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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
CN0375
Open Patient
Specimen ID
F725
Open Specimen
Sample ID
V1-organoid
Disease Body Location
Digestive/Gastrointestinal
OncoTree Code
COAD
CTEP SDC Code
10009951 - Adenocarcinoma - colon
PDM Type
Organoid Culture
Required Media
Media 6A
Culture Origin
PDX Fragment
FACS
Characterization
mMHC-, hHLA+, mCD9-, hCD9+, hCD90-, hEpCAM+, hCD24+
Growth Properties
Organoids
Proliferation Rate
in Complete Media
NA
Sub-culture
Recommendations
1 Frozen Stock Vial can be used to generate: 4 wells in a 24-well plate
Culture Derivation
Derived from passage 6 PDX material
Tumorigenic in
NSG Mice
Yes
No
Spheroid Growth
Yes
No
Spheroid Growth
Notes
NA
Soft Agar Growth
Yes
No
Soft Agar
Growth Notes
NA
Fibroblast qRT-PCR
C1 Corr
-0.33
Fibroblast qRT-PCR
C2 Corr
-0.41
Fibroblast qRT-PCR
Top Hits
KRT18,KRT8,EPCAM,CEACAM5,CD24
Images (if available)
In Vitro Images
View
Image Type
Notes
In Vitro Image
Light Microscopy
Image of total well, bar shows 2mm size, Passage 9, 7 days in culture
Light Microscopy
Magnified image- note 500µm bar, Passage 9, 7 days in culture
Organoid H&E
10x image of embedded Patient-derived organoids
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:
2.0.1.51.0
Whole Exome FASTQ (*.FASTQ.gz; for paired-end sequence, download both files)
Download Read1 FASTQ
Download Read2 FASTQ
Ver:
2.0.1.51.0
RNASeq FASTQ (*.FASTQ.gz; for paired-end sequence, download both files)
Download Read1 FASTQ
Download Read2 FASTQ
Ver:
2.0.1.4.0
RNASeq Transcripts per Million (TPM; *.RSEM.genes.results and *.RSEM.isoforms.results tab-delimited text file)
Download RSEM (genes)
Download RSEM (isoforms)
Ver:
2.0.1.4.0
OncoKB Gene Panel
View
Hugo
Symbol
HGVS Protein
Change
Variant Allele
Frequency
Total
Reads
Variant
Class
Oncogenicity
Predicted
Functional Effect
OncoKB
Version
AMER1
p.S501Efs*39
1.0000
80
Frame_Shift_Del
Likely Oncogenic
Likely Loss-of-function
-
APC
p.Q1477*
1.0000
361
Nonsense_Mutation
Likely Oncogenic
Likely Loss-of-function
-
KRAS
p.A146T
0.5672
67
Missense_Mutation
Oncogenic
Gain-of-function
-
SMAD4
p.P356L
1.0000
63
Missense_Mutation
Likely Oncogenic
Unknown
-
SOX9
p.E400*
0.4615
234
Nonsense_Mutation
Likely Oncogenic
Likely Loss-of-function
-
TP53
p.R175H
1.0000
84
Missense_Mutation
Oncogenic
Loss-of-function
-
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