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
P4	PDAC	3	69	22.9	Female	6037.37

Mutation Profiles

Primary Tumor

ID	Gene	CHROM	POS	REF	ALT	Consequence	HGVSc	HGVSp	VAF
P4-Tissue	CPT2	1	53676713	T	C	Missense_Mutation	ENST00000371486.3:c.1367T>C	ENSP00000360541.3:p.Leu456Pro	0.04237288
P4-Tissue	HRNR	1	152192163	G	T	Missense_Mutation	ENST00000368801.2:c.1942C>A	ENSP00000357791.2:p.Arg648Ser	0.15923566
P4-Tissue	RETSAT	2	85570849	C	T	Missense_Mutation	ENST00000457495.2:c.1423G>A	ENSP00000405040.2:p.Gly475Arg	0.04678362
P4-Tissue	RETSAT	2	85570857	G	A	Missense_Mutation	ENST00000457495.2:c.1415C>T	ENSP00000405040.2:p.Ala472Val	0.04320987
P4-Tissue	THSD7B	2	138421009	C	A	Missense_Mutation	ENST00000413152.2:c.4431C>A	ENSP00000413841.2:p.Phe1477Leu	0.05555555
P4-Tissue	PODXL2	3	127379547	G	A	Missense_Mutation	ENST00000342480.6:c.676G>A	ENSP00000345359.6:p.Gly226Arg	0.08029197
P4-Tissue	SLC2A2	3	170724992	C	A	Missense_Mutation	ENST00000382808.4:c.200G>T	ENSP00000372258.4:p.Gly67Val	0.07070707
P4-Tissue	SPRY4	5	141694525	T	C	Missense_Mutation	ENST00000434127.2:c.149A>G	ENSP00000399468.2:p.Asn50Ser	0.09677419
P4-Tissue	FOXQ1	6	1313078	G	A	Missense_Mutation	ENST00000296839.2:c.139G>A	ENSP00000296839.2:p.Ala47Thr	0.42105263
P4-Tissue	CDSN	6	31084047	CA	TG	Missense_Mutation	ENST00000376288.2:c.1344_1345inv	ENSP00000365465.2:p.Gly449Ser	0.04385964
P4-Tissue	PXDNL	8	52321567	G	A	Missense_Mutation	ENST00000543296.1:c.2617C>T	ENSP00000444865.1:p.Arg873Cys	0.06097561
P4-Tissue	CDKN2A	9	21971111	G	A	Missense_Mutation	ENST00000579755.1:c.290C>T	ENSP00000462950.1:p.Ala97Val	0.08547008
P4-Tissue	UBAP2	9	33953402	T	C	Missense_Mutation	ENST00000539807.1:c.202A>G	ENSP00000439329.1:p.Thr68Ala	0.04605263
P4-Tissue	POLR3A	10	79785392	T	C	Missense_Mutation	ENST00000372371.3:c.306A>G	ENSP00000361446.3:p.Ile102Met	0.04424778
P4-Tissue	RRP12	10	99160960	C	T	Missense_Mutation	ENST00000414986.1:c.29G>A	ENSP00000414863.1:p.Gly10Asp	0.03313253
P4-Tissue	TECTA	11	120998619	G	A	Missense_Mutation	ENST00000392793.1:c.1933G>A	ENSP00000376543.1:p.Val645Ile	0.08321167
P4-Tissue	HEPACAM	11	124793631	C	T	Missense_Mutation	ENST00000298251.4:c.703G>A	ENSP00000298251.4:p.Val235Ile	0.04301075
P4-Tissue	TPTE2	13	20000613	AT	GA	Missense_Mutation	ENST00000457266.2:c.1013_1014delinsTC	ENSP00000442218.1:p.Tyr338Phe	0.04854368
P4-Tissue	TPTE2	13	20000621	T	C	Missense_Mutation	ENST00000457266.2:c.1006A>G	ENSP00000442218.1:p.Asn336Asp	0.02970297
P4-Tissue	VWA3A	16	22144263	G	A	Missense_Mutation	ENST00000389398.5:c.1915G>A	ENSP00000374049.5:p.Asp639Asn	0.08300395
P4-Tissue	GDPD3	16	30119734	A	T	Missense_Mutation	ENST00000406256.3:c.727T>A	ENSP00000384363.3:p.Cys243Ser	0.05347593
P4-Tissue	TP53	17	7577498	C	A	Splice_Site	ENST00000455263.2:c.782+1G>T		0.04487179
P4-Tissue	PTPRS	19	5211653	G	A	Missense_Mutation	ENST00000592099.1:c.3841C>T	ENSP00000467398.1:p.Arg1281Trp	0.10043668
P4-Tissue	MIS18A	21	33651108	G	A	Missense_Mutation	ENST00000290130.3:c.218C>T	ENSP00000290130.3:p.Ala73Val	0.06
P4-Tissue	KRTAP10-7	21	46021011	A	G	Missense_Mutation	ENST00000380102.2:c.490A>G	ENSP00000369445.2:p.Ile164Val	0.03276131
P4-Tissue	LONRF3	X	118109402	C	A	Missense_Mutation	ENST00000371628.3:c.659C>A	ENSP00000360690.3:p.Pro220Gln	0.10559006
P4-Tissue	MAGEC1	X	140994462	A	C	Missense_Mutation	ENST00000285879.4:c.1272A>C	ENSP00000285879.4:p.Leu424Phe	0.07288629
P4-Tissue	GABRQ	X	151820163	G	A	Missense_Mutation	ENST00000370306.2:c.1076G>A	ENSP00000359329.2:p.Arg359Gln	0.10052910

Organoid

ID	Gene	CHROM	POS	REF	ALT	Consequence	HGVSc	HGVSp	VAF
P4-Organoid	ARID1A	1	27101258	A	T	Missense_Mutation	ENST00000374152.2:c.3391A>T	ENSP00000363267.2:NA	0.02415458
P4-Organoid	CSMD2	1	34076762	C	A	Missense_Mutation	ENST00000373388.2:c.519G>T	ENSP00000362486.2:NA	0.02912621
P4-Organoid	SZT2	1	43888215	A	T	Missense_Mutation	ENST00000562955.1:c.1834A>T	ENSP00000457168.1:NA	0.04597701
P4-Organoid	HRNR	1	152192163	G	T	Missense_Mutation	ENST00000368801.2:c.1942C>A	ENSP00000357791.2:p.Arg648Ser	0.15347334
P4-Organoid	OBSCN	1	228547770	G	A	Missense_Mutation	ENST00000366709.4:c.10534G>A	ENSP00000355670.4:p.Gly3512Ser	0.17661691
P4-Organoid	MLK4	1	233464299	C	A	Missense_Mutation	ENST00000366624.3:c.525C>A	ENSP00000355583.3:p.Phe175Leu	0.2
P4-Organoid	ANXA4	2	70047911	CT	C	Frame_Shift_Del	ENST00000536030.1:c.614del	ENSP00000441931.1:p.Phe205SerfsTer51	0.14705882
P4-Organoid	RETSAT	2	85570857	G	A	Missense_Mutation	ENST00000457495.2:c.1415C>T	ENSP00000405040.2:p.Ala472Val	0.03550295
P4-Organoid	UNC80	2	210650836	A	T	Missense_Mutation	ENST00000439458.1:c.647A>T	ENSP00000391088.1:p.Gln216Leu	0.20737327
P4-Organoid	BHLHE40	3	5024820	G	A	Missense_Mutation	ENST00000256495.3:c.682G>A	ENSP00000256495.3:p.Ala228Thr	0.12183908
P4-Organoid	SLAIN2	4	48380044	A	T	Missense_Mutation	ENST00000512093.1:c.91A>T	ENSP00000425923.1:p.Ile31Leu	0.04444444
P4-Organoid	GPRIN3	4	90170735	CCTCCCACAGGA	C	Frame_Shift_Del	ENST00000609438.1:c.516_526del	ENSP00000476603.1:p.Cys172TrpfsTer5	0.10410958
P4-Organoid	TRIP13	5	896897	G	C	Missense_Mutation	ENST00000166345.3:c.376G>C	ENSP00000166345.3:p.Val126Leu	0.03448275
P4-Organoid	PCDHB8	5	140559743	G	A	Missense_Mutation	ENST00000239444.2:c.2128G>A	ENSP00000239444.2:p.Val710Met	0.14492753
P4-Organoid	PCDHB10	5	140574103	T	G	Missense_Mutation	ENST00000239446.4:c.1978T>G	ENSP00000239446.4:p.Leu660Val	0.14492753
P4-Organoid	SYCP2L	6	10894381	G	A	Missense_Mutation	ENST00000283141.6:c.280G>A	ENSP00000283141.6:p.Val94Ile	0.05882352
P4-Organoid	SLC4A2	7	150768923	C	T	Missense_Mutation	ENST00000485713.1:c.2339C>T	ENSP00000419412.1:p.Ser780Leu	0.02341137
P4-Organoid	SLC25A37	8	23423760	C	T	Missense_Mutation	ENST00000519973.1:c.350C>T	ENSP00000429200.1:p.Ala117Val	0.04
P4-Organoid	RABEPK	9	127996034	G	A	Missense_Mutation	ENST00000394125.4:c.894G>A	ENSP00000377683.4:p.Met298Ile	0.03448275
P4-Organoid	ZSWIM8	10	75557606	CACTTCT	C	In_Frame_Del	ENST00000605216.1:c.3721_3726del	ENSP00000474748.1:p.Tyr1241_Phe1242del	0.01793722
P4-Organoid	KDELC2	11	108352848	C	A	Missense_Mutation	ENST00000434945.2:c.618G>T	ENSP00000413429.2:p.Trp206Cys	0.02941176
P4-Organoid	ITPR2	12	26809319	C	T	Missense_Mutation	ENST00000381340.3:c.2355G>A	ENSP00000370744.3:p.Met785Ile	0.25
P4-Organoid	C15orf59	15	74032845	C	T	Missense_Mutation	ENST00000569673.1:c.295G>A	ENSP00000457205.1:p.Asp99Asn	0.03278688
P4-Organoid	CES4A	16	67039264	A	G	Missense_Mutation	ENST00000541479.1:c.1271A>G	ENSP00000443175.1:p.Tyr424Cys	0.046875
P4-Organoid	FAM222B	17	27086225	A	T	Missense_Mutation	ENST00000581407.1:c.752T>A	ENSP00000462419.1:p.Leu251His	0.01822323
P4-Organoid	KCNH4	17	40328171	C	T	Missense_Mutation	ENST00000607371.1:c.730G>A	ENSP00000475564.1:p.Val244Ile	0.02117647
P4-Organoid	ETV4	17	41606558	T	A	Missense_Mutation	ENST00000591713.1:c.1175A>T	ENSP00000465718.1:p.Tyr392Phe	0.08666666
P4-Organoid	GATA6	18	19752055	G	A	Missense_Mutation	ENST00000581694.1:c.950G>A	ENSP00000462313.1:p.Arg317Gln	0.03804347
P4-Organoid	LAMA3	18	21390399	G	A	Missense_Mutation	ENST00000399516.3:c.1673G>A	ENSP00000382432.2:p.Arg558Gln	0.05498281
P4-Organoid	MALT1	18	56414719	T	C	Missense_Mutation	ENST00000348428.3:c.2120T>C	ENSP00000319279.4:p.Val707Ala	0.03045685
P4-Organoid	CGB2	19	49535810	A	G	Missense_Mutation	ENST00000359342.6:c.59A>G	ENSP00000352295.6:p.Lys20Arg	0.15135135
P4-Organoid	KLK14	19	51582907	G	T	Missense_Mutation	ENST00000391802.1:c.313C>A	ENSP00000375678.1:p.Gln105Lys	0.05660377
P4-Organoid	HAS1	19	52217317	G	A	Missense_Mutation	ENST00000601714.1:c.1121C>T	ENSP00000472821.1:p.Ser374Leu	0.04690831
P4-Organoid	LILRB4	19	55175016	A	G	Missense_Mutation	ENST00000430952.2:c.61A>G	ENSP00000408995.2:p.Met21Val	0.11304347
P4-Organoid	ZNF446	19	58991785	A	T	Missense_Mutation	ENST00000596341.1:c.892A>T	ENSP00000472219.1:p.Ile298Phe	0.01757812
P4-Organoid	TOX2	20	42694484	C	T	Missense_Mutation	ENST00000423191.2:c.967C>T	ENSP00000390278.1:p.Arg323Cys	0.05434782
P4-Organoid	ZGPAT	20	62340429	G	A	Missense_Mutation	ENST00000448100.2:c.497G>A	ENSP00000391176.1:p.Arg166His	0.06722689
P4-Organoid	ACTRT1	X	127185306	G	A	Missense_Mutation	ENST00000371124.3:c.880C>T	ENSP00000360165.3:p.Leu294Phe	0.14411764

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
P4	AZD2014	169.2
P4	AZD3759	205.6
P4	AZD4547	~ 450617644533
P4	AZD5363	~ 1.295e-018
P4	AZD6738	~ 6.433e+014
P4	AZD9291	94.59
P4	I.BET.762	437.9
P4	Rapamycin..Sirolimus.	~ 359330
P4	AZD1775..MK.1775.	11071
P4	Triptolide..PG490.	61.48
P4	Simvastatin	~ 1085830138
P4	Temozolomide	~ 2.366e+015
P4	Imatinib.Mesylate..STI571.	~ 5886
P4	Pazopanib..GW786034.	~ 4.789e-006
P4	Sunitinib.Malate	~ 5008
P4	Olaparib..AZD2281..KU0059436.	~ 7.711e-011
P4	Regorafenib..BAY.73.4506.	~ 5174
P4	Erlotinib	837.3
P4	Gefitinib	393
P4	Afatinib	~ 0.001331
P4	OTX.015	109.1
P4	BKM120..NVP.BKM120.	~ 1.884e+020
P4	BYL719	3981
P4	Cediranib..AZD2171.	45156
P4	Ceritinib.LDK378.	201.2
P4	Crizotinib...PF.02341066.	~ 21267126645
P4	Dabrafenib	~ 283.7
P4	Dacomitinib	~ 0.0004920
P4	Everolimus..RAD001.	147.6
P4	Ibrutinib..PCI.32765.	111.3
P4	Lapatinib	~ 1.642e-012
P4	LY2835219	515.5
P4	Brivanib..BMS.582664.	2995
P4	Panobinostat	95.67
P4	Selumetinib..AZD6244.	~ 47445596091285
P4	Sorafenib	~ 12276
P4	Trametinib	~ 74.47
P4	Vandetanib..ZD6474.	1322
P4	Vemurafenib	730601
P4	AZD5153	119.9
P4	ABT.199..GDC.0199..	~ 3.521e-005
P4	ABT.888..Veliparib..NSC.737664.	~ 4859
P4	Avagacestat..BMS.708163.	~ 6.455e-008
P4	Axitinib...AG.013736.	1890
P4	Bosutinib..SKI.606.	918.4
P4	Cabozantinib..XL184.	~ 5331
P4	Dasatinib..BMS.354825.	~ 4.187e-022
P4	decitabine	~ 0.0003188
P4	defactinib	~ 4120
P4	Dovitinib..TKI258.CHIR258.	2769
P4	Fluorouracil..5.Fluoracil..5.FU.	~ 5464
P4	Foretinib..XL880.	1201
P4	Tivantinib..ARQ.197.	2243
P4	Abraxane	~ 0.02352
P4	AZD2461.olaparib.analog.	~ 76.58
P4	Olaparib.	4261
P4	Idelalisib	~ 8596
P4	Irinotecan	10465
P4	Nilotinib..AMN.107.	~ 0.000
P4	NVP.AEW541	807.2
P4	Oxaliplatin	~ 284.9
P4	PLX3397	8739
P4	Quizartinib..AC220.	9956
P4	Saracatinib..AZD0530.	1974
P4	Semagacestat..LY450139.	~ 86636
P4	TGX.221	~ 8.241e+014
P4	tozasertib	~ 3.164e+027
P4	Vorinostat..SAHA..MK0683.	~ 1.012e+016
P4	XAV939	~
P4	gemcitabine	90.7
P4	palbociclib	~ 245302831
P4	Neratinib..HKI.272.	179