PDX Model DetailsJ000100646

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PDX Model Summary
Model Details	Model ID J000100646 Initial Diagnosis Urinary bladder cancer Final Diagnosis Urinary bladder cancer Stage/Grade Not Specified / Grade:high Primary Site Bladder Sample Site Bladder Tumor Type Primary Malignancy
Publications citing this model	Malcolm, J; et al. Factors that influence response classifications in chemotherapy treated patient-derived xenografts (PDX). PeerJ. 2019 Mar 28;7:e6586. 10.7717/peerj.6586
Patient	Sex Male Age (at time of tissue collection) 72 Race/Ethnicity White / Not Reported Treatment Naïve? Yes Current Smoker/Former Smoker Unknown / Unknown
Engraftment	Host Strain NOD.Cg-Prkdc^scid Il2rg^tm1Wjl/SzJ (aka NSG or NOD Scid gamma) Sample Type Surgical resection (fragment) Engraftment Site Right Flank

Molecular Data (Engrafted Tumor)
Variants	no variation plots
Gene Expression	Platforms: RNA_Seq Hatched bars indicate genes with expression levels determined to be mildly affected by alignment calculations. Details.
Gene CNV
CNV Plots
Tumor Mutation Burden	Sample J000102432 from passage P0 has a TMB score of 4.85 Sample J000102435 from passage P0 has a TMB score of 4.85 Sample J000103693 from passage P1 has a TMB score of 4.04 TMB Range 0.0-304.42 (across all JAX PDX models; TMB > 22 is considered high)
Microsatellite Instability	Sample:J000102432 from passage P0 Score:MSI-S Sample:J000102435 from passage P0 Score:MSI-S Sample:J000103693 from passage P1 Score:MSI-S
Gene Fusion	no data

Model Characterization

Histology

Summary:
Patient tumor is a high grade urothelial carcinoma. P0, P1 pathology consistent with high grade carcinomas. P0 and P1 have excellent concordance to PT. P2 pathology consistent with adenocarcinoma.
Pathologist:
Dr. Regina Gandour-Edwards, University of California, Davis

Patient tumor for PDX model J000100646 stained for H&E.	P0 tumor F001 for PDX model J000100646 stained for H&E.
P1 tumor ID006 for PDX model J000100646 stained for H&E.	P2 tumor F001 ID015 for PDX model J000100646 stained for H&E.
P2 tumor F001 ID015 for PDX model J000100646 stained for AE1/AE3. Staining was positive.	P2 tumor F001 ID015 for PDX model J000100646 stained for CD45. Staining was negative.
P2 tumor F001 ID015 for PDX model J000100646 stained for Ki67. Staining was positive.