PDX Model DetailsJ000094707

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PDX Model Summary

Model Details
Model ID
J000094707
Initial Diagnosis
Rectum adenocarcinoma
Final Diagnosis
Rectum adenocarcinoma
Stage/Grade
AJCC IIA / Grade:2
Primary Site
Rectum
Sample Site
Rectum
Tumor Type
Primary Malignancy

Patient
Sex
Male
Age (at time of tissue collection)
59
Race/Ethnicity
Not Reported / Not Reported
Treatment Naïve?
No
Current Smoker/Former Smoker
Unknown / Unknown

Engraftment
Host Strain
NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ
(aka NSG or NOD Scid gamma)
Sample Type
Surgical resection (fragment)
Engraftment Site
Right Flank

Molecular Data (Engrafted Tumor)

Variants

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 J000101139 from passage P0 has a TMB score of 4.85
Sample J000101141 from passage P0 has a TMB score of 5.66
Sample J000102913 from passage P1 has a TMB score of 7.27
Sample J000103479 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:J000101139 from passage P0     Score:MSI-S
Sample:J000101141 from passage P0     Score:MSI-S
Sample:J000102913 from passage P1     Score:MSI-S
Sample:J000103479 from passage P1     Score:MSI-S

Gene Fusion
Fusion Genes
Sample J000102912 has fusion genes PVT1--PCAT1, ZFHX3--PMFBP1, PVT1--POU5F1B, CAPN8--CAPN2, KANSL1--ARL17A, POLR2J3--UPK3BL1, CCL15--CCL14, SAMD5--AL033504.1
Sample J000101142 has fusion genes AC004967.1--AC079781.5, LAMC2--AL354953.1, RNASEH1--AC108488.1, ZNF738--AC010615.1, ZFHX3--PMFBP1, AP000347.1--ASLP1, KANSL1--ARL17A, POLR2J2--AC004951.2, STX16--NPEPL1, ASLP1--AP000346.2, CCL15--CCL14, SAMD5--AL033504.1
Sample J000103478 has fusion genes AC004066.1--PPA2, LAMC2--AL354953.1, PDXDC1--NPIPB14P, CRYBB2P1--GRK3, TVP23C--CDRT4, AL079338.1--PSORS1C3, SMBD1P--MUC20P1, CA13--CA3, SMURF2P1--LRRC37B, KANSL1--ARL17B, PCDHA4--PCDHAC2, ARHGEF5--OR2A7, CCL15--CCL14, AZGP1--GJC3, AC004967.1--AC079781.5, GON4L--AL353807.5, BOLA2B--SMG1, BPTF--LRRC37A3, RALGAPB--TOP1, STX16--NPEPL1, TPTEP2--CSNK1E

Model Characterization

Histology

 Summary:
P0, P1 and P2 pathology consistent with adenocarcinoma.
Pathologist:
Dr. Regina Gandour-Edwards, University of California, Davis

Patient tumor for PDX model J000094707 stained with H&E.
P0 tumor F001 for PDX model J000094707 stained for H&E.

P0 tumor F001 for PDX model J000094707 stained for AE1AE3. Staining was positive.
P0 tumor F001 for PDX model J000094707 stained for CD45. Staining was negative.

P0 tumor F001 for PDX model J000094707 stained for Ki67. Staining was positive.
P1 tumor F001 P1 ID014 for PDX model J000094707 stained for H&E.

P1 tumor F001 P1 ID014 for PDX model J000094707 stained for AE1AE3. Staining was positive.
P1 tumor F001 P1 ID014 for PDX model J000094707 stained for CD45. Staining was negative.

P2 tumor F001 ID017 for PDX model J000094707 stained for H&E.
P2 tumor F001 ID017 for PDX model J000094707 stained for AE1AE3. Staining was positive.

P2 tumor F001 ID017 for PDX model J000094707 stained for CD45. Staining was negative.
P2 tumor F001 ID017 for PDX model J000094707 stained for Ki67. Staining was positive.

Dosing Studies

 no data

Circos Plots

 no data