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Patient Specimen
Sample (PDX or In Vitro Culture)
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Patient ID
425362
Open Patient
Specimen ID
245-T
Open Specimen
Sample ID
V1-organoid
Disease Body Location
Skin
OncoTree Code
MEL
CTEP SDC Code
10053571 - Melanoma
PDM Type
Organoid Culture
Required Media
Media 6A
Culture Origin
PDX Fragment
FACS
Characterization
mMHC-, hHLA+, mCD9-, hCD9+, hCD90+ hEpCAM-, hCD24-
Growth Properties
Aggregate Clusters
Proliferation Rate
in Complete Media
NA
Sub-culture
Recommendations
1 Frozen Stock Vial can be used to generate: 6 wells (Lot# CK7176) / 4 wells (Lot# CK1510) in a 24-well plate
Culture Derivation
Derived from passage 2 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
0.56
Fibroblast qRT-PCR
C2 Corr
0.45
Fibroblast qRT-PCR
Top Hits
VIM,KRT5,FN1,COL1A2,CD45
Images (if available)
In Vitro Images
View
Image Type
Notes
In Vitro Image
Light Microscopy
Image of total well, 1 mm scale bar, Passage 14, 7 days in culture
Light Microscopy
Magnified image, 500 micron scale bar, Passage 14, 7 days in culture
Organoid H&E
10X image of embedded Patient-derived organoids, Melanin A IHC
Xenograft from In Vitro Culture
20x image of organoid-derived xenograft
Xenograft from In Vitro Culture
20x image of organoid-derived xenograft, Melanin A IHC
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
ARID1A
p.Q405*
0.4369
499
Nonsense_Mutation
Likely Oncogenic
Likely Loss-of-function
v7.1
BRAF
p.V600E
0.6075
107
Missense_Mutation
Oncogenic
Gain-of-function
v7.1
CDK4
p.R24H
1.0000
236
Missense_Mutation
Likely Oncogenic
Likely Gain-of-function
v7.1
PIK3R1
p.X582_splice
0.2218
284
Splice_Site
Likely Oncogenic
Likely Loss-of-function
v7.1
PTPRT
p.W691*
0.3478
161
Nonsense_Mutation
Likely Oncogenic
Likely Loss-of-function
v7.1
TP53
p.C277Y
0.9907
216
Missense_Mutation
Likely Oncogenic
Likely Loss-of-function
v7.1
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