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
P12	PDAC	IIB	63	19.2	Male	16.9

Mutation Profiles

Primary Tumor

ID	Gene	CHROM	POS	REF	ALT	Consequence	HGVSc	HGVSp	VAF
P12-Tissue	NBAS	2	15374862	G	A	Nonsense_Mutation	ENST00000441750.1:c.5593C>T	ENSP00000413201.1:p.Gln1865Ter	0.03174603
P12-Tissue	SLC9B1	4	103822431	G	T	Missense_Mutation	ENST00000296422.7:c.1391C>A	ENSP00000296422.7:p.Pro464Gln	0.35526315
P12-Tissue	VPS13A	9	79898363	A	T	Missense_Mutation	ENST00000376634.4:c.3211A>T	ENSP00000365821.4:p.Asn1071Tyr	0.06097561
P12-Tissue	C10orf12	10	98742211	C	T	Missense_Mutation	ENST00000286067.2:c.1064C>T	ENSP00000286067.2:p.Pro355Leu	0.00591716
P12-Tissue	SETD1A	16	30991110	G	A	Missense_Mutation	ENST00000262519.8:c.4003G>A	ENSP00000262519.8:p.Val1335Ile	0.01930501
P12-Tissue	RP4-583P15.14	20	62369695	C	T	Missense_Mutation	ENST00000467211.1:c.73C>T	ENSP00000477118.1:p.Ala25Val	0.046875
P12-Tissue	C21orf58	21	47742645	C	T	Missense_Mutation	ENST00000291691.7:c.8G>A	ENSP00000291691.7:p.Arg3Gln	0.04494382

Organoid

ID	Gene	CHROM	POS	REF	ALT	Consequence	HGVSc	HGVSp	VAF
P12-Organoid	ASXL2	2	25972742	C	A	Missense_Mutation	ENST00000435504.4:c.1683G>T	ENSP00000391447.3:p.Gln561His	0.03100775
P12-Organoid	B3GNT2	2	62450083	A	G	Missense_Mutation	ENST00000405767.1:c.728A>G	ENSP00000384692.1:p.Lys243Arg	0.03436426
P12-Organoid	POLR1B	2	113310289	A	C	Missense_Mutation	ENST00000541869.1:c.1168A>C	ENSP00000444136.1:p.Lys390Gln	0.04545454
P12-Organoid	ERBB4	2	212576871	A	G	Missense_Mutation	ENST00000436443.1:c.1028T>C	ENSP00000403204.1:p.Met343Thr	0.05027933
P12-Organoid	SCN11A	3	38936183	C	A	Missense_Mutation	ENST00000456224.3:c.2676G>T	ENSP00000416757.3:p.Glu892Asp	0.02816901
P12-Organoid	KPNA4	3	160225993	G	A	Missense_Mutation	ENST00000334256.4:c.1274C>T	ENSP00000334373.4:p.Ala425Val	0.12844036
P12-Organoid	SEPT11	4	77941786	G	T	Missense_Mutation	ENST00000541121.1:c.946G>T	ENSP00000443701.1:p.Gly316Trp	0.01760563
P12-Organoid	SLC9B1	4	103822431	G	T	Missense_Mutation	ENST00000296422.7:c.1391C>A	ENSP00000296422.7:p.Pro464Gln	0.1875
P12-Organoid	TENM3	4	183694720	T	C	Missense_Mutation	ENST00000511685.1:c.4988T>C	ENSP00000424226.1:p.Ile1663Thr	0.03323262
P12-Organoid	SORBS2	4	186548093	T	C	Missense_Mutation	ENST00000449407.2:c.1028A>G	ENSP00000397262.2:p.Gln343Arg	0.08467741
P12-Organoid	SLC36A1	5	150867631	C	A	Missense_Mutation	ENST00000520701.1:c.1247C>A	ENSP00000428140.1:p.Pro416Gln	0.00775193
P12-Organoid	TRERF1	6	42236862	C	A	Missense_Mutation	ENST00000541110.1:c.467G>T	ENSP00000439689.1:p.Arg156Leu	0.02419354
P12-Organoid	C7orf63	7	89917578	G	A	Missense_Mutation	ENST00000497910.1:c.1633G>A	ENSP00000419549.1:p.Val545Ile	0.18032786
P12-Organoid	SNTG1	8	51617181	C	T	Missense_Mutation	ENST00000522124.1:c.1060C>T	ENSP00000429842.1:p.Arg354Trp	0.05050505
P12-Organoid	C10orf2	10	102750687	C	A	Missense_Mutation	ENST00000370228.1:c.1654C>A	ENSP00000359248.1:p.His552Asn	0.04219409
P12-Organoid	COL17A1	10	105793794	C	T	Missense_Mutation	ENST00000369733.3:c.3819G>A	ENSP00000358748.3:p.Met1273Ile	0.06796116
P12-Organoid	DMBT1	10	124389946	C	G	Missense_Mutation	ENST00000368956.2:c.3694C>G	ENSP00000357952.2:p.Arg1232Gly	0.15695067
P12-Organoid	DEAF1	11	694961	GGCCGCCGCCGCCACAGCGGCCGCGGCC	G	In_Frame_Del	ENST00000382409.3:c.60_86del	ENSP00000371846.3:p.Val25_Ala33del	0.09803921
P12-Organoid	INSC	11	15260560	G	A	Missense_Mutation	ENST00000530161.1:c.1333G>A	ENSP00000436194.1:p.Val445Met	0.02832861
P12-Organoid	OR5R1	11	56185579	C	A	Missense_Mutation	ENST00000312253.1:c.130G>T	ENSP00000308595.1:p.Gly44Trp	0.01209677
P12-Organoid	TRIM29	11	120008421	C	A	Missense_Mutation	ENST00000341846.5:c.319G>T	ENSP00000343129.5:p.Ala107Ser	0.01851851
P12-Organoid	KCNH3	12	49937058	G	T	Missense_Mutation	ENST00000257981.6:c.580G>T	ENSP00000257981.5:p.Gly194Trp	0.03947368
P12-Organoid	NACA	12	57114788	A	T	Missense_Mutation	ENST00000550952.1:c.526T>A	ENSP00000448035.1:p.Ser176Thr	0.03030303
P12-Organoid	ARHGAP9	12	57867929	C	A	Missense_Mutation	ENST00000550288.1:c.2051G>T	ENSP00000473445.1:p.Trp684Leu	0.02469135
P12-Organoid	USP8	15	50784950	C	T	Missense_Mutation	ENST00000433963.1:c.2287C>T	ENSP00000405537.1:p.Arg763Trp	0.16363636
P12-Organoid	USP8	15	50784955	C	A	Missense_Mutation	ENST00000433963.1:c.2292C>A	ENSP00000405537.1:p.Asn764Lys	0.16574585
P12-Organoid	WFIKKN1	16	683474	C	A	Missense_Mutation	ENST00000319070.2:c.1064C>A	ENSP00000324763.2:p.Pro355His	0.01648351
P12-Organoid	MED1	17	37604067	A	C	Missense_Mutation	ENST00000394287.3:c.116T>G	ENSP00000377828.3:p.Leu39Arg	0.08955223
P12-Organoid	MUC16	19	9066866	C	A	Missense_Mutation	ENST00000397910.4:c.20580G>T	ENSP00000381008.2:p.Leu6860Phe	0.03252032
P12-Organoid	LRFN1	19	39804790	G	A	Missense_Mutation	ENST00000248668.4:c.1187C>T	ENSP00000248668.4:p.Pro396Leu	0.04333333
P12-Organoid	LILRB1	19	55147987	GA	CC	Missense_Mutation	ENST00000434867.2:c.1690_1691delinsCC	ENSP00000405243.2:p.Glu564Pro	0.35952848
P12-Organoid	ELMO2	20	45002114	TC	AA	Missense_Mutation	ENST00000454865.2:c.535_536delinsTT	ENSP00000415641.2:p.Glu179Leu	0.01298701
P12-Organoid	NTSR1	20	61341261	G	T	Missense_Mutation	ENST00000370501.3:c.702G>T	ENSP00000359532.3:p.Lys234Asn	0.01724137
P12-Organoid	DYRK1A	21	38845110	G	T	Missense_Mutation	ENST00000451934.1:c.135G>T	ENSP00000416089.1:p.Gln45His	0.14393939
P12-Organoid	RBMX2	X	129546749	C	A	Missense_Mutation	ENST00000305536.6:c.896C>A	ENSP00000339090.4:p.Ser299Tyr	0.025
P12-Organoid	PLXNA3	X	153689836	C	A	Missense_Mutation	ENST00000369682.3:c.992C>A	ENSP00000358696.3:p.Pro331Gln	0.08163265

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
P12	AZD2014	1915
P12	AZD3759	214.1
P12	AZD4547	~ 6081
P12	AZD5363	9.715E+57
P12	AZD6738	1517
P12	AZD9291	197.7
P12	I.BET.762	1678
P12	Rapamycin..Sirolimus.	2464
P12	AZD1775..MK.1775.	~ 1.425e-010
P12	Triptolide..PG490.	33.49
P12	Simvastatin	2701
P12	Temozolomide	~ 7.508
P12	Imatinib.Mesylate..STI571.	~ 5911
P12	Pazopanib..GW786034.	~ 46061643
P12	Sunitinib.Malate	~ 4856
P12	Olaparib..AZD2281..KU0059436.	~ 3.028e-011
P12	Regorafenib..BAY.73.4506.	~ 93574786
P12	Erlotinib	383.7
P12	Gefitinib	70.9
P12	Afatinib	~ 4.711e-044
P12	OTX.015	334.2
P12	BKM120..NVP.BKM120.	4171
P12	BYL719	~ 137794706
P12	Cediranib..AZD2171.	~ 5102
P12	Ceritinib.LDK378.	1523
P12	Crizotinib...PF.02341066.	39386
P12	Dabrafenib	20.93
P12	Dacomitinib	~ 2.821e-047
P12	Everolimus..RAD001.	~ 306.9
P12	Ibrutinib..PCI.32765.	181.2
P12	Lapatinib	2677
P12	LY2835219	~ 1562899524
P12	Brivanib..BMS.582664.
P12	Panobinostat	91.12
P12	Selumetinib..AZD6244.	~ 4.396e+017
P12	Sorafenib	~ 2.980e-147
P12	Trametinib	106.5
P12	Vandetanib..ZD6474.	873.5
P12	Vemurafenib	~ 0.000
P12	AZD5153	~ 1.629e-006
P12	ABT.199..GDC.0199..	1230
P12	ABT.888..Veliparib..NSC.737664.	~ 1405
P12	Avagacestat..BMS.708163.	88.99
P12	Axitinib...AG.013736.	39694
P12	Bosutinib..SKI.606.	1126
P12	Cabozantinib..XL184.	~ 5294
P12	Dasatinib..BMS.354825.	~ 6.284e-019
P12	decitabine	~ 2.218e-006
P12	defactinib	~ 3.799e+016
P12	Dovitinib..TKI258.CHIR258.	4910
P12	Fluorouracil..5.Fluoracil..5.FU.	~ 8.803e+014
P12	Foretinib..XL880.	3771
P12	Tivantinib..ARQ.197.	8423
P12	Abraxane	99.68
P12	AZD2461.olaparib.analog.	~ 2.426
P12	Olaparib.	~ 0.009000
P12	Idelalisib	~ 1387820143
P12	Irinotecan	8439
P12	Nilotinib..AMN.107.	~ 5.317e+052
P12	NVP.AEW541	32101
P12	Oxaliplatin	~ 19762
P12	PLX3397	5418
P12	Quizartinib..AC220.	~ 67008
P12	Saracatinib..AZD0530.	835.4
P12	Semagacestat..LY450139.	~ 1081
P12	TGX.221	~ 4137
P12	tozasertib	618.5
P12	Vorinostat..SAHA..MK0683.	141461
P12	XAV939	7778
P12	gemcitabine	85.18
P12	palbociclib	~ 18985
P12	Neratinib..HKI.272.	79.75