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
P11	PDAC	4	64	29.9	Female	69.9

Mutation Profiles

Primary Tumor

ID	Gene	CHROM	POS	REF	ALT	Consequence	HGVSc	HGVSp	VAF
P11-Tissue	PRAMEF22	1	13038350	T	C	Missense_Mutation	ENST00000376187.1:c.1415T>C	ENSP00000365358.1:p.Phe472Ser	0.29850746
P11-Tissue	LYPLA2	1	24121214	CCTGT	C	Frame_Shift_Del	ENST00000374514.3:c.691_694del	ENSP00000363638.3:NA	0.03278688
P11-Tissue	RC3H1	1	173952772	G	A	Nonsense_Mutation	ENST00000367696.2:c.376C>T	ENSP00000356669.2:p.Gln126Ter	0.16216216
P11-Tissue	TARBP1	1	234596068	T	C	Missense_Mutation	ENST00000040877.1:c.1474A>G	ENSP00000040877.1:p.Lys492Glu	0.12021857
P11-Tissue	LHCGR	2	48982761	A	T	Missense_Mutation	ENST00000405626.1:c.50T>A	ENSP00000386033.1:p.Leu17Gln	0.02649006
P11-Tissue	TTN	2	179432192	G	T	Missense_Mutation	ENST00000591111.1:c.73744C>A	ENSP00000465570.1:p.Pro24582Thr	0.10778443
P11-Tissue	SETD2	3	47162702	C	A	Nonsense_Mutation	ENST00000409792.3:c.3424G>T	ENSP00000386759.3:p.Glu1142Ter	0.09722222
P11-Tissue	SEC62	3	169693395	G	T	Splice_Site	ENST00000480708.1:c.37-1G>T		0.03623188
P11-Tissue	SYNPO2	4	119978759	CCAGGAATCCATTGTG	C	In_Frame_Del	ENST00000307142.4:c.3457_3471del	ENSP00000306015.4:p.Gln1153_Val1157del	0.09677419
P11-Tissue	FRG1	4	190878589	A	G	Missense_Mutation	ENST00000226798.4:c.469A>G	ENSP00000226798.4:p.Ile157Val	0.08547008
P11-Tissue	TRPC7	5	135587435	AG	CT	Missense_Mutation	ENST00000513104.1:c.1480_1481inv	ENSP00000426070.1:p.Leu494Arg	0.02054794
P11-Tissue	RNF14	5	141357877	C	G	Missense_Mutation	ENST00000394520.2:c.316C>G	ENSP00000378028.2:p.Leu106Val	0.09333333
P11-Tissue	TFAP2B	6	50791226	C	G	Missense_Mutation	ENST00000393655.3:c.188C>G	ENSP00000377265.2:p.Ser63Trp	0.065625
P11-Tissue	SOGA3	6	127797102	G	A	Missense_Mutation	ENST00000556132.1:c.2069C>T	ENSP00000451768.1:p.Ala690Val	0.05109489
P11-Tissue	CNBD1	8	88365922	A	T	Missense_Mutation	ENST00000518476.1:c.1211A>T	ENSP00000430073.1:p.Glu404Val	0.12987013
P11-Tissue	TUBAL3	10	5437430	G	A	Missense_Mutation	ENST00000479328.1:c.136C>T	ENSP00000418799.1:p.Arg46Trp	0.03347280
P11-Tissue	TRIM3	11	6479476	A	G	Missense_Mutation	ENST00000537602.1:c.182T>C	ENSP00000441091.1:p.Val61Ala	0.10404624
P11-Tissue	OR5L1	11	55579307	G	A	Missense_Mutation	ENST00000333973.2:c.365G>A	ENSP00000335529.2:p.Arg122His	0.08843537
P11-Tissue	OR1S1	11	57982317	A	T	Missense_Mutation	ENST00000309433.6:c.101A>T	ENSP00000311688.6:p.Asp34Val	0.05957446
P11-Tissue	KRAS	12	25398284	C	A	Missense_Mutation	ENST00000557334.1:c.35G>T	ENSP00000452512.1:p.Gly12Val	0.16666666
P11-Tissue	KMT2D	12	49434018	CT	C	Frame_Shift_Del	ENST00000301067.7:c.7534del	ENSP00000301067.7:p.Ser2512ValfsTer31	0.04639175
P11-Tissue	RB1	13	48916747	C	T	Nonsense_Mutation	ENST00000267163.4:c.277C>T	ENSP00000267163.4:p.Gln93Ter	0.225
P11-Tissue	DIAPH3	13	60737862	T	A	Missense_Mutation	ENST00000400330.1:c.39A>T	ENSP00000383184.1:p.Gln13His	0.15686274
P11-Tissue	NDFIP2	13	80055604	A	T	Missense_Mutation	ENST00000218652.7:c.266A>T	ENSP00000218652.7:p.Asp89Val	0.11864406
P11-Tissue	C15orf26	15	81436026	G	C	Missense_Mutation	ENST00000286732.4:c.501G>C	ENSP00000286732.4:p.Arg167Ser	0.08053691
P11-Tissue	ZNF213	16	3187465	G	A	Missense_Mutation	ENST00000576416.1:c.184G>A	ENSP00000459177.1:p.Ala62Thr	0.13930348
P11-Tissue	ALG1	16	5132659	C	T	Missense_Mutation	ENST00000588623.1:c.839C>T	ENSP00000468118.1:p.Ala280Val	0.07166123
P11-Tissue	TP53	17	7577506	C	A	Missense_Mutation	ENST00000455263.2:c.775G>T	ENSP00000398846.2:p.Asp259Tyr	0.15723270
P11-Tissue	MYH13	17	10258269	C	T	Missense_Mutation	ENST00000418404.3:c.844G>A	ENSP00000404570.3:p.Glu282Lys	0.07738095
P11-Tissue	BPTF	17	65850452	A	G	Missense_Mutation	ENST00000424123.3:c.593A>G	ENSP00000388405.3:p.Asp198Gly	0.10559006
P11-Tissue	ENGASE	17	77078018	A	G	Missense_Mutation	ENST00000579016.1:c.911A>G	ENSP00000462333.1:p.Tyr304Cys	0.078125
P11-Tissue	SLC14A2	18	43262402	C	T	Missense_Mutation	ENST00000589658.1:c.1112C>T	ENSP00000465349.1:p.Ala371Val	0.07142857

Organoid

ID	Gene	CHROM	POS	REF	ALT	Consequence	HGVSc	HGVSp	VAF
P11-Organoid	PLEKHN1	1	901915	G	T	Missense_Mutation	ENST00000379410.3:c.4G>T	ENSP00000368720.3:NA	0.02083333
P11-Organoid	PRAMEF4	1	12943166	C	T	Missense_Mutation	ENST00000235349.5:c.50G>A	ENSP00000235349.5:NA	0.39790575
P11-Organoid	LYPLA2	1	24121214	CCTGT	C	Frame_Shift_Del	ENST00000374514.3:c.691_694del	ENSP00000363638.3:NA	0.18012422
P11-Organoid	SPTA1	1	158605779	C	A	Missense_Mutation	ENST00000368147.4:c.5356G>T	ENSP00000357129.4:p.Gly1786Trp	0.09223301
P11-Organoid	RC3H1	1	173952772	G	A	Nonsense_Mutation	ENST00000367696.2:c.376C>T	ENSP00000356669.2:p.Gln126Ter	0.56756756
P11-Organoid	TARBP1	1	234596068	T	C	Missense_Mutation	ENST00000040877.1:c.1474A>G	ENSP00000040877.1:p.Lys492Glu	0.58095238
P11-Organoid	TBCE	1	235594030	C	CT	Frame_Shift_Ins	ENST00000543662.1:c.572dup	ENSP00000439170.1:p.Phe193IlefsTer28	0.54950495
P11-Organoid	PPM1G	2	27607572	C	A	Missense_Mutation	ENST00000350803.4:c.793G>T	ENSP00000264714.4:p.Asp265Tyr	0.01869158
P11-Organoid	TTN	2	179432192	G	T	Missense_Mutation	ENST00000591111.1:c.73744C>A	ENSP00000465570.1:p.Pro24582Thr	0.47448979
P11-Organoid	SETD2	3	47162702	C	A	Nonsense_Mutation	ENST00000409792.3:c.3424G>T	ENSP00000386759.3:p.Glu1142Ter	0.17647058
P11-Organoid	MYNN	3	169492309	CTG	C	Frame_Shift_Del	ENST00000544106.1:c.228_229del	ENSP00000440637.1:p.Leu77GlyfsTer11	0.04545454
P11-Organoid	CRIPAK	4	1388757	T	C	Missense_Mutation	ENST00000324803.4:c.458T>C	ENSP00000323978.4:p.Met153Thr	0.26960784
P11-Organoid	SYNPO2	4	119978759	CCAGGAATCCATTGTG	C	In_Frame_Del	ENST00000307142.4:c.3457_3471del	ENSP00000306015.4:p.Gln1153_Val1157del	0.23648648
P11-Organoid	FRG1	4	190878589	A	G	Missense_Mutation	ENST00000226798.4:c.469A>G	ENSP00000226798.4:p.Ile157Val	0.03990610
P11-Organoid	RNF14	5	141357877	C	G	Missense_Mutation	ENST00000394520.2:c.316C>G	ENSP00000378028.2:p.Leu106Val	0.616
P11-Organoid	ZFAND3	6	38084383	C	T	Missense_Mutation	ENST00000373391.2:c.331C>T	ENSP00000362489.2:p.Arg111Trp	0.08585858
P11-Organoid	TFAP2D	6	50696688	C	A	Missense_Mutation	ENST00000008391.3:c.718C>A	ENSP00000008391.3:p.Pro240Thr	0.025
P11-Organoid	TFAP2B	6	50791226	C	G	Missense_Mutation	ENST00000393655.3:c.188C>G	ENSP00000377265.2:p.Ser63Trp	0.39884393
P11-Organoid	SOGA3	6	127797102	G	A	Missense_Mutation	ENST00000556132.1:c.2069C>T	ENSP00000451768.1:p.Ala690Val	0.41935483
P11-Organoid	PLEKHG1	6	151139353	G	A	Splice_Site	ENST00000367328.1:c.1312+1G>A		0.40588235
P11-Organoid	SCIN	7	12689144	T	A	Missense_Mutation	ENST00000519209.1:c.1193T>A	ENSP00000430997.1:p.Val398Asp	0.11458333
P11-Organoid	ABCA13	7	48559842	T	G	Missense_Mutation	ENST00000544596.1:c.1193T>G	ENSP00000442634.1:p.Leu398Arg	0.05426356
P11-Organoid	CNBD1	8	88365922	A	T	Missense_Mutation	ENST00000518476.1:c.1211A>T	ENSP00000430073.1:p.Glu404Val	0.64532019
P11-Organoid	TOP1MT	8	144408459	G	A	Missense_Mutation	ENST00000523676.1:c.122C>T	ENSP00000429181.1:p.Thr41Met	0.13838120
P11-Organoid	PPAPDC2	9	4663187	A	G	Missense_Mutation	ENST00000381883.2:c.812A>G	ENSP00000371307.2:p.Gln271Arg	0.125
P11-Organoid	OR13C4	9	107289207	G	T	Missense_Mutation	ENST00000277216.3:c.284C>A	ENSP00000277216.3:p.Ser95Tyr	0.17525773
P11-Organoid	TUBAL3	10	5437430	G	A	Missense_Mutation	ENST00000479328.1:c.136C>T	ENSP00000418799.1:p.Arg46Trp	0.20821917
P11-Organoid	ADAMTS14	10	72520449	C	T	Missense_Mutation	ENST00000373208.1:c.3521C>T	ENSP00000362304.1:p.Pro1174Leu	0.06140350
P11-Organoid	CYP2E1	10	135347332	G	T	Missense_Mutation	ENST00000463117.2:c.898G>T	ENSP00000440689.1:p.Gly300Trp	0.01226993
P11-Organoid	TRIM3	11	6479476	A	G	Missense_Mutation	ENST00000537602.1:c.182T>C	ENSP00000441091.1:p.Val61Ala	0.45185185
P11-Organoid	OR1S1	11	57982317	A	T	Missense_Mutation	ENST00000309433.6:c.101A>T	ENSP00000311688.6:p.Asp34Val	0.32777777
P11-Organoid	TENM4	11	78498042	C	T	Missense_Mutation	ENST00000278550.7:c.2266G>A	ENSP00000278550.7:p.Asp756Asn	0.12173913
P11-Organoid	KRAS	12	25398284	C	A	Missense_Mutation	ENST00000557334.1:c.35G>T	ENSP00000452512.1:p.Gly12Val	0.59643916
P11-Organoid	KMT2D	12	49434018	CT	C	Frame_Shift_Del	ENST00000301067.7:c.7534del	ENSP00000301067.7:p.Ser2512ValfsTer31	0.44311377
P11-Organoid	WDR66	12	122392233	A	G	Missense_Mutation	ENST00000397454.2:c.1528A>G	ENSP00000380595.2:p.Ile510Val	0.42452830
P11-Organoid	RB1	13	48916747	C	T	Nonsense_Mutation	ENST00000267163.4:c.277C>T	ENSP00000267163.4:p.Gln93Ter	0.92045454
P11-Organoid	DIAPH3	13	60737862	T	A	Missense_Mutation	ENST00000400330.1:c.39A>T	ENSP00000383184.1:p.Gln13His	0.92237442
P11-Organoid	NDFIP2	13	80055604	A	T	Missense_Mutation	ENST00000218652.7:c.266A>T	ENSP00000218652.7:p.Asp89Val	0.92248062
P11-Organoid	BMP4	14	54417115	G	A	Missense_Mutation	ENST00000559087.1:c.862C>T	ENSP00000453485.1:p.Arg288Trp	0.24812030
P11-Organoid	C15orf26	15	81436026	G	C	Missense_Mutation	ENST00000286732.4:c.501G>C	ENSP00000286732.4:p.Arg167Ser	0.23529411
P11-Organoid	RGMA	15	93588749	C	T	Missense_Mutation	ENST00000557301.1:c.856G>A	ENSP00000452126.1:p.Gly286Ser	0.02097902
P11-Organoid	ZNF213	16	3187465	G	A	Missense_Mutation	ENST00000576416.1:c.184G>A	ENSP00000459177.1:p.Ala62Thr	0.48258706
P11-Organoid	ATP6V0D1	16	67472954	G	A	Missense_Mutation	ENST00000602876.1:c.505C>T	ENSP00000473515.1:p.Arg169Trp	0.01141226
P11-Organoid	TP53	17	7577506	C	A	Missense_Mutation	ENST00000455263.2:c.775G>T	ENSP00000398846.2:p.Asp259Tyr	0.84403669
P11-Organoid	MYH13	17	10258269	C	T	Missense_Mutation	ENST00000418404.3:c.844G>A	ENSP00000404570.3:p.Glu282Lys	0.79069767
P11-Organoid	CCR7	17	38711920	C	T	Missense_Mutation	ENST00000579344.1:c.193G>A	ENSP00000462631.1:p.Val65Met	0.06060606
P11-Organoid	SPPL2C	17	43924263	C	T	Missense_Mutation	ENST00000329196.5:c.1991C>T	ENSP00000332488.5:p.Ala664Val	0.26633165
P11-Organoid	BPTF	17	65850452	A	G	Missense_Mutation	ENST00000424123.3:c.593A>G	ENSP00000388405.3:p.Asp198Gly	0.50980392
P11-Organoid	ENGASE	17	77078018	A	G	Missense_Mutation	ENST00000579016.1:c.911A>G	ENSP00000462333.1:p.Tyr304Cys	0.50145772
P11-Organoid	ZNF521	18	22930900	C	T	Missense_Mutation	ENST00000538137.2:c.11G>A	ENSP00000440768.2:p.Arg4His	0.14649681
P11-Organoid	SLC14A2	18	43262402	C	T	Missense_Mutation	ENST00000589658.1:c.1112C>T	ENSP00000465349.1:p.Ala371Val	0.29794520
P11-Organoid	FFAR3	19	35850261	G	T	Missense_Mutation	ENST00000594310.1:c.469G>T	ENSP00000469522.1:p.Gly157Trp	0.01079136
P11-Organoid	FFAR3	19	35850345	C	T	Missense_Mutation	ENST00000594310.1:c.553C>T	ENSP00000469522.1:p.Arg185Trp	0.02608695
P11-Organoid	POLD1	19	50919960	G	A	Missense_Mutation	ENST00000599857.1:c.3047G>A	ENSP00000473052.1:p.Arg1016His	0.08119658
P11-Organoid	LILRA1	19	55107376	G	A	Missense_Mutation	ENST00000251372.3:c.934G>A	ENSP00000251372.3:p.Asp312Asn	0.06325301
P11-Organoid	BCORL1	X	129190032	CTG	C	Frame_Shift_Del	ENST00000540052.1:c.5060_5061del	ENSP00000437775.1:p.Val1687GlyfsTer57	0.10661764
P11-Organoid	ZNF449	X	134494558	C	T	Missense_Mutation	ENST00000339249.4:c.1114C>T	ENSP00000339585.4:p.Leu372Phe	0.35714285

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
P11	AZD2014	66.09
P11	AZD3759	~ 1.959e+020
P11	AZD4547	20556
P11	AZD5363	~ 1.137e+020
P11	AZD6738	8258
P11	AZD9291	314311
P11	I.BET.762	778.4
P11	Rapamycin..Sirolimus.	14224
P11	AZD1775..MK.1775.	615.2
P11	Triptolide..PG490.	~ 0.002906
P11	Simvastatin	67.45
P11	Temozolomide	~ 2.138e-014
P11	Imatinib.Mesylate..STI571.	~ 14922680799
P11	Pazopanib..GW786034.	1432
P11	Sunitinib.Malate	~ 4980
P11	Olaparib..AZD2281..KU0059436.	~ 4944
P11	Regorafenib..BAY.73.4506.	6045
P11	Erlotinib	~ 4206
P11	Gefitinib	~ 9.703e+020
P11	Afatinib	~ 551729261
P11	OTX.015	151.5
P11	BKM120..NVP.BKM120.	1182
P11	BYL719	88933
P11	Cediranib..AZD2171.	16859
P11	Ceritinib.LDK378.	1703
P11	Crizotinib...PF.02341066.	2707
P11	Dabrafenib	~ 42.99
P11	Dacomitinib	21364
P11	Everolimus..RAD001.	~ 1481275
P11	Ibrutinib..PCI.32765.	~ 5476
P11	Lapatinib	3818
P11	LY2835219	4468
P11	Brivanib..BMS.582664.	~ 21033
P11	Panobinostat	64.91
P11	Selumetinib..AZD6244.	575.1
P11	Sorafenib	~ 210426
P11	Trametinib	67.16
P11	Vandetanib..ZD6474.	3045
P11	Vemurafenib	5351
P11	AZD5153	61.83
P11	ABT.199..GDC.0199..	~ 4875
P11	ABT.888..Veliparib..NSC.737664.	~ 4750
P11	Avagacestat..BMS.708163.	~ 1.739e-018
P11	Axitinib...AG.013736.	2612
P11	Bosutinib..SKI.606.	3406
P11	Cabozantinib..XL184.	5681
P11	Dasatinib..BMS.354825.	1.005E-43
P11	decitabine	6264
P11	defactinib	~ 1.131e+020
P11	Dovitinib..TKI258.CHIR258.	543.4
P11	Fluorouracil..5.Fluoracil..5.FU.	4935
P11	Foretinib..XL880.	922.8
P11	Tivantinib..ARQ.197.	221.3
P11	Abraxane	2.136
P11	AZD2461.olaparib.analog.	~ 75054541111961
P11	Olaparib.	~ 4186
P11	Idelalisib	7783
P11	Irinotecan	402.3
P11	Nilotinib..AMN.107.	4977
P11	NVP.AEW541	742
P11	Oxaliplatin	~ 22932
P11	PLX3397	8599
P11	Quizartinib..AC220.	372.1
P11	Saracatinib..AZD0530.	1778
P11	Semagacestat..LY450139.	3665
P11	TGX.221	14325
P11	tozasertib	~ 3272339869801
P11	Vorinostat..SAHA..MK0683.	2521
P11	XAV939	1580
P11	gemcitabine	~ 0.2483
P11	palbociclib	~ 128005008829
P11	Neratinib..HKI.272.	765