PDX Model DetailsJ000100675

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PDX Model Summary
Model Details	Model ID J000100675 Initial Diagnosis Invasive ductal carcinoma Final Diagnosis Invasive ductal carcinoma Stage/Grade AJCC IIB / Grade:3 Primary Site Breast Sample Site Breast 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 Female Age (at time of tissue collection) 56 Race/Ethnicity White / Not Hispanic or Latino Treatment Naïve? Yes Current Smoker/Former Smoker No / Yes
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, stRNA_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 J000102704 from passage P0 has a TMB score of 4.85 Sample J000104167 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:J000102704 from passage P0 Score:MSI-S Sample:J000104167 from passage P1 Score:MSI-S
Gene Fusion	no data

Model Characterization

Histology

Summary:
P0, P1 pathology consistent with Poorly differentiated carcinoma. P0 pathology consistent with a high grade mammary carcinoma. P0 pathology consistent with Triple negative Breast Cancer. P2 pathology consistent with carcinoma.
Pathologist:
Dr. Regina Gandour-Edwards, University of California, Davis

Patient tumor for PDX model J000100675 stained with H&E.	P0 tumor F001 for PDX model J000100675 stained with H&E.
P0 tumor F001 for PDX model J000100675 stained for ER. Staining was negative.	P0 tumor F001 for PDX model J000100675 stained for PR. Staining was negative.
P0 tumor F001 for PDX model J000100675 stained for ERBB2 (HER2). Staining was negative.	P1 tumor ID007 for PDX model J000100675 stained for H&E.
P2 tumor F001 ID012 for PDX model J000100675 stained for H&E.	P2 tumor F001 ID012 for PDX model J000100675 stained for AE1AE3. Staining was positive.
P2 tumor F001 ID012 for PDX model J000100675 stained for CD45. Staining was negative.	P2 tumor F001 ID012 for PDX model J000100675 stained for Ki67. Staining was positive.
P2 tumor F001 ID012 for PDX model J000100675 stained for ER. Staining was negative.	P2 tumor F001 ID012 for PDX model J000100675 stained for PR. Staining was negative.
P2 tumor F001 ID012 for PDX model J000100675 stained for ERBB2 (HER2). Staining was negative.	P2 tumor F001 ID012 for PDX model J000100675 stained for AR. Staining was negative.