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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
121662
Open Patient
Specimen ID
129-R
Open Specimen
Sample ID
V1-organoid
Disease Body Location
Respiratory/Thoracic
OncoTree Code
LUAD
CTEP SDC Code
10025032 - Lung adenocarcinoma
PDM Type
Organoid Culture
Required Media
Media 6A
Culture Origin
PDX Fragment
FACS
Characterization
mMHC-, hHLA+, mCD9-, hCD9+, hCD90-, hEpCAM+, CD24+
Growth Properties
Organoids
Proliferation Rate
in Complete Media
N/A
Sub-culture
Recommendations
1 Frozen Stock Vial can be used to generate: 8 wells in a 24-well plate
Culture Derivation
Derived from passage 0 PDX material.
Tumorigenic in
NSG Mice
Yes
No
Spheroid Growth
Yes
No
Spheroid Growth
Notes
N/A
Soft Agar Growth
Yes
No
Soft Agar
Growth Notes
N/A
Fibroblast qRT-PCR
C1 Corr
0.00
Fibroblast qRT-PCR
C2 Corr
-0.04
Fibroblast qRT-PCR
Top Hits
KRT8,KRT18,KRT19,KRT7,EPCAM
Images (if available)
In Vitro Images
View
Image Type
Notes
In Vitro Image
Light Microscopy
Image of total well, 1 mm scale bar, Passage 12, 7 days in culture
Light Microscopy
Magnified image, 500 micron scale bar, Passage 12, 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:
2.0.2.51.0
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:
2.0.2.21.0
RNASeq Transcripts per Million (TPM; *.RSEM.genes.results and *.RSEM.isoforms.results tab-delimited text file)
Download RSEM (genes)
Download RSEM (isoforms)
Ver:
2.0.2.21.0
OncoKB Gene Panel
View
Hugo
Symbol
HGVS Protein
Change
Variant Allele
Frequency
Total
Reads
Variant
Class
Oncogenicity
Predicted
Functional Effect
OncoKB
Version
None Found
p.R463*
0.6012
168
Nonsense_Mutation
Likely Oncogenic
Likely Loss-of-function
v4.30
ATM
p.F858L
0.3108
296
Missense_Mutation
Likely Neutral
Likely Neutral
v4.30
KRAS
p.G12C
0.4225
426
Missense_Mutation
Oncogenic
Gain-of-function
v4.30
LATS2
p.P477_A480dup
0.3061
49
In_Frame_Ins
Likely Oncogenic
Unknown
v4.30
MST1
p.D475Qfs*52
0.1440
389
Frame_Shift_Ins
Likely Oncogenic
Likely Loss-of-function
v4.30
TP53
p.E298*
0.4921
382
Nonsense_Mutation
Likely Oncogenic
Likely Loss-of-function
v4.30
TP53
p.P152Rfs*18
0.4684
190
Frame_Shift_Del
Likely Oncogenic
Likely Loss-of-function
v4.30
Export
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