Organoidomics

Please contact Prof. Semin Lee, Jinho Jang or Web-master for any inquires.

3D Organoids

RAMP

Clinical Information

ID	Diagnosis	Stage	Age	BMI	Sex	CA19-9
P9	PDAC	IIB	84	22.5	Male	57

Mutation Profiles

Primary Tumor

ID	Gene	CHROM	POS	REF	ALT	Consequence	HGVSc	HGVSp	VAF
P9-Tissue	PTCHD2	1	11561569	G	A	Missense_Mutation	ENST00000389575.3:c.520G>A	ENSP00000374226.3:p.Val174Ile	0.05797101
P9-Tissue	SH2D5	1	21050683	G	A	Missense_Mutation	ENST00000444387.2:c.692C>T	ENSP00000406026.2:p.Ser231Leu	0.04964539
P9-Tissue	SZT2	1	43896014	A	T	Missense_Mutation	ENST00000562955.1:c.4263A>T	ENSP00000457168.1:p.Lys1421Asn	0.10638297
P9-Tissue	IGSF3	1	117142641	G	A	Missense_Mutation	ENST00000369486.3:c.1951C>T	ENSP00000358498.3:p.Arg671Trp	0.09939759
P9-Tissue	NBPF20	1	148343792	C	A	Missense_Mutation	ENST00000414710.2:c.295G>T	ENSP00000389520.2:p.Val99Phe	0.21428571
P9-Tissue	OR10J3	1	159284018	T	A	Missense_Mutation	ENST00000332217.5:c.432A>T	ENSP00000331789.5:p.Gln144His	0.03240740
P9-Tissue	MIA3	1	222806547	G	A	Missense_Mutation	ENST00000344922.5:c.3433G>A	ENSP00000340900.5:p.Ala1145Thr	0.07142857
P9-Tissue	OR14A16	1	247978414	G	T	Missense_Mutation	ENST00000357627.1:c.618C>A	ENSP00000350248.1:p.Phe206Leu	0.11464968
P9-Tissue	NEB	2	152348788	T	C	Missense_Mutation	ENST00000604864.1:c.24881A>G	ENSP00000474498.1:p.Tyr8294Cys	0.02962963
P9-Tissue	NEB	2	152348795	CC	GG	Splice_Site	ENST00000604864.1:c.24874-1_24874inv		0.03508771
P9-Tissue	FSIP2	2	186670987	T	G	Missense_Mutation	ENST00000424728.1:c.16954T>G	ENSP00000401306.1:p.Ser5652Ala	0.11111111
P9-Tissue	PLOD2	3	145788596	A	C	Missense_Mutation	ENST00000494950.1:c.2020T>G	ENSP00000420094.1:p.Phe674Val	0.06111111
P9-Tissue	TMEM165	4	56277874	A	G	Missense_Mutation	ENST00000542052.1:c.112A>G	ENSP00000437816.1:p.Ile38Val	0.09947644
P9-Tissue	METTL14	4	119631238	C	CTTGACTGGTTGTACACT	Frame_Shift_Ins	ENST00000506780.1:c.1053_1054insCTTTGACTGGTTGTACA	ENSP00000424111.1:p.Glu352LeufsTer2	0.02721088
P9-Tissue	FAT4	4	126370280	A	T	Missense_Mutation	ENST00000394329.3:c.8109A>T	ENSP00000377862.3:p.Leu2703Phe	0.07633587
P9-Tissue	PCDHGC5	5	140870054	C	A	Missense_Mutation	ENST00000252087.1:c.1247C>A	ENSP00000252087.1:p.Ala416Asp	0.09933774
P9-Tissue	SYNPO	5	150029215	C	T	Missense_Mutation	ENST00000522122.1:c.2110C>T	ENSP00000428378.1:p.Arg704Cys	0.09677419
P9-Tissue	RREB1	6	7248893	G	A	Missense_Mutation	ENST00000379938.2:c.4921G>A	ENSP00000369270.2:p.Glu1641Lys	0.10313901
P9-Tissue	USP49	6	41773784	G	A	Missense_Mutation	ENST00000394253.3:c.938C>T	ENSP00000377797.2:p.Thr313Met	0.04712041
P9-Tissue	CDKN2A	9	21974714	G	C	Missense_Mutation	ENST00000579122.1:c.113C>G	ENSP00000464202.1:p.Pro38Arg	0.09813084
P9-Tissue	OR5M9	11	56230138	G	A	Missense_Mutation	ENST00000279791.1:c.740C>T	ENSP00000279791.1:p.Ser247Phe	0.05752212
P9-Tissue	KRAS	12	25398284	C	T	Missense_Mutation	ENST00000557334.1:c.35G>A	ENSP00000452512.1:p.Gly12Asp	0.05844155
P9-Tissue	MARCH9	12	58152427	A	G	Missense_Mutation	ENST00000548358.1:c.449A>G	ENSP00000446758.1:p.Asn150Ser	0.18333333
P9-Tissue	RIMBP2	12	130927074	C	T	Missense_Mutation	ENST00000536002.1:c.496G>A	ENSP00000439159.1:p.Gly166Ser	0.04641350
P9-Tissue	RYR3	15	33928584	G	A	Missense_Mutation	ENST00000415757.3:c.3389G>A	ENSP00000399610.3:p.Arg1130His	0.05217391
P9-Tissue	CACNA1H	16	1203777	C	T	Missense_Mutation	ENST00000565831.1:c.40C>T	ENSP00000455840.1:p.Pro14Ser	0.16326530
P9-Tissue	TP53	17	7579385	TTC	T	Frame_Shift_Del	ENST00000455263.2:c.300_301del	ENSP00000398846.2:p.Lys101AsnfsTer47	0.08771929
P9-Tissue	MYH1	17	10404746	C	T	Missense_Mutation	ENST00000226207.5:c.3419G>A	ENSP00000226207.5:p.Arg1140His	0.04471544
P9-Tissue	PSG4	19	43697534	A	G	Missense_Mutation	ENST00000433626.2:c.971T>C	ENSP00000387864.2:p.Ile324Thr	0.25316455
P9-Tissue	SLC24A3	20	19673940	GCCGCTGAGTT	G	Frame_Shift_Del	ENST00000328041.6:c.1363_1372del	ENSP00000333519.5:p.Pro455SerfsTer21	0.13513513
P9-Tissue	CSNK1E	22	38690489	G	A	Missense_Mutation	ENST00000403904.1:c.937C>T	ENSP00000384074.1:p.Arg313Cys	0.11453744
P9-Tissue	ZNF280C	X	129373639	G	A	Missense_Mutation	ENST00000370978.4:c.410C>T	ENSP00000360017.4:p.Ser137Leu	0.25531914

Organoid

ID	Gene	CHROM	POS	REF	ALT	Consequence	HGVSc	HGVSp	VAF
P9-Organoid	PTCHD2	1	11561569	G	A	Missense_Mutation	ENST00000389575.3:c.520G>A	ENSP00000374226.3:p.Val174Ile	0.38926174
P9-Organoid	SH2D5	1	21050683	G	A	Missense_Mutation	ENST00000444387.2:c.692C>T	ENSP00000406026.2:p.Ser231Leu	0.40579710
P9-Organoid	YBX1	1	43166460	C	T	Missense_Mutation	ENST00000321358.7:c.749C>T	ENSP00000361626.3:NA	0.15126050
P9-Organoid	SZT2	1	43896014	A	T	Missense_Mutation	ENST00000562955.1:c.4263A>T	ENSP00000457168.1:p.Lys1421Asn	0.47089947
P9-Organoid	GBP1	1	89525903	C	T	Missense_Mutation	ENST00000370473.4:c.295G>A	ENSP00000359504.4:NA	0.05163043
P9-Organoid	WDR77	1	111989740	T	A	Missense_Mutation	ENST00000235090.5:c.470A>T	ENSP00000235090.5:NA	0.04854368
P9-Organoid	NBPF20	1	148343792	C	A	Missense_Mutation	ENST00000414710.2:c.295G>T	ENSP00000389520.2:p.Val99Phe	0.16216216
P9-Organoid	OR10J3	1	159284018	T	A	Missense_Mutation	ENST00000332217.5:c.432A>T	ENSP00000331789.5:p.Gln144His	0.32575757
P9-Organoid	MIA3	1	222806547	G	A	Missense_Mutation	ENST00000344922.5:c.3433G>A	ENSP00000340900.5:p.Ala1145Thr	0.37162162
P9-Organoid	OR14A16	1	247978414	G	T	Missense_Mutation	ENST00000357627.1:c.618C>A	ENSP00000350248.1:p.Phe206Leu	1
P9-Organoid	ANXA4	2	70046424	G	T	Missense_Mutation	ENST00000536030.1:c.485G>T	ENSP00000441931.1:p.Arg162Met	0.04651162
P9-Organoid	TTN	2	179410814	C	T	Missense_Mutation	ENST00000591111.1:c.90226G>A	ENSP00000465570.1:p.Val30076Ile	0.33898305
P9-Organoid	FSIP2	2	186670987	T	G	Missense_Mutation	ENST00000424728.1:c.16954T>G	ENSP00000401306.1:p.Ser5652Ala	0.45985401
P9-Organoid	PLOD2	3	145788596	A	C	Missense_Mutation	ENST00000494950.1:c.2020T>G	ENSP00000420094.1:p.Phe674Val	0.31123919
P9-Organoid	TMEM165	4	56277874	A	G	Missense_Mutation	ENST00000542052.1:c.112A>G	ENSP00000437816.1:p.Ile38Val	0.40784313
P9-Organoid	METTL14	4	119631238	C	CTTGACTGGTTGTACACT	Frame_Shift_Ins	ENST00000506780.1:c.1053_1054insCTTTGACTGGTTGTACA	ENSP00000424111.1:p.Glu352LeufsTer2	0.21008403
P9-Organoid	FAT4	4	126370280	A	T	Missense_Mutation	ENST00000394329.3:c.8109A>T	ENSP00000377862.3:p.Leu2703Phe	0.42911877
P9-Organoid	KIAA0922	4	154507363	T	G	Missense_Mutation	ENST00000440693.1:c.1314T>G	ENSP00000409663.1:p.Ile438Met	0.42424242
P9-Organoid	EPB41L4A	5	111519807	C	A	Missense_Mutation	ENST00000261486.5:c.1528G>T	ENSP00000261486.5:p.Asp510Tyr	0.48672566
P9-Organoid	PCDHGC5	5	140870054	C	A	Missense_Mutation	ENST00000252087.1:c.1247C>A	ENSP00000252087.1:p.Ala416Asp	0.46368715
P9-Organoid	SYNPO	5	150029215	C	T	Missense_Mutation	ENST00000522122.1:c.2110C>T	ENSP00000428378.1:p.Arg704Cys	0.47899159
P9-Organoid	RREB1	6	7248893	G	A	Missense_Mutation	ENST00000379938.2:c.4921G>A	ENSP00000369270.2:p.Glu1641Lys	1
P9-Organoid	TRIM40	6	30105062	G	T	Missense_Mutation	ENST00000396581.1:c.249G>T	ENSP00000379826.1:p.Glu83Asp	0.05747126
P9-Organoid	USP49	6	41773784	G	A	Missense_Mutation	ENST00000394253.3:c.938C>T	ENSP00000377797.2:p.Thr313Met	0.48260869
P9-Organoid	SENP6	6	76423246	TGGACTCACTCCGAGGCCCTTCTC	T	Frame_Shift_Del	ENST00000447266.2:c.2930_2952del	ENSP00000402527.2:p.Asp977ValfsTer18	0.25
P9-Organoid	MARCKS	6	114181528	G	A	Missense_Mutation	ENST00000368635.4:c.772G>A	ENSP00000357624.4:p.Ala258Thr	0.41129032
P9-Organoid	FOXK1	7	4801932	C	T	Missense_Mutation	ENST00000446823.1:c.1550C>T	ENSP00000394442.1:p.Ala517Val	0.01572327
P9-Organoid	STK31	7	23751758	G	A	Missense_Mutation	ENST00000433467.2:c.91G>A	ENSP00000411852.2:p.Asp31Asn	0.28813559
P9-Organoid	MOS	8	57026243	C	A	Missense_Mutation	ENST00000311923.1:c.299G>T	ENSP00000310722.1:p.Arg100Leu	0.50520833
P9-Organoid	CDKN2A	9	21974714	G	C	Missense_Mutation	ENST00000579122.1:c.113C>G	ENSP00000464202.1:p.Pro38Arg	1
P9-Organoid	ADARB2	10	1779344	T	C	Translation_Start_Site	ENST00000381312.1:c.1A>G	ENSP00000370713.1:p.Met1?	0.53061224
P9-Organoid	JAKMIP3	10	133967465	C	T	Missense_Mutation	ENST00000298622.4:c.2185C>T	ENSP00000298622.4:p.Arg729Trp	0.25764192
P9-Organoid	OR5M9	11	56230138	G	A	Missense_Mutation	ENST00000279791.1:c.740C>T	ENSP00000279791.1:p.Ser247Phe	0.41666666
P9-Organoid	UBXN1	11	62444997	C	A	Missense_Mutation	ENST00000533000.1:c.218G>T	ENSP00000432189.1:p.Arg73Leu	0.01923076
P9-Organoid	RBM4	11	66411363	AGCTGCTGCTGCAGCAGCAGCC	A	In_Frame_Del	ENST00000514361.3:c.791_811del	ENSP00000425446.3:p.Ala264_Ala270del	0.01754386
P9-Organoid	KRAS	12	25398284	C	T	Missense_Mutation	ENST00000557334.1:c.35G>A	ENSP00000452512.1:p.Gly12Asp	0.43579766
P9-Organoid	MARCH9	12	58152427	A	G	Missense_Mutation	ENST00000548358.1:c.449A>G	ENSP00000446758.1:p.Asn150Ser	0.39130434
P9-Organoid	RIMBP2	12	130927074	C	T	Missense_Mutation	ENST00000536002.1:c.496G>A	ENSP00000439159.1:p.Gly166Ser	0.57819905
P9-Organoid	RYR3	15	33928584	G	A	Missense_Mutation	ENST00000415757.3:c.3389G>A	ENSP00000399610.3:p.Arg1130His	0.48322147
P9-Organoid	MGA	15	42003389	C	T	Nonsense_Mutation	ENST00000570161.1:c.2926C>T	ENSP00000457035.1:p.Gln976Ter	0.42379182
P9-Organoid	CACNA1H	16	1203777	C	T	Missense_Mutation	ENST00000565831.1:c.40C>T	ENSP00000455840.1:p.Pro14Ser	0.55913978
P9-Organoid	TP53	17	7579385	TTC	T	Frame_Shift_Del	ENST00000455263.2:c.300_301del	ENSP00000398846.2:p.Lys101AsnfsTer47	0.856
P9-Organoid	MYH1	17	10404746	C	T	Missense_Mutation	ENST00000226207.5:c.3419G>A	ENSP00000226207.5:p.Arg1140His	0.53703703
P9-Organoid	EMR2	19	14877816	T	A	Missense_Mutation	ENST00000601345.1:c.461A>T	ENSP00000471297.1:p.Lys154Ile	1
P9-Organoid	EMR2	19	14877820	G	A	Missense_Mutation	ENST00000601345.1:c.457C>T	ENSP00000471297.1:p.Leu153Phe	1
P9-Organoid	DLL3	19	39998562	C	T	Missense_Mutation	ENST00000205143.4:c.1766C>T	ENSP00000205143.3:p.Thr589Met	0.04761904
P9-Organoid	SNRPB	20	2444461	C	A	Missense_Mutation	ENST00000438552.2:c.352G>T	ENSP00000412566.2:p.Val118Phe	0.53669724
P9-Organoid	SLC24A3	20	19673940	GCCGCTGAGTT	G	Frame_Shift_Del	ENST00000328041.6:c.1363_1372del	ENSP00000333519.5:p.Pro455SerfsTer21	0.404
P9-Organoid	MCM3AP	21	47704204	G	A	Missense_Mutation	ENST00000397708.1:c.997C>T	ENSP00000380820.1:p.Arg333Trp	0.20958083
P9-Organoid	IGLL1	22	23917235	T	C	Missense_Mutation	ENST00000330377.2:c.241A>G	ENSP00000329312.2:p.Arg81Gly	0.08673469
P9-Organoid	CSNK1E	22	38690489	G	A	Missense_Mutation	ENST00000403904.1:c.937C>T	ENSP00000384074.1:p.Arg313Cys	0.52264808
P9-Organoid	ZNF280C	X	129373639	G	A	Missense_Mutation	ENST00000370978.4:c.410C>T	ENSP00000360017.4:p.Ser137Leu	1

Somatic Copy Number Alterations

Primary Tumor

Organoid

Concordance between Primary tumor and Organoid

VAF-VAF Plot

Number of Shared Mutations between Primary tumor and organoid (All mutations)

Number of Shared Mutations between Primary tumor and organoid (Functional mutations)

Drug Responses

ID	Drug	IC50
P9	AZD2014	485.4
P9	AZD3759	~ 7.381e+018
P9	AZD4547	~ 5451
P9	AZD5363	~ 3195747961
P9	AZD6738	2602
P9	AZD9291	~ 15322523
P9	I.BET.762	1668
P9	Rapamycin..Sirolimus.	~ 6.185e-010
P9	AZD1775..MK.1775.	148.2
P9	Triptolide..PG490.	~ 7.696e-005
P9	Simvastatin	8821
P9	Temozolomide	~ 218213
P9	Imatinib.Mesylate..STI571.	~ 74119949
P9	Pazopanib..GW786034.	14581
P9	Sunitinib.Malate	2723
P9	Olaparib..AZD2281..KU0059436.	5.283E+82
P9	Regorafenib..BAY.73.4506.	~ 2.219e+034
P9	Erlotinib	~ 6.317e+020
P9	Gefitinib	~ 1.395e+016
P9	Afatinib	~ 37050430535
P9	OTX.015	268.1
P9	BKM120..NVP.BKM120.	1802
P9	BYL719	5421
P9	Cediranib..AZD2171.	2930
P9	Ceritinib.LDK378.	1042
P9	Crizotinib...PF.02341066.	2471
P9	Dabrafenib	3847
P9	Dacomitinib	~ 1.531e+015
P9	Everolimus..RAD001.	~ 5722
P9	Ibrutinib..PCI.32765.	1841
P9	Lapatinib	9845
P9	LY2835219	286
P9	Brivanib..BMS.582664.	~ 19259
P9	Panobinostat	58.65
P9	Selumetinib..AZD6244.	1017
P9	Sorafenib	8851
P9	Trametinib	46.5
P9	Vandetanib..ZD6474.	1514
P9	Vemurafenib	~ 0.004421
P9	AZD5153	108.4
P9	ABT.199..GDC.0199..	323.1
P9	ABT.888..Veliparib..NSC.737664.	~ 5199
P9	Avagacestat..BMS.708163.	~ 1565781
P9	Axitinib...AG.013736.	1747
P9	Bosutinib..SKI.606.	1355
P9	Cabozantinib..XL184.	18718
P9	Dasatinib..BMS.354825.	5400
P9	decitabine	1511
P9	defactinib	4373
P9	Dovitinib..TKI258.CHIR258.	1467
P9	Fluorouracil..5.Fluoracil..5.FU.	5172
P9	Foretinib..XL880.	1283
P9	Tivantinib..ARQ.197.	365.4
P9	Abraxane	4.84
P9	AZD2461.olaparib.analog.	~ 1.032e-009
P9	Olaparib.	~ 2.516e+036
P9	Idelalisib	~ 58933
P9	Irinotecan	648.6
P9	Nilotinib..AMN.107.	1260
P9	NVP.AEW541	686.9
P9	Oxaliplatin	~ 6.060e-021
P9	PLX3397	~ 1155456
P9	Quizartinib..AC220.	11452
P9	Saracatinib..AZD0530.	3618
P9	Semagacestat..LY450139.	~ 21032
P9	TGX.221	~ 6431
P9	tozasertib	~ 1.012e+038
P9	Vorinostat..SAHA..MK0683.	~ 4131
P9	XAV939	1333
P9	gemcitabine	~ 2.164e-025
P9	palbociclib	11738
P9	Neratinib..HKI.272.	2776