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Sample (PDX or In Vitro Culture)
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Patient ID
463943
Open Patient
Specimen ID
066-T
Open Specimen
Sample ID
J2-PDC
Disease Body Location
Digestive/Gastrointestinal
OncoTree Code
COAD
CTEP SDC Code
10009951 - Adenocarcinoma - colon
PDM Type
PDC: Mixed Tumor Culture
Required Media
Complete DMEM/F12
Culture Origin
PDX-Derived Organoid
FACS
Characterization
mMHC-, hHLA+; mCD9-, hCD9+; hEpCAM+, hCD90-; hCD24+
Growth Properties
Adherent Monolayer
Proliferation Rate
in Complete Media
46 hrs
Sub-culture
Recommendations
Split ratio: 1 : 3 to 1:4
Culture Derivation
Isolated from an organoid culture. Determined to be a tumor by FACS analysis, QRT-PCR, cell morphology and a 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
-0.30
Fibroblast qRT-PCR
C2 Corr
-0.38
Fibroblast qRT-PCR
Top Hits
KRT8,KRT19,KRT18,CD24,EPCAM
Images (if available)
In Vitro Images
View
Image Type
Notes
In Vitro Image
Light Microscopy
20x magnification, Passage 21
Xenograft from In Vitro Culture
Cell-line 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:
2.0.2.4.0
RNASeq Transcripts per Million (TPM; *.RSEM.genes.results and *.RSEM.isoforms.results tab-delimited text file)
Download RSEM (genes)
Download RSEM (isoforms)
Ver:
2.0.2.4.0
OncoKB Gene Panel
View
Hugo
Symbol
HGVS Protein
Change
Variant Allele
Frequency
Total
Reads
Variant
Class
Oncogenicity
Predicted
Functional Effect
OncoKB
Version
APC
p.S1068*
0.6788
386
Nonsense_Mutation
Likely Oncogenic
Likely Loss-of-function
v3.14
APC
p.T1493Rfs*14
0.2686
566
Frame_Shift_Del
Likely Oncogenic
Likely Loss-of-function
v3.14
CDKN1B
p.G97Vfs*22
0.2868
394
Frame_Shift_Del
Likely Oncogenic
Likely Loss-of-function
v3.14
KRAS
p.G12V
0.6000
350
Missense_Mutation
Oncogenic
Gain-of-function
v3.14
SMAD3
p.*426Yext*6
0.6159
276
Nonstop_Mutation
Likely Oncogenic
Likely Loss-of-function
v3.14
SOX9
p.P241Qfs*10
0.7928
526
Frame_Shift_Del
Likely Oncogenic
Likely Loss-of-function
v3.14
TCF7L2
p.S82Vfs*26
0.3789
570
Frame_Shift_Del
Likely Oncogenic
Likely Loss-of-function
v3.14
EPHB1
p.R351Q
0.2763
485
Missense_Mutation
Likely Oncogenic
Likely Loss-of-function
v3.14
Export
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