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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
885512
Open Patient
Specimen ID
296-R
Open Specimen
Sample ID
V1-organoid
Disease Body Location
Breast
OncoTree Code
MMBC
CTEP SDC Code
10006190 - Invasive breast carcinoma
PDM Type
Organoid Culture
Required Media
Breast #2
Culture Origin
PDX Fragment
FACS
Characterization
mMHC-, hHLA+, mCD9-, hCD9+, hCD90-, hEpCAM+, hCD24+
Growth Properties
Organoids
Proliferation Rate
in Complete Media
N/A
Sub-culture
Recommendations
1 Frozen Stock Vial can be used to generate: 6 wells in a 24-well plate
Culture Derivation
Derived from passage 0 PDX material. Sorted twice for hCD9 positive cells
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
-0.24
Fibroblast qRT-PCR
C2 Corr
-0.22
Fibroblast qRT-PCR
Top Hits
KRT17,KRT5,KRT8,KRT14,CD24
Images (if available)
In Vitro Images
View
Image Type
Notes
In Vitro Image
Light Microscopy
Magnified image, 500 micron scale bar, Passage 20, 7 days in culture
Light Microscopy
Image of total well, 1 mm scale bar, Passage 20, 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
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:
2.0.2.4.0
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
KMT2C
p.R2028*
1.0000
274
Nonsense_Mutation
Likely Oncogenic
Likely Loss-of-function
v3.14
KMT2D
p.Q3845*
0.3165
297
Nonsense_Mutation
Likely Oncogenic
Likely Loss-of-function
v3.14
RB1
p.S565*
1.0000
66
Nonsense_Mutation
Likely Oncogenic
Likely Loss-of-function
v3.14
STK11
p.G251D
0.9908
434
Missense_Mutation
Likely Oncogenic
Unknown
v3.14
TP53
p.I195T
0.9958
476
Missense_Mutation
Likely Oncogenic
Likely Loss-of-function
v3.14
Export
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