PDX Portal

Model Details

Patient Information for Model: BCM-15115

Model Contact

Model: BCM-15115
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-15115

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
AFF3	chr2	99601548	99601551	CGCT	C	c.1330_1332del	AGC/-	p.S444del	0.159	56	43	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000409579.5		COSV57843239		.	56	43	ENST00000409579.5		COSV57843239	.
AKAP9	chr7	92001306	92001306	G	T	c.1389G>T	atG/atT	p.M463I	0.47	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	0.991	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	0.476	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	0.499	115	73	In-frame Insertion	In-frame Insertion	MODERATE	ENST00000356239.8		COSV62337888		rs10644111	115	73	ENST00000356239.8		COSV62337888	rs10644111
ALK	chr2	29193706	29193706	T	C	c.4381A>G	Atc/Gtc	p.I1461V	0.995	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	0.983	100	100	Missense Variant	Missense Variant	MODERATE	ENST00000257430.9	Benign	COSV57321643	0.794920000000	rs459552	100	100	ENST00000257430.9	Benign	COSV57321643	rs459552
APC	chr5	112842245	112842249	TCAAG	T	c.6655_6658del	CAAGca/ca	p.A2219Tfs*11	0.076	100	1	Frameshift Mutation	Frameshift Mutation	HIGH	ENST00000257430.9				.	100	1	ENST00000257430.9			.
APOBEC3B	chr22	38991390	38991391	TG	T	c.784del	ctG/ct	p.V262Ffs*42	0.927	15	6	Frameshift Mutation	Frameshift Mutation	HIGH	ENST00000333467.4		COSV59840725		rs368511533	15	6	ENST00000333467.4		COSV59840725	rs368511533
AR	chrX	67545316	67545316	T	TGCAGCA	c.234_239dup	ctg/ctGCAGCAg	p.Q79_Q80dup	0.834	101	15	In-frame Insertion	In-frame Insertion	MODERATE	ENST00000374690.9		COSV65953707		.	101	15	ENST00000374690.9		COSV65953707	.
ARHGEF10	chr8	1909390	1909390	G	A	c.2063G>A	aGc/aAc	p.S688N	0.404	43	1	Missense Variant	Missense Variant	MODERATE	ENST00000349830.8	Conflicting_interpretations_of_pathogenicity		0.000818752000	rs143290224	43	1	ENST00000349830.8	Conflicting_interpretations_of_pathogenicity		rs143290224
ARHGEF10L	chr1	17619364	17619365	GC	G	c.862del	Ctc/tc	p.L288Sfs*23	0.041	14	1	Frameshift Mutation	Frameshift Mutation	HIGH	ENST00000361221.8				.	14	1	ENST00000361221.8			.
ARID1B	chr6	156777879	156777879	G	A	c.199G>A	Ggc/Agc	p.G67S	0.4	80	6	Missense Variant	Missense Variant	MODERATE	ENST00000636930.2	Benign			rs566121493	80	6	ENST00000636930.2	Benign		rs566121493
ARID2	chr12	45904929	45904934	TGCAGA	T	c.5364-4_5364del			0.108	20	1	Splice Acceptor Variant	Splice Acceptor Variant; Coding Sequence Variant; Intronic Variant	HIGH	ENST00000334344.11				rs1411931579	20	1	ENST00000334344.11			rs1411931579
ARID2	chr12	45904937	45904937	G	T	c.5367G>T	ttG/ttT	p.L1789F	0.108	20	1	Missense Variant	Missense Variant	MODERATE	ENST00000334344.11				rs1444599005	20	1	ENST00000334344.11			rs1444599005

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-15115

There are no histology images for this model.

Metastasis Information for Model: BCM-15115

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-15115

Event Id	Treatment	Treatment Setting	Age at Start	Age at End	Duration	Clinical Response	Pathologic Response	Reason Stopped
10	Anastrozole	Neoadjuvant	63.84	64.13	106 days	Not Reported	Not Reported	Treatment Completed
20	Paclitaxel	Adjuvant	64.37	64.51	51 days	Not Reported	Not Applicable	Treatment Completed
25	Radiation Therapy	Adjuvant	64.57	64.64	26 days	Not Reported	Not Applicable	Treatment Completed