Sample Editor (PDX or In Vitro Culture)

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NIH, National Cancer

Institute, Division of Cancer Treatment and Diagnosis (DCTD)

Sample

292921

168-R

Value Required

V1-organoid

Disease Body Location

Digestive/Gastrointestinal

PAAD

10052747 - Adenocarcinoma - pancreas

Value Required

Organoid Culture

Panc

PDX Fragment

FACS
Characterization

mMHC-, hHLA+, mCD9-, hCD9+, hCD90-, hEpCAM+, hCD24-

Growth Properties

Organoids

Proliferation Rate
in Complete Media

NA

Sub-culture
Recommendations

1 Frozen Stock Vial can be used to generate: 8 wells in a 24-well plate

Culture Derivation

Derived from passage 2 PDX material

Tumorigenic in
NSG Mice

Spheroid Growth

Spheroid Growth
Notes

NA

Soft Agar Growth

Soft Agar
Growth Notes

NA

Fibroblast qRT-PCR
C1 Corr

-0.12

Fibroblast qRT-PCR
C2 Corr

-0.18

Fibroblast qRT-PCR
Top Hits

KRT18,KRT8,KRT19,CEACAM5,KRT7

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Images (if available)

In Vitro Images

View	Image Type	Notes	In Vitro Image
	Light Microscopy	Image of total well, bar shows 1mm size, Passage 12, 7 days in culture
	Light Microscopy	Magnified image- note 500µm bar, Passage 12, 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

Genomic Analysis

External Genetic Analysis Data

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

2.0.1.51.0

Download Read1 FASTQ

Download Read2 FASTQ

2.0.1.51.0

Download Read1 FASTQ

Download Read2 FASTQ

2.0.1.4.0

Download RSEM (genes)

Download RSEM (isoforms)

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
	APC	p.E582Gfs*20	0.3478	92	Frame_Shift_Ins	Likely Oncogenic	Likely Loss-of-function	v3.14
	APC	p.P1594Afs*38	0.5756	410	Frame_Shift_Ins	Likely Oncogenic	Likely Loss-of-function	v3.14
	APC	p.K2248*	0.6110	347	Nonsense_Mutation	Likely Oncogenic	Likely Loss-of-function	v3.14
	ARID1A	p.S617Qfs*2	0.3299	97	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	ARID1A	p.R1461*	0.4786	468	Nonsense_Mutation	Likely Oncogenic	Likely Loss-of-function	v3.14
	ARID1B	p.R1944*	0.1803	305	Nonsense_Mutation	Likely Oncogenic	Likely Loss-of-function	v3.14
	ARID1B	p.N2124Tfs*21	0.5118	340	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	ASXL1	p.G646Wfs*12	0.3952	167	Frame_Shift_Ins	Likely Oncogenic	Likely Loss-of-function	v3.14
	AXIN2	p.G665Afs*24	0.4949	198	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	BCORL1	p.P1681Qfs*20	1.0000	103	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	BRCA2	p.R3384*	0.4615	286	Nonsense_Mutation	Likely Oncogenic	Likely Loss-of-function	v3.14
	CD58	p.Q59Tfs*4	0.4557	79	Frame_Shift_Ins	Likely Oncogenic	Likely Loss-of-function	v3.14
	CIITA	p.G655Rfs*94	0.4291	289	Frame_Shift_Ins	Likely Oncogenic	Likely Loss-of-function	v3.14
	DNMT3A	p.F414Lfs*7	0.3890	383	Frame_Shift_Ins	Likely Oncogenic	Likely Loss-of-function	v3.14
	ELF3	p.X200_splice	0.4649	185	Splice_Site	Likely Oncogenic	Likely Loss-of-function	v3.14
	FANCC	p.X444_splice	0.8400	25	Splice_Site	Likely Oncogenic	Likely Loss-of-function	v3.14
	FAT1	p.K2139Sfs*8	0.4730	389	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	GATA3	p.S237Afs*28	0.4575	424	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	GNAS	p.R201H	0.4379	306	Missense_Mutation	Oncogenic	Gain-of-function	v3.14
	KMT2B	p.K553Nfs*52	0.4986	1039	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	KMT2B	p.V788*	0.5271	332	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	KMT2B	p.G1879Vfs*16	0.4462	186	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	KMT2C	p.F4496Lfs*21	0.2185	270	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	KMT2C	p.K2797Rfs*26	0.5799	169	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	KMT2C	p.R2609*	0.3959	293	Nonsense_Mutation	Likely Oncogenic	Likely Loss-of-function	v3.14
	KMT2D	p.L2331*	0.6094	233	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	KRAS	p.G12D	0.6462	260	Missense_Mutation	Oncogenic	Gain-of-function	v3.14
	MEN1	p.R521Gfs*43	0.0000	128	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	MET	p.T992I	0.5924	238	Missense_Mutation	Inconclusive	Likely Gain-of-function	v3.14
	MSH2	p.W345*	0.9862	145	Nonsense_Mutation	Likely Oncogenic	Likely Loss-of-function	v3.14
	NPM1	p.V156Sfs*6	0.4074	135	Frame_Shift_Ins	Likely Oncogenic	Likely Loss-of-function	v3.14
	PAX5	p.A322Rfs*19	0.4815	270	Frame_Shift_Ins	Likely Oncogenic	Likely Loss-of-function	v3.14
	RAD50	p.E723Gfs*5	0.3071	407	Frame_Shift_Ins	Likely Oncogenic	Likely Loss-of-function	v3.14
	SETD2	p.X2477_splice	0.5667	90	Splice_Site	Likely Oncogenic	Likely Loss-of-function	v3.14
	SETD2	p.T305Qfs*35	0.3279	61	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	SH2B3	p.A111Pfs*86	0.2899	207	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	SPEN	p.A2251Qfs*102	0.4076	395	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	TP53	p.R273C	0.2262	84	Missense_Mutation	Likely Oncogenic	Likely Loss-of-function	v3.14
	TP53	p.R267Q	0.4500	60	Missense_Mutation	Likely Oncogenic	Likely Loss-of-function	v3.14
	TP53	p.G244C	0.5694	209	Missense_Mutation	Likely Oncogenic	Likely Loss-of-function	v3.14
	TSC2	p.G654Lfs*2	0.4438	178	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	TSC2	p.X1690_splice	0.4198	243	Splice_Site	Likely Oncogenic	Likely Loss-of-function	v3.14
	ZFHX3	p.R1893Gfs*35	0.4093	215	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	ZFHX3	p.E763Sfs*61	0.2099	324	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14

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