PDX Portal

Model Details

Patient Information for Model: BCM-15006

Model Contact

Model: BCM-15006
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-15006

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
ACVR1	chr2	157765946	157765949	ATTC	A	c.1038_1040del	aaGAAt/aat	p.K346del	0.26	2	1	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000434821.7					2	1	ENST00000434821.7
AKAP9	chr7	92097327	92097330	TAGA	T	c.10373_10375del	AGA/-	p.R3458del	0.184	50	3	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000356239.8				rs757087367	50	3	ENST00000356239.8			rs757087367
ARID1A	chr1	26696849	26696849	G	A	c.446G>A	gGc/gAc	p.G149D	0.861	19	3	Missense Variant	Missense Variant	MODERATE	ENST00000324856.13	Uncertain_significance	COSV61376273		rs2080267760	19	3	ENST00000324856.13	Uncertain_significance	COSV61376273	rs2080267760
ATRX	chrX	77682471	77682471	C	G	c.2785G>C	Gag/Cag	p.E929Q	0.233	59	56	Missense Variant	Missense Variant	MODERATE	ENST00000373344.10	Benign			rs3088074	59	56	ENST00000373344.10	Benign		rs3088074
BARD1	chr2	214767531	214767532	CA	TG	c.1518_1519inv	caTGtg/caCAtg	p.V507M	0.486	34	24	Missense Variant	Missense Variant	MODERATE	ENST00000260947.9		COSV105837301		rs386654966	34	24	ENST00000260947.9		COSV105837301	rs386654966
BCR	chr22	23314599	23314599	C	G	c.3611C>G	gCc/gGc	p.A1204G	0.175	7	2	Missense Variant	Missense Variant	MODERATE	ENST00000305877.13		COSV59925974	0.000060068300	rs56265970	7	2	ENST00000305877.13		COSV59925974	rs56265970
BIRC6	chr2	32515477	32515480	ATTC	A	c.11059_11061del	aTTCtt/att	p.L3687del	0.211	15	3	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000421745.6					15	3	ENST00000421745.6
CDK12	chr17	39462615	39462618	GAGA	G	c.548_550del	gAGAag/gag	p.K183del	0.982	8	3	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000447079.6					8	3	ENST00000447079.6
CIC	chr19	42291340	42291340	C	T	c.2572C>T	Ccc/Tcc	p.P858S	0.97	11	3	Missense Variant	Missense Variant	MODERATE	ENST00000575354.6		COSV99360636	0.000175355000	rs139895527	11	3	ENST00000575354.6		COSV99360636	rs139895527
CIITA	chr16	10909070	10909070	A	G	c.2702A>G	cAg/cGg	p.Q901R	0.96	85	84	Missense Variant	Missense Variant	MODERATE	ENST00000618327.4	Benign		0.983235000000	rs7197779	85	84	ENST00000618327.4	Benign		rs7197779
CREB3L2	chr7	137928167	137928170	CTGG	C	c.299_301del	aCCAgt/agt	p.T100del	0.855	49	49	In-frame Deletion	In-frame Deletion	MODERATE	ENST00000330387.11		COSV57791862		rs3217268	49	49	ENST00000330387.11		COSV57791862	rs3217268
ERBB3	chr12	56101214	56101214	A	T	c.3355A>T	Agc/Tgc	p.S1119C	0.95	14	9	Missense Variant	Missense Variant	MODERATE	ENST00000267101.8	Benign	COSV57247854	0.088057000000	rs773123	14	9	ENST00000267101.8	Benign	COSV57247854	rs773123
ERCC5	chr13	102846322	102846322	C	T	c.56C>T	cCc/cTc	p.P19L	0.954	14	3	Missense Variant	Missense Variant	MODERATE	ENST00000652225.2	Uncertain_significance	COSV99053842	0.000582552000	rs34291397	14	3	ENST00000652225.2	Uncertain_significance	COSV99053842	rs34291397
ERCC5	chr13	102862407	102862407	C	T	c.1258C>T	Cgt/Tgt	p.R420C	0.317	14	3	Missense Variant	Missense Variant	MODERATE	ENST00000652225.2			0.000012670500	rs374911899	14	3	ENST00000652225.2			rs374911899
FAM135B	chr8	138153029	138153030	TG	CA	c.1445_1446inv	cCA/cTG	p.P482L	0.657	35	29	Missense Variant	Missense Variant	MODERATE	ENST00000395297.6				rs71505459	35	29	ENST00000395297.6			rs71505459

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-15006

Patient

PDX

H&E

HER2

Metastasis Information for Model: BCM-15006

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-15006

Event Id	Treatment	Treatment Setting	Age at Start	Age at End	Duration	Clinical Response	Pathologic Response	Reason Stopped
20	Cyclophosphamide,Doxorubicin	Neoadjuvant	33.95	34.07	44 days	Partial Response	Not Reported	Treatment Completed
25	Carboplatin,Paclitaxel	Neoadjuvant	34.11	34.32	77 days	Progressive Disease	Not Reported	Treatment Completed
40	Radiation Therapy	Neoadjuvant	34.37	34.5	47 days	Complete Response	Pathological Complete Response	Treatment Completed
45	Cisplatin	Neoadjuvant	34.38	34.45	26 days	Complete Response	Pathological Complete Response	Treatment Completed
55	Capecitabine	Metastatic	34.78	35.28	183 days	Not Reported	Not Applicable	Treatment Completed
70	Radiation Therapy	Metastatic	35.78	35.85	26 days	Not Reported	Not Applicable	Treatment Completed
75	Capecitabine	Metastatic	35.8	35.92	44 days	Not Reported	Not Applicable	Disease Progression
80	Eribulin	Metastatic	35.93	35.94	4 days	Not Reported	Not Applicable	Disease Progression