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PDMR Database User Guide
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Patient Specimen
Sample (PDX or In Vitro Culture)
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Patient ID
116655
Open Patient
Specimen ID
072-R
Open Specimen
Sample ID
J2-PDC
Disease Body Location
Digestive/Gastrointestinal
OncoTree Code
MACR
CTEP SDC Code
10009951 - Adenocarcinoma - colon
PDM Type
PDC: Mixed Tumor Culture
Required Media
Media 6C/Colon 1B
Culture Origin
PDX-Derived Organoid
FACS
Characterization
mMHC-, hHLA+, mCD9-, hCD9+; hEpCAM+, hCD90-, hCD24+
Growth Properties
Adherent Monolayer
Proliferation Rate
in Complete Media
28 hrs
Sub-culture
Recommendations
Split ratio: 1:4 to 1:5
Culture Derivation
Prepared from a PDX-derived organoid culture. Determined to be a tumor by FACS analysis, QRT-PCR, cell morphology, and positive tumorigenicity test.
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
-0.51
Fibroblast qRT-PCR
C2 Corr
-0.56
Fibroblast qRT-PCR
Top Hits
KRT8,EPCAM,KRT18,CEACAM5,KRT19
Images (if available)
In Vitro Images
View
Image Type
Notes
In Vitro Image
Light Microscopy
20x magnification, Passage 23
Xenograft from In Vitro Culture
20X image of cell culture-derived xenograft
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
ANKRD11
p.A2265Rfs*8
0.4018
112
Frame_Shift_Ins
Likely Oncogenic
Likely Loss-of-function
v3.19
APC
p.V452Sfs*7
0.3832
107
Frame_Shift_Del
Likely Oncogenic
Likely Loss-of-function
v3.19
APC
p.T1556Nfs*3
0.4574
223
Frame_Shift_Ins
Likely Oncogenic
Likely Loss-of-function
v3.19
BRAF
p.V600E
0.6927
179
Missense_Mutation
Oncogenic
Gain-of-function
v3.19
BRIP1
p.R173C
0.5938
128
Missense_Mutation
Inconclusive
Inconclusive
v3.19
FBXW7
p.R465C
0.4764
296
Missense_Mutation
Oncogenic
Loss-of-function
v3.19
HIST1H1D
p.A186Lfs*?
0.4251
207
Frame_Shift_Del
Likely Oncogenic
Likely Loss-of-function
v3.19
INHA
p.L189Cfs*2
0.5447
872
Frame_Shift_Ins
Likely Oncogenic
Likely Loss-of-function
v3.19
KEAP1
p.F478Lfs*2
0.5178
338
Frame_Shift_Ins
Likely Oncogenic
Likely Loss-of-function
v3.19
KMT2C
p.K2797Rfs*26
0.6464
280
Frame_Shift_Del
Likely Oncogenic
Likely Loss-of-function
v3.19
NOTCH3
p.K2069Rfs*16
0.4561
171
Frame_Shift_Del
Likely Oncogenic
Likely Loss-of-function
v3.19
NOTCH3
p.X715_splice
0.4756
164
Splice_Site
Likely Oncogenic
Likely Gain-of-function
v3.19
RAD50
p.K722Rfs*14
0.5763
236
Frame_Shift_Del
Likely Oncogenic
Likely Loss-of-function
v3.19
RNF43
p.G659Vfs*41
0.5520
250
Frame_Shift_Del
Likely Oncogenic
Likely Loss-of-function
v3.19
RNF43
p.P192Rfs*11
0.0000
684
Frame_Shift_Del
Likely Oncogenic
Likely Loss-of-function
v3.19
TGFBR2
p.K153Afs*3
0.0000
316
Frame_Shift_Del
Likely Oncogenic
Likely Loss-of-function
v3.19
TSC2
p.T1247Sfs*74
0.5020
247
Frame_Shift_Del
Likely Oncogenic
Likely Loss-of-function
v3.19
ZFP36L2
p.G107Afs*80
0.4740
289
Frame_Shift_Del
Likely Oncogenic
Likely Loss-of-function
v3.19
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