		0.000005067700	rs587778049	8	1	ENST00000645722.2	not_provided		rs587778049
ARHGEF10	chr8	1928541	1928541	G	A	c.2812G>A	Gtt/Att	p.V938I	0.978	43	2	Missense Variant	Missense Variant	MODERATE	ENST00000349830.8	Likely_benign	COSV50664968	0.005334550000	rs61752020	43	2	ENST00000349830.8	Likely_benign	COSV50664968	rs61752020
ARID1A	chr1	26697480	26697480	C	A	c.1077C>A	caC/caA	p.H359Q	0.329	48	1	Missense Variant	Missense Variant	MODERATE	ENST00000324856.13				.	48	1	ENST00000324856.13			.
ATIC	chr2	215325297	215325297	C	G	c.347C>G	aCt/aGt	p.T116S	0.959	52	43	Missense Variant	Missense Variant	MODERATE	ENST00000236959.14	Benign	COSV52691660	0.326476000000	rs2372536	52	43	ENST00000236959.14	Benign	COSV52691660	rs2372536
ATR	chr3	142562770	142562770	A	G	c.632T>C	aTg/aCg	p.M211T	0.475	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
ATR	chr3	142459302	142459302	C	T	c.7274G>A	cGa/cAa	p.R2425Q	0.124	101	24	Missense Variant	Missense Variant	MODERATE	ENST00000350721.9	Benign	COSV63383988	0.130080000000	rs2229032	101	24	ENST00000350721.9	Benign	COSV63383988	rs2229032
ATRX	chrX	77682471	77682471	C	G	c.2785G>C	Gag/Cag	p.E929Q	0.568	91	73	Missense Variant	Missense Variant	MODERATE	ENST00000373344.10	Benign			rs3088074	91	73	ENST00000373344.10	Benign		rs3088074

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-0104

Patient

PDX

H&E

HER2

Metastasis Information for Model: BCM-0104

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-0104

Event Id	Treatment	Treatment Setting	Age at Start	Age at End	Duration	Clinical Response	Pathologic Response	Reason Stopped
15	Paclitaxel	Neoadjuvant	58.27	58.46	69 days	Partial Response	Not Reported	Other
20	Paclitaxel	Neoadjuvant	58.67	58.7	11 days	Progressive Disease	No Response	Disease Progression
30	Radiation Therapy	Metastatic	59.29	59.42	47 days	Not Reported	Not Applicable	Treatment Completed
45	Radiation Therapy	Metastatic	59.96	59.96	1	Not Reported	Not Applicable	Disease Progression