PDX Model DetailsTM00090

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PDX Model Summary

Model Details
Model ID (Previous ID)
TM00090 (BR0744F)
Initial Diagnosis
Breast metaplastic carcinoma
Final Diagnosis
Breast metaplastic carcinoma
Stage/Grade
AJCC IV / 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
Wang, M; et al. Humanized mice in studying efficacy and mechanisms of PD-1-targeted cancer immunotherapy. 2018 FASEB 2018 Mar;32(3):1537-1549.  10.1096/fj.201700740R

Patient
Sex
Female
Age (at time of tissue collection)
43
Race/Ethnicity
White / Not Hispanic or Latino
Treatment Naïve?
Yes
Current Smoker/Former Smoker
No / No

Engraftment
Host Strain
NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ
(aka NSG or NOD Scid gamma)
Sample Type
Surgical resection (fragment)
Engraftment Site
no data

Molecular Data (Engrafted Tumor)

Variants

Gene Expression

Platforms: RNA_Seq, hg10st, 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 BR0744F098P0 from passage P0 has a TMB score of 8.08
TMB Range
0.0-304.42 (across all JAX PDX models; TMB > 22 is considered high)

Microsatellite Instability
Sample:BR0744F098P0 from passage P0     Score:MSI-S

Gene Fusion
Fusion Genes
Sample BR0744F098P0 has fusion genes MTG1--SCART1, AL450332.1--HDDC2, PDXDC1--NPIPB14P, PKD1--NPIPP1, LDLRAP1--AL606491.1, LYRM4--AL359643.2, SYS1--DBNDD2, LEPROT--LEPR, BOLA2B--SMG1P2, BACE2--FAM3B, EIF4G3--HP1BP3, H2BC20P--H4C14, NR2F2--AC087477.2, USP34--ZNF512, CROCCP2--NBPF1, STEAP1B--RAPGEF5, TMED7--TICAM2, DBT--LRRC39, HERC2P10--AC087481.2, CFAP298--TCP10L, CHCHD10--VPREB3, CNRIP1--PPP3R1, SOGA3--KIAA0408, C6orf47--BAG6, GDAP1--MIR2052HG, TBC1D23--NIT2, EFCAB14--ATPAF1, ZFP41--GLI4, AC005100.1--AC003985.1, HDAC8--CITED1, AC006427.2--TAPT1-AS1, AL390860.1--TRIM58, AP003555.2--ANO1, TNFSF12--TNFSF13, KANSL1--ARL17A, STX6--KIAA1614-AS1, VTI1B--AL049779.4, U73166.1--SEMA3B, SYNCRIP--SNX14, CLN6--CALML4, KIAA0232--LINC01483, VAMP1--CD27-AS1, AIG1--AL136116.3, ZNF736--AC073270.2, EEF1AKMT2--FAM53B, ADIRF--BMS1P3, FOXA2--LINC00261, STX16--NPEPL1, ATF2--CHN1, LINC01305--SP9, TEX30--HS6ST3, CDC73--AL138778.1, AC138409.2--AP000346.2, SMG1--ARL6IP1, H2BC19P--H4C14, TRIM58--OR2W3, NOS1AP--C1orf226, SMURF2P1--LRRC37B, CCSER2--AL157400.2, PARG--AGAP4, VPS45--PLEKHO1, LINC01483--LINC01497, POLD3--RNF169, HNRNPUL2--BSCL2, FBXW7--FER1L5, PRKAA1--TTC33, CENPS--CORT, RBM14--RBM4, UBE2J1--GABRR2, AC006001.3--GTF2IRD1P1, CYTOR--ANAPC1P4, RBM14--RBM4B, PARL--MAP6D1, CTNNAL1--PTPN3, KIAA0232--LINC01497, FGF13--NALF1, PMF1--BGLAP, CENPBD1P1--IL9RP4, CXCL12--AL137026.3, OTUD6B--LRRC69, HIVEP1--LINC00315, ZHX1--C8orf76, POLA2--CDC42EP2, SHPRH--FBXO30, UAP1--DDR2, SMG1P1--ZNF766, FKBP1A--SDCBP2, HS2ST1--LINC01140, SLC39A1--CRTC2, NRIP1--LINC02246, PITPNM2--ZNF641

Model Characterization

Histology

 Summary:
P0 pathology consistent with metaplastic breast carcinoma. P2, P3 pathology consistent with high grade breast carcinoma.
Pathologist:
Dr. Regina Gandour-Edwards, University of California, Davis

Patient tumor for PDX model TM00090. Sheets of epithelial cells in a pseudoglandular pattern with abundant bluish mucin in the intercellular spaces.
P0 tumor #098 for PDX model TM00090. Sheets of epithelial cells in with abundant bluish mucin in the intercellular spaces.

P0 tumor #098 for PDX model TM00090; IHC for PR
P0 tumor #098 for PDX model TM00090; IHC for ER

P2 tumor F098 ID0111 for PDX model TM00090 stained for H&E.
P3 tumor F098 ID016 for PDX model TM00090 stained for H&E.

P3 tumor F098 ID016 for PDX model TM00090 stained for AE1AE3. Staining was positive but patchy.
P3 tumor F098 ID016 for PDX model TM00090 stained for CD45. Staining was negative.

P3 tumor F098 ID016 for PDX model TM00090 stained for Ki67. Staining was positive.

Dosing Studies

Circos Plots

Circos Plot for P0 tumor #097 from PDX Model TM00090 (aka, BR0744F)
Circos plot for P0 tumor #098 from TM00090 (aka, BR0744F)