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Last Database Update
2019-09-15
MTB 3.0
 
HelpHelp and Documentation PDX Model Details
Model Details
Model ID:TM00089 Previous ID:BR0620F
Primary Site:Breast Initial Diagnosis:invasive ductal carcinoma Final Diagnosis:invasive ductal carcinoma
Tumor Site:Breast Tumor Type:Primary Malignancy Stage / Grade:AJCC IIA / Grade:3
Patient
Sex:Female Age:68 Race / Ethnicity:Asian or Pacific Islander / Not Hispanic or Latino
Treatment Naive:Yes
Engraftment Host
Strain:NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ
(aka NSG or NOD Scid gamma)
Implantation Site: Sample Type:Surgical resection (fragment)
Publications citing this model
Tumor Mutation Burden
Sample from passage P0 has a TMB score of 4.04
TMB Range:0.81-305.22  (across all JAX PDX models)
TMB > 22 is considered high.
Variant Summary Help

Gene Expression Help Platforms:RNA_Seq, hg10st
Hatched bars indicate genes with expression levels determined to be mildly affected by alignment calculations. Details.
Gene CNV Help
CNV Plots Help
Model Characterization
Histology: Tumor Markers:
Patient and PDX tumor markers differ. IHC results show PDX model TM00089 is ER positive/PR negative/ERBB2 negative for lineage 039 while it is ER negative/PR negative/ERBB2 negative for lineage 037. Patient tumor reported as ER positive/PR negative/ERBB2 negative.
Summary:
P2 and P5 pathology consistent with poorly differentiated carcinoma.
Pathologist:
Dr. Regina Gandour-Edwards, University of California, Davis.

Patient tumor for PDX model TM00089.

Patient tumor for PDX model TM00089.

Patient tumor for PDX model TM00089.

Patient tumor for PDX model TM00089; Ki67 marker

Patient tumor for PDX model TM00089; PR marker (negative)

Patient tumor for PDX model TM00089; ER marker (positive).

P0 tumor #037 for PDX model TM00089; estradiol supplemented

P0 tumor #037 for PDX model TM00089; estradiol supplemented; PR marker

P0 tumor #037 for PDX model TM00089; estradiol supplemented; ER marker

P1 tumor for PDX model TM00089; estradiol supplemented

P1 tumor for PDX model TM00089; estradiol supplemented; PR marker (negative)

P1 tumor for PDX model TM00089; estradiol supplemented; ER marker (negative)

P1 tumor #039 from PDX model TM00089.

P1 tumor #039 from PDX model TM00089; PR marker (negative)

P1 tumor #039 for PDX model TM00089; ER marker (focal positive)

P2 tumor F037 ID013 for PDX model TM00089 stained for H&E.

P2 tumor F037 ID013 for PDX model TM00089 stained for AE1AE3. Staining was positive.

P2 F037 ID013 tumor for PDX model TM00089 stained for CD45. Staining was negative.

P2 F037 ID013 tumor for PDX model TM00089 stained for Ki67. Staining was positive.

P2 F037 ID013 tumor for PDX model TM00089 stained for ER. Staining was negative.

P2 F037 ID013 tumor for PDX model TM00089 stained for PR. Staining was negative.

P2 F037 ID013 tumor for PDX model TM00089 stained for ERBB2 (HER2). Staining was negative.

P5 F037 ID027 tumor for PDX model TM00089 stained for H&E.

P5 F037 ID027 tumor for PDX model TM00089 stained for AE1/AE3. Staining was positive.

P5 F037 ID027 tumor for PDX model TM00089 stained for CD45. Staining was negative.

P5 F037 ID027 tumor for PDX model TM00089 stained for Ki67. Staining was positive.

P5 F037 ID027 tumor for PDX model TM00089 stained for AR. Staining was negative.

P5 F037 ID027 tumor for PDX model TM00089 stained for ER. Staining was negative.

P5 F037 ID027 tumor for PDX model TM00089 stained for ERBB2 (HER2). Staining was negative.

P5 F037 ID027 tumor for PDX model TM00089 stained for PR. Staining was negative.
Circos Plots:

Circos plot for P0 tumor #037 from PDX model TM00089 (aka, BR0620)

Circos plot for P0 tumor #039 from PDX model TM00089 (aka, BR0620)

Circos plot for P1 tumor #001 from PDX model TM00089 (aka, BR0620F)