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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
128783
Open Patient
Specimen ID
104-T
Open Specimen
Sample ID
V2-organoid
Disease Body Location
Digestive/Gastrointestinal
OncoTree Code
COAD
CTEP SDC Code
10009951 - Adenocarcinoma - colon
PDM Type
Organoid Culture
Required Media
Media 6C/Colon 1B
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: 12 wells in a 24-well plate
Culture Derivation
Derived from passage 3 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
-0.34
Fibroblast qRT-PCR
C2 Corr
-0.42
Fibroblast qRT-PCR
Top Hits
CEACAM5,KRT8,KRT18,KRT19,EPCAM
Images (if available)
In Vitro Images
View
Image Type
Notes
In Vitro Image
Light Microscopy
Image of total well, bar shows 1 mm size, Passage 13, 7 days in culture
Light Microscopy
Magnified image- note 500µm bar, Passage 13, 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
APC
p.E1309Dfs*4
0.4172
163
Frame_Shift_Del
Likely Oncogenic
Likely Loss-of-function
v3.14
APC
p.H1349Tfs*5
0.5570
149
Frame_Shift_Ins
Likely Oncogenic
Likely Loss-of-function
v3.14
KRAS
p.G13D
0.4305
151
Missense_Mutation
Oncogenic
Gain-of-function
v3.14
PIK3CA
p.E542K
0.4522
115
Missense_Mutation
Oncogenic
Gain-of-function
v3.14
SOX9
-
0.4346
474
Frame_Shift_Del
Likely Oncogenic
Likely Loss-of-function
v3.14
TCF7L2
p.R471C
0.4500
280
Missense_Mutation
Likely Oncogenic
Unknown
v3.14
TP53
p.P152L
1.0000
82
Missense_Mutation
Likely Oncogenic
Likely Loss-of-function
v3.14
Export
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