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	99593875	99593880	CTGAGG	C	c.1856_1860del	aCCTCA/a	p.T619Sfs*72	0.426	12	2	Frameshift Mutation	Frameshift Mutation	HIGH	ENST00000409579.5		COSV57864141		rs199557232	12	2	ENST00000409579.5		COSV57864141	rs199557232
AFF3	chr2	99593872	99593873	CG	C	c.1863del	gcC/gc	p.D623Tfs*48	0.426	12	5	Frameshift Mutation	Frameshift Mutation	HIGH	ENST00000409579.5		COSV57841232		rs201754690	12	5	ENST00000409579.5		COSV57841232	rs201754690
AKAP9	chr7	92105709	92105709	G	C	c.11362G>C	Gtc/Ctc	p.V3788L	0.403	50	1	Missense Variant	Missense Variant	MODERATE	ENST00000356239.8	Conflicting_interpretations_of_pathogenicity		0.000139277000	rs199527737	50	1	ENST00000356239.8	Conflicting_interpretations_of_pathogenicity		rs199527737
ANK1	chr8	41695291	41695291	G	A	c.3001C>T	Cgt/Tgt	p.R1001C	0.262	9	1	Missense Variant	Missense Variant	MODERATE	ENST00000289734.13			0.000008442020	rs148222043	9	1	ENST00000289734.13			rs148222043
AR	chrX	67545316	67545322	TGCAGCA	T	c.234_239del	ctGCAGCAg/ctg	p.Q79_Q80del	0.743	48	8	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000374690.9		COSV65952724			48	8	ENST00000374690.9		COSV65952724
ATM	chr11	108247071	108247071	C	T	c.1009C>T	Cgt/Tgt	p.R337C	0.4	10	1	Missense Variant	Missense Variant	MODERATE	ENST00000278616.8	Uncertain_significance	COSV53723836	0.000080277800	rs138398778	10	1	ENST00000278616.8	Uncertain_significance	COSV53723836	rs138398778
ATRX	chrX	77682471	77682471	C	G	c.2785G>C	Gag/Cag	p.E929Q	0.961	59	56	Missense Variant	Missense Variant	MODERATE	ENST00000373344.10	Benign			rs3088074	59	56	ENST00000373344.10	Benign		rs3088074
BRCA1	chr17	43091492	43091492	T	C	c.4039A>G	Aga/Gga	p.R1347G	0.588	19	1	Missense Variant	Missense Variant	MODERATE	ENST00000357654.9	Benign	COSV100524757	0.003703270000	rs28897689	19	1	ENST00000357654.9	Benign	COSV100524757	rs28897689
CBLB	chr3	105702216	105702216	C	A	c.1837G>T	Ggc/Tgc	p.G613C	0.321	7	1	Missense Variant	Missense Variant	MODERATE	ENST00000394030.8			0.000004224150	rs1476818648	7	1	ENST00000394030.8			rs1476818648
CDKN1A	chr6	36684194	36684194	C	A	c.93C>A	agC/agA	p.S31R	0.631	4	2	Missense Variant	Missense Variant	MODERATE	ENST00000244741.10	Benign	COSV55187247	0.156476000000	rs1801270	4	2	ENST00000244741.10	Benign	COSV55187247	rs1801270
CIC	chr19	42290854	42290854	C	T	c.2086C>T	Cgg/Tgg	p.R696W	0.481	11	1	Missense Variant	Missense Variant	MODERATE	ENST00000575354.6		COSV50547794	0.000030632200	rs550975604	11	1	ENST00000575354.6		COSV50547794	rs550975604
CIITA	chr16	10909070	10909070	A	G	c.2702A>G	cAg/cGg	p.Q901R	0.979	85	84	Missense Variant	Missense Variant	MODERATE	ENST00000618327.4	Benign		0.983235000000	rs7197779	85	84	ENST00000618327.4	Benign		rs7197779
COL2A1	chr12	47997874	47997874	T	A	c.426A>T	gaA/gaT	p.E142D	0.597	9	1	Missense Variant	Missense Variant	MODERATE	ENST00000380518.8	Benign		0.037236200000	rs34392760	9	1	ENST00000380518.8	Benign		rs34392760
CREB1	chr2	207560248	207560248	C	T	c.137C>T	gCa/gTa	p.A46V	0.407	1	1	Missense Variant	Missense Variant	MODERATE	ENST00000353267.8			0.000199305000	rs143117860	1	1	ENST00000353267.8			rs143117860
CSMD3	chr8	112573521	112573521	C	T	c.4022G>A	gGc/gAc	p.G1341D	0.137	24	1	Missense Variant	Missense Variant	MODERATE	ENST00000297405.10					24	1	ENST00000297405.10

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