PDX Portal

Model Details

Patient Information for Model: BCM-15029

Model Contact

Model: BCM-15029
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-15029

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	92001306	92001306	G	T	c.1389G>T	atG/atT	p.M463I	0.638	115	73	Missense Variant	Missense Variant	MODERATE	ENST00000356239.8	Benign	COSV62345589	0.376835000000	rs6964587	115	73	ENST00000356239.8	Benign	COSV62345589	rs6964587
AKAP9	chr7	92085597	92085597	C	T	c.8935C>T	Cct/Tct	p.P2979S	0.986	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
AKAP9	chr7	92083384	92083384	A	G	c.8375A>G	aAt/aGt	p.N2792S	0.733	115	62	Missense Variant	Missense Variant	MODERATE	ENST00000356239.8	Benign/Likely_benign	COSV62339152	0.357813000000	rs6960867	115	62	ENST00000356239.8	Benign/Likely_benign	COSV62339152	rs6960867
AKAP9	chr7	92022864	92022864	A	AAAC	c.4004_4006dup	aaa/aAACaa	p.K1335_L1336insQ	0.579	115	73	In-frame Insertion	In-frame Insertion	MODERATE	ENST00000356239.8		COSV62337888		rs10644111	115	73	ENST00000356239.8		COSV62337888	rs10644111
ALK	chr2	29193500	29193500	G	C	c.4587C>G	gaC/gaG	p.D1529E	0.605	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	0.997	115	115	Missense Variant	Missense Variant	MODERATE	ENST00000389048.8	Benign	COSV101201052	0.997594000000	rs1670283	115	115	ENST00000389048.8	Benign	COSV101201052	rs1670283
ALK	chr2	29193615	29193615	T	C	c.4472A>G	aAg/aGg	p.K1491R	0.603	115	51	Missense Variant	Missense Variant	MODERATE	ENST00000389048.8	Benign	COSV66555753	0.349007000000	rs1881420	115	51	ENST00000389048.8	Benign	COSV66555753	rs1881420
APC	chr5	112828868	112828869	GT	G	c.1643del	gTt/gt	p.L548*	0.493	100	1	Frameshift Mutation	Frameshift Mutation	HIGH	ENST00000257430.9		COSV57325795		rs1554082091	100	1	ENST00000257430.9		COSV57325795	rs1554082091
APC	chr5	112841059	112841059	T	A	c.5465T>A	gTc/gAc	p.V1822D	0.988	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	0.516	101	35	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000374690.9		COSV65954886		.	101	35	ENST00000374690.9		COSV65954886	.
AR	chrX	67545316	67545325	TGCAGCAGCA	T	c.231_239del	ctGCAGCAGCAg/ctg	p.Q78_Q80del	0.448	101	16	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000374690.9		COSV65958085		.	101	16	ENST00000374690.9		COSV65958085	.
ARHGEF10	chr8	1929314	1929314	T	G	c.2950T>G	Tcc/Gcc	p.S984A	0.971	43	10	Missense Variant	Missense Variant	MODERATE	ENST00000349830.8	Benign	COSV50664117	0.053800200000	rs17683288	43	10	ENST00000349830.8	Benign	COSV50664117	rs17683288
ARID1B	chr6	157190043	157190043	G	C	c.4064G>C	aGt/aCt	p.S1355T	0.98	80	4	Missense Variant	Missense Variant	MODERATE	ENST00000636930.2		COSV104368469		.	80	4	ENST00000636930.2		COSV104368469	.
ATIC	chr2	215325297	215325297	C	G	c.347C>G	aCt/aGt	p.T116S	0.985	52	43	Missense Variant	Missense Variant	MODERATE	ENST00000236959.14	Benign	COSV52691660	0.326476000000	rs2372536	52	43	ENST00000236959.14	Benign	COSV52691660	rs2372536
ATR	chr3	142459302	142459302	C	T	c.7274G>A	cGa/cAa	p.R2425Q	0.233	101	24	Missense Variant	Missense Variant	MODERATE	ENST00000350721.9	Benign	COSV63383988	0.130080000000	rs2229032	101	24	ENST00000350721.9	Benign	COSV63383988	rs2229032

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-15029

Patient

PDX

HER2

Metastasis Information for Model: BCM-15029

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-15029

Event Id	Treatment	Treatment Setting	Age at Start	Age at End	Duration	Clinical Response	Pathologic Response	Reason Stopped
10	Cyclophosphamide,Doxorubicin,Radiation Therapy	Adjuvant	46.89	47.56	245 days	Not Reported	Not Reported	Treatment Completed
30	Carboplatin,Docetaxel	Neoadjuvant	63.05	63.28	84 days	Partial Response	Partial Response	Side Effects