Sample Editor (PDX or In Vitro Culture)

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NIH, National Cancer

Institute, Division of Cancer Treatment and Diagnosis (DCTD)

Sample

116655

072-R

Value Required

V1-organoid

Disease Body Location

Digestive/Gastrointestinal

MACR

10009951 - Adenocarcinoma - colon

Value Required

Organoid Culture

Media 6C/Colon 1B

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: 12 wells in a 24-well plate

Culture Derivation

Derived from passage 0 PDX material.

Tumorigenic in
NSG Mice

Spheroid Growth

Spheroid Growth
Notes

N/A

Soft Agar Growth

Soft Agar
Growth Notes

N/A

Fibroblast qRT-PCR
C1 Corr

-0.14

Fibroblast qRT-PCR
C2 Corr

-0.23

Fibroblast qRT-PCR
Top Hits

KRT8,KRT18,KRT19,EPCAM,KRT16

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Images (if available)

In Vitro Images

View	Image Type	Notes	In Vitro Image
	Light Microscopy	Image of total well, 1 mm scale bar, Passage 11, 7 days in culture
	Light Microscopy	Magnified image, 500 micron scale bar, Passage 11, 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. Highly mucinous tumor.

Genomic Analysis

External Genetic Analysis Data

A data file is available if a Download link is displayed:

2.0.2.51.0

Download Read1 FASTQ

Download Read2 FASTQ

2.0.2.51.0

Download Read1 FASTQ

Download Read2 FASTQ

2.0.2.6.0

Download RSEM (genes)

Download RSEM (isoforms)

2.0.2.6.0

OncoKB Gene Panel

View	Hugo Symbol	HGVS Protein Change	Variant Allele Frequency	Total Reads	Variant Class	Oncogenicity	Predicted Functional Effect	OncoKB Version
	ANKRD11	p.A2265Rfs*8	0.5385	13	Frame_Shift_Ins	Likely Oncogenic	Likely Loss-of-function	v3.19
	APC	p.V452Sfs*7	0.4819	83	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.19
	APC	p.T1556Nfs*3	0.4868	152	Frame_Shift_Ins	Likely Oncogenic	Likely Loss-of-function	v3.19
	BRAF	p.V600E	0.3482	112	Missense_Mutation	Oncogenic	Gain-of-function	v3.19
	BRIP1	p.R173C	0.4052	116	Missense_Mutation	Inconclusive	Inconclusive	v3.19
	FBXW7	p.R465C	0.4943	174	Missense_Mutation	Oncogenic	Loss-of-function	v3.19
	HIST1H1D	p.A186Lfs*?	0.4975	203	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.19
	INHA	p.L189Cfs*2	0.4725	273	Frame_Shift_Ins	Likely Oncogenic	Likely Loss-of-function	v3.19
	KEAP1	p.F478Lfs*2	0.4522	230	Frame_Shift_Ins	Likely Oncogenic	Likely Loss-of-function	v3.19
	KMT2B	p.P174Qfs*20	0.2423	293	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.19
	KMT2C	p.K2797Rfs*26	0.4016	254	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.19
	NOTCH3	p.K2069Rfs*16	0.3913	23	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.19
	RAD50	p.K722Rfs*14	0.5174	230	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.19
	RNF43	p.G659Vfs*41	0.5168	149	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.19
	RNF43	p.P192Rfs*11	0.0000	573	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.19
	TSC2	p.T1247Sfs*74	0.4082	98	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.19
	ZFP36L2	p.G107Afs*80	0.4667	135	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.19

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