PDX Portal

Model Details

Patient Information for Model: BCM-0113

Model Contact

Model: BCM-0113
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-0113

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	99593872	99593873	CG	C	c.1863del	gcC/gc	p.D623Tfs*48	0.429	56	6	Frameshift Mutation	Frameshift Mutation	HIGH	ENST00000409579.5		COSV57841232		rs201754690	56	6	ENST00000409579.5		COSV57841232	rs201754690
AFF3	chr2	99593875	99593880	CTGAGG	C	c.1856_1860del	aCCTCA/a	p.T619Sfs*72	0.429	56	6	Frameshift Mutation	Frameshift Mutation	HIGH	ENST00000409579.5		COSV57864141		rs199557232	56	6	ENST00000409579.5		COSV57864141	rs199557232
AKAP9	chr7	92001306	92001306	G	T	c.1389G>T	atG/atT	p.M463I	0.367	115	73	Missense Variant	Missense Variant	MODERATE	ENST00000356239.8	Benign	COSV62345589	0.376835000000	rs6964587	115	73	ENST00000356239.8	Benign	COSV62345589	rs6964587
AKAP9	chr7	92105709	92105709	G	C	c.11362G>C	Gtc/Ctc	p.V3788L	0.408	115	1	Missense Variant	Missense Variant	MODERATE	ENST00000356239.8	Conflicting_interpretations_of_pathogenicity		0.000139277000	rs199527737	115	1	ENST00000356239.8	Conflicting_interpretations_of_pathogenicity		rs199527737
AKAP9	chr7	92085597	92085597	C	T	c.8935C>T	Cct/Tct	p.P2979S	0.952	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	0.556	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	0.667	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	0.992	115	115	Missense Variant	Missense Variant	MODERATE	ENST00000389048.8	Benign	COSV101201052	0.997594000000	rs1670283	115	115	ENST00000389048.8	Benign	COSV101201052	rs1670283
ANK1	chr8	41695291	41695291	G	A	c.3001C>T	Cgt/Tgt	p.R1001C	0.227	37	1	Missense Variant	Missense Variant	MODERATE	ENST00000289734.13			0.000008442020	rs148222043	37	1	ENST00000289734.13			rs148222043
AR	chrX	67545316	67545322	TGCAGCA	T	c.234_239del	ctGCAGCAg/ctg	p.Q79_Q80del	0.935	101	24	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000374690.9		COSV65952724		.	101	24	ENST00000374690.9		COSV65952724	.
ARHGEF10L	chr1	17697181	17697181	C	T	c.3641C>T	gCc/gTc	p.A1214V	0.025	14	1	Missense Variant	Missense Variant	MODERATE	ENST00000361221.8				.	14	1	ENST00000361221.8			.
ARID2	chr12	45850443	45850443	C	T	c.2320C>T	Cca/Tca	p.P774S	0.073	20	1	Missense Variant	Missense Variant	MODERATE	ENST00000334344.11				.	20	1	ENST00000334344.11			.
ATM	chr11	108247071	108247071	C	T	c.1009C>T	Cgt/Tgt	p.R337C	0.407	51	1	Missense Variant	Missense Variant	MODERATE	ENST00000278616.8	Uncertain_significance	COSV53723836	0.000080277800	rs138398778	51	1	ENST00000278616.8	Uncertain_significance	COSV53723836	rs138398778
ATM	chr11	108292644	108292644	T	TAACG	c.4462_4463insAACG	tta/tAACGta	p.L1488*	0.032	51	1	Frameshift Mutation	Frameshift Mutation; Nonsense Mutation	HIGH	ENST00000278616.8				.	51	1	ENST00000278616.8			.
ATR	chr3	142562770	142562770	A	G	c.632T>C	aTg/aCg	p.M211T	0.312	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

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-0113

Patient

PDX

H&E

HER2

Metastasis Information for Model: BCM-0113

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-0113

Event Id	Treatment	Treatment Setting	Age at Start	Age at End	Duration	Clinical Response	Pathologic Response	Reason Stopped
10	Doxorubicin	Neoadjuvant	63.46	63.54	29 days	Not Reported	Not Reported	Unknown
15	Cyclophosphamide,Doxorubicin	Neoadjuvant	63.62	63.79	62 days	Not Reported	Not Reported	Treatment Completed
20	Docetaxel	Neoadjuvant	63.85	63.85	1	Not Reported	Not Reported	Side Effects
25	Paclitaxel	Neoadjuvant	63.91	63.99	29 days	Not Reported	Not Reported	Side Effects
35	Carboplatin	Adjuvant	64.16	64.34	66 days	Not Reported	Not Applicable	Treatment Completed
50	Capecitabine,Ixabepilone	Metastatic	64.49	64.68	69 days	Not Reported	Not Applicable	Unknown