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Patient ID
447624
Open Patient
Specimen ID
303-R
Open Specimen
Sample ID
J1-PDC
Disease Body Location
Digestive/Gastrointestinal
OncoTree Code
ANSC
CTEP SDC Code
10041840 - Squamous cell carcinoma - anus
PDM Type
PDC: Mixed Tumor Culture
Required Media
Media 6C/Colon 1B
Culture Origin
PDX-Derived Organoid
FACS
Characterization
mMHC-, hHLA+; mCD9-, hCD9+; hEpCAM+, hCD90-; hCD24+
Growth Properties
Adherent Monolayer
Proliferation Rate
in Complete Media
48 hrs
Sub-culture
Recommendations
Split ratio: 1:4 to 1:5
Culture Derivation
Isolated from a PDX-derived organoid culture. Determined to be a tumor by FACS analysis, QRT-PCR, cell morphology, and a positive tumorgenicity test.
Tumorigenic in
NSG Mice
Yes
No
Spheroid Growth
Yes
No
Spheroid Growth
Notes
Soft Agar Growth
Yes
No
Soft Agar
Growth Notes
Fibroblast qRT-PCR
C1 Corr
-0.30
Fibroblast qRT-PCR
C2 Corr
-0.34
Fibroblast qRT-PCR
Top Hits
KRT5,KRT19,KRT7,KRT8,KRT16
Images (if available)
In Vitro Images
View
Image Type
Notes
In Vitro Image
Light Microscopy
20x magnification, Passage 40
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:
2.0.2.16.0
RNASeq Transcripts per Million (TPM; *.RSEM.genes.results and *.RSEM.isoforms.results tab-delimited text file)
Download RSEM (genes)
Download RSEM (isoforms)
Ver:
2.0.2.16.0
OncoKB Gene Panel
View
Hugo
Symbol
HGVS Protein
Change
Variant Allele
Frequency
Total
Reads
Variant
Class
Oncogenicity
Predicted
Functional Effect
OncoKB
Version
ATXN2
p.Q180Hfs*26
0.2222
171
Frame_Shift_Del
Likely Oncogenic
Likely Loss-of-function
v3.14
ATXN2
p.Q177Afs*69
0.2032
187
Frame_Shift_Del
Likely Oncogenic
Likely Loss-of-function
v3.14
KMT2D
p.E847*
0.4986
367
Nonsense_Mutation
Likely Oncogenic
Likely Loss-of-function
v3.14
LATS2
p.P477_A480dup
1.0000
12
In_Frame_Ins
Likely Oncogenic
Unknown
v3.14
PTEN
p.G127E
1.0000
339
Missense_Mutation
Oncogenic
Loss-of-function
v3.14
RB1
p.X830_splice
1.0000
25
Splice_Site
Likely Oncogenic
Likely Loss-of-function
v3.14
Export
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