Skip to Content
Contact PDMR
|
PDMR Database User Guide
Home
Patient
Patient Specimen
Sample (PDX or In Vitro Culture)
Distribution Lots
Genomic Analysis
Reports
Search
Sample
Cancel
Patient ID
415267
Open Patient
Specimen ID
285-R
Open Specimen
Sample ID
J2-PDC
Disease Body Location
Breast
OncoTree Code
IBC
CTEP SDC Code
10021980 - Inflammatory breast carcinoma
PDM Type
PDC: Mixed Tumor Culture
Required Media
Breast #2
Culture Origin
PDX-Derived Organoid
FACS
Characterization
mMHC-, hHLA+; mCD9-, hCD9+; hEpCAM+, hCD90-; hCD24+
Growth Properties
Adherent Monolayer
Proliferation Rate
in Complete Media
43 hrs
Sub-culture
Recommendations
Split ratio: 1:4 to 1:5
Culture Derivation
Isolated from PDX-derived organoid culture. Determined to be a tumor by FACS analysis, QRT-PCR, cell morphology, and tumorigenicity
Tumorigenic in
NSG Mice
Yes
No
Spheroid Growth
Yes
No
Spheroid Growth
Notes
Soft Agar Growth
Yes
No
Soft Agar
Growth Notes
Fibroblast qRT-PCR
C1 Corr
-0.19
Fibroblast qRT-PCR
C2 Corr
-0.22
Fibroblast qRT-PCR
Top Hits
CD24,EPCAM,KRT19,KRT7,KRT8
Images (if available)
In Vitro Images
View
Image Type
Notes
In Vitro Image
Light Microscopy
20x magnification, Passage 28
Spheroid Culture
20X magnification, Passage 17
Xenograft from In Vitro Culture
20X image of cell culture-derived xenograft; Implantation Site: Mammary Fat Pad
Export
Genomic Analysis
External Genetic Analysis Data
A data file is available if a Download link is displayed:
Somatic Mutations Associated with Cancer (*.vcf and *.maf)
Whole Exome Sequencing (*.vcf)
Download
Ver:
2.0.2.51.0
Whole Exome FASTQ (*.FASTQ.gz; for paired-end sequence, download both files)
Download Read1 FASTQ
Download Read2 FASTQ
Ver:
2.0.2.51.0
RNASeq FASTQ (*.FASTQ.gz; for paired-end sequence, download both files)
Download Read1 FASTQ
Download Read2 FASTQ
Ver:
2.0.2.16.0
RNASeq Transcripts per Million (TPM; *.RSEM.genes.results and *.RSEM.isoforms.results tab-delimited text file)
Download RSEM (genes)
Download RSEM (isoforms)
Ver:
2.0.2.16.0
OncoKB Gene Panel
View
Hugo
Symbol
HGVS Protein
Change
Variant Allele
Frequency
Total
Reads
Variant
Class
Oncogenicity
Predicted
Functional Effect
OncoKB
Version
KMT2C
p.S4677*
0.5789
95
Nonsense_Mutation
Likely Oncogenic
Likely Loss-of-function
v3.14
KMT2C
p.W3183_Q3194delins*
0.4156
231
Nonsense_Mutation
Likely Oncogenic
Likely Loss-of-function
v3.14
KMT2D
p.S2312*
0.5251
219
Nonsense_Mutation
Likely Oncogenic
Likely Loss-of-function
v3.14
PALB2
p.K18R
0.5153
196
Missense_Mutation
Likely Neutral
Likely Neutral
v3.14
TP53
p.R273H
1.0000
131
Missense_Mutation
Oncogenic
Loss-of-function
v3.14
Export
1 - 5