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PDMR Database User Guide
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Patient
Patient Specimen
Sample (PDX or In Vitro Culture)
Distribution Lots
Genomic Analysis
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Sample
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Patient ID
894883
Open Patient
Specimen ID
131-R
Open Specimen
Sample ID
ND8W86EA1_RG-YJ5
Disease Body Location
Digestive/Gastrointestinal
OncoTree Code
ANSC
CTEP SDC Code
10041840 - Squamous cell carcinoma - anus
PDM Type
PDX
Tissue Type
Resection
Patient/Originating
Specimen
Yes
No
Passage of this Sample
3
Sample
Notes
Pathology Data (if available)
Pathology Data
View
Tumor
Grade
Tumor
Content
Necrosis
Stromal
Inflammatory
Cells
Low Magnification Image
High Magnification Image
Intermediate grade or moderately differentiated
80%
%
20%
<Unknown>
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:
1.2
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
ATM
p.F858L
0.4581
334
Missense_Mutation
Likely Neutral
Likely Neutral
v3.14
KMT2C
p.X338_splice
0.0883
317
Splice_Site
Likely Oncogenic
Likely Loss-of-function
v3.14
STK11
p.D194N
1.0000
144
Missense_Mutation
Likely Oncogenic
Likely Loss-of-function
v3.14
TGFBR2
p.C92*
1.0000
133
Nonsense_Mutation
Likely Oncogenic
Likely Loss-of-function
v3.14
Export
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