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
P2	PDAC	3	59	22.2	Male	50955

Mutation Profiles

Primary Tumor

ID	Gene	CHROM	POS	REF	ALT	Consequence	HGVSc	HGVSp	VAF
P2-Tissue	FLG2	1	152327668	G	A	Missense_Mutation	ENST00000388718.5:c.2594C>T	ENSP00000373370.4:p.Ser865Leu	0.00867302
P2-Tissue	CRIPAK	4	1389360	TCACACGTGCCCATGTGGAGTGCCCGCCTGCTCACACACGTGCCCATGTGGAGTGCCCGCCTGCTCACACGTGCCCATGTGGAGTGCCTGCCTGCTCA	T	Frame_Shift_Del	ENST00000324803.4:c.1099_1195del	ENSP00000323978.4:p.Arg367LysfsTer30	0.00190114
P2-Tissue	TNXB	6	32030024	C	T	Missense_Mutation	ENST00000375247.2:c.7078G>A	ENSP00000364396.2:p.Gly2360Ser	0.02095238
P2-Tissue	MUC5B	11	1268488	C	T	Missense_Mutation	ENST00000529681.1:c.10378C>T	ENSP00000436812.1:p.Pro3460Ser	0.20085470
P2-Tissue	SLC25A39	17	42398561	G	A	Missense_Mutation	ENST00000590194.1:c.532C>T	ENSP00000467681.1:p.Arg178Trp	0.01978022
P2-Tissue	DMKN	19	36003596	C	T	Missense_Mutation	ENST00000451297.2:c.523G>A	ENSP00000409513.2:p.Gly175Arg	0.01724137

Organoid

ID	Gene	CHROM	POS	REF	ALT	Consequence	HGVSc	HGVSp	VAF
P2-Organoid	HSPG2	1	22188550	C	G	Missense_Mutation	ENST00000374695.3:c.4799G>C	ENSP00000363827.3:NA	1
P2-Organoid	TMEM53	1	45120448	G	A	Missense_Mutation	ENST00000372237.3:c.617C>T	ENSP00000361311.3:NA	0.26595744
P2-Organoid	MIER1	1	67411908	G	A	Missense_Mutation	ENST00000401042.3:c.110G>A	ENSP00000383821.3:p.Arg37Gln	1
P2-Organoid	ASPM	1	197059118	C	G	Missense_Mutation	ENST00000367409.4:c.9926G>C	ENSP00000356379.4:p.Ser3309Thr	0.35802469
P2-Organoid	PPFIA4	1	203024615	C	T	Missense_Mutation	ENST00000599966.1:c.367C>T	ENSP00000471264.1:p.Arg123Cys	0.30582010
P2-Organoid	USH2A	1	216419944	C	T	Missense_Mutation	ENST00000366943.2:c.2792G>A	ENSP00000355910.2:p.Cys931Tyr	0.02463054
P2-Organoid	OR6F1	1	247875926	AG	A	Frame_Shift_Del	ENST00000302084.2:c.131del	ENSP00000305640.2:p.Ala44ValfsTer3	0.23938223
P2-Organoid	ASAP2	2	9347277	A	T	Missense_Mutation	ENST00000315273.4:c.44A>T	ENSP00000316404.4:p.His15Leu	0.05027173
P2-Organoid	IFT172	2	27684338	A	C	Missense_Mutation	ENST00000260570.3:c.2240T>G	ENSP00000260570.3:p.Leu747Arg	0.47839506
P2-Organoid	CLASP1	2	122285420	C	T	Missense_Mutation	ENST00000541377.1:c.425G>A	ENSP00000441625.1:p.Arg142His	0.44827586
P2-Organoid	TTN	2	179498672	C	T	Missense_Mutation	ENST00000591111.1:c.37631G>A	ENSP00000465570.1:p.Arg12544Lys	0.14948453
P2-Organoid	RAPH1	2	204355961	G	C	Missense_Mutation	ENST00000457812.1:c.202C>G	ENSP00000392854.1:p.Arg68Gly	0.28846153
P2-Organoid	ERBB4	2	212522706	T	G	Missense_Mutation	ENST00000402597.1:c.1885A>C	ENSP00000385565.1:p.Ser629Arg	0.54615384
P2-Organoid	TTLL4	2	219602823	G	GA	Frame_Shift_Ins	ENST00000442769.1:c.430dup	ENSP00000396555.1:p.Ser144LysfsTer71	0.37272727
P2-Organoid	SLC4A3	2	220502893	G	A	Missense_Mutation	ENST00000373762.3:c.2855G>A	ENSP00000362867.3:p.Arg952His	0.49418604
P2-Organoid	KPNA1	3	122156036	C	T	Missense_Mutation	ENST00000344337.6:c.1103G>A	ENSP00000343701.6:p.Gly368Glu	0.60869565
P2-Organoid	DEPDC1B	5	59899244	G	A	Missense_Mutation	ENST00000545085.1:c.1135C>T	ENSP00000438320.1:p.Arg379Cys	0.46341463
P2-Organoid	EPHA7	6	93967847	C	T	Missense_Mutation	ENST00000369303.4:c.2080G>A	ENSP00000358309.4:p.Val694Ile	0.43786982
P2-Organoid	SUGCT	7	40900005	T	G	Missense_Mutation	ENST00000401647.2:c.1121T>G	ENSP00000385222.2:p.Val374Gly	0.43674698
P2-Organoid	KCNK9	8	140630863	G	A	Missense_Mutation	ENST00000520439.1:c.763C>T	ENSP00000430676.1:p.Arg255Trp	0.95
P2-Organoid	BAI1	8	143558817	C	T	Missense_Mutation	ENST00000517894.1:c.1294C>T	ENSP00000430945.1:p.Arg432Cys	0.33462282
P2-Organoid	CYP11B2	8	143996298	G	A	Missense_Mutation	ENST00000323110.2:c.622C>T	ENSP00000325822.2:p.Arg208Trp	0.46166950
P2-Organoid	CEL	9	135946015	T	C	Missense_Mutation	ENST00000372080.4:c.1463T>C	ENSP00000361151.4:p.Ile488Thr	0.08984375
P2-Organoid	MUC5B	11	1268488	C	T	Missense_Mutation	ENST00000529681.1:c.10378C>T	ENSP00000436812.1:p.Pro3460Ser	0.16521739
P2-Organoid	OR5T3	11	56019901	G	C	Missense_Mutation	ENST00000303059.3:c.226G>C	ENSP00000305403.3:p.Val76Leu	0.46305418
P2-Organoid	OR8D4	11	123777232	T	G	Missense_Mutation	ENST00000321355.2:c.94T>G	ENSP00000325381.2:p.Leu32Val	0.52173913
P2-Organoid	GLB1L3	11	134163054	A	G	Missense_Mutation	ENST00000431683.2:c.827A>G	ENSP00000396615.2:p.Asn276Ser	0.44660194
P2-Organoid	ACRBP	12	6756507	A	C	Missense_Mutation	ENST00000536350.1:c.26T>G	ENSP00000443153.1:p.Leu9Arg	0.61904761
P2-Organoid	KRAS	12	25398284	C	T	Missense_Mutation	ENST00000557334.1:c.35G>A	ENSP00000452512.1:p.Gly12Asp	0.3
P2-Organoid	KMT2D	12	49445979	GGA	G	Frame_Shift_Del	ENST00000301067.7:c.1485_1486del	ENSP00000301067.7:p.Pro496AlafsTer3	0.42211055
P2-Organoid	DUOX1	15	45427329	G	C	Missense_Mutation	ENST00000389037.3:c.335G>C	ENSP00000373689.3:p.Ser112Thr	0.46045918
P2-Organoid	DMXL2	15	51772927	G	A	Missense_Mutation	ENST00000543779.2:c.6376C>T	ENSP00000441858.2:p.Arg2126Cys	0.48958333
P2-Organoid	CLEC16A	16	11260318	C	A	Missense_Mutation	ENST00000409790.1:c.2715C>A	ENSP00000387122.1:p.Ser905Arg	0.12186379
P2-Organoid	TP53	17	7577539	G	A	Missense_Mutation	ENST00000455263.2:c.742C>T	ENSP00000398846.2:p.Arg248Trp	1
P2-Organoid	TBX2	17	59482881	C	T	Missense_Mutation	ENST00000240328.3:c.1370C>T	ENSP00000240328.3:p.Ala457Val	0.55121951
P2-Organoid	ARID3A	19	932476	G	A	Missense_Mutation	ENST00000263620.3:c.427G>A	ENSP00000263620.2:p.Glu143Lys	0.55405405
P2-Organoid	XAB2	19	7688662	G	C	Missense_Mutation	ENST00000534844.1:c.1065C>G	ENSP00000438225.1:p.His355Gln	0.49264705
P2-Organoid	GPATCH1	19	33581694	C	T	Missense_Mutation	ENST00000170564.2:c.217C>T	ENSP00000170564.1:p.Pro73Ser	0.41346153
P2-Organoid	IRGC	19	44223415	C	A	Missense_Mutation	ENST00000244314.5:c.705C>A	ENSP00000244314.5:p.Asp235Glu	0.49014778
P2-Organoid	BCR	22	23653975	T	TCCGG	Frame_Shift_Ins	ENST00000359540.3:c.3143_3146dup	ENSP00000352535.3:p.Val1050ArgfsTer17	0.5
P2-Organoid	TCEAL2	X	101382371	C	T	Missense_Mutation	ENST00000372780.1:c.569C>T	ENSP00000361866.1:p.Ala190Val	1
P2-Organoid	MECP2	X	153363111	G	GGCGGCGGTGGCGGCA	In_Frame_Ins	ENST00000453960.2:c.11_12insTGCCGCCACCGCCGC	ENSP00000395535.2:p.Ala6_Ala7insThrAlaAlaAlaAla	0.01212121

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
P2	AZD2014	~ 8.475e-117
P2	AZD3759	~ 4737
P2	AZD4547	~ 9755
P2	AZD5363	~ 4.978e-038
P2	AZD6738	2054
P2	AZD9291	~ 760496408
P2	I.BET.762	2061
P2	Rapamycin..Sirolimus.	3103
P2	AZD1775..MK.1775.	1927
P2	Triptolide..PG490.	28.98
P2	Simvastatin	6520
P2	Temozolomide	12881
P2	Imatinib.Mesylate..STI571.	~ 7408
P2	Pazopanib..GW786034.	~ 5259
P2	Sunitinib.Malate	~ 0.000
P2	Olaparib..AZD2281..KU0059436.	~ 1399
P2	Regorafenib..BAY.73.4506.	~ 1543
P2	Erlotinib	978
P2	Gefitinib	200
P2	Afatinib	~ 3.260e-027
P2	OTX.015	980.6
P2	BKM120..NVP.BKM120.	5867
P2	BYL719	~ 85.20
P2	Cediranib..AZD2171.	~ 5903
P2	Ceritinib.LDK378.	4565
P2	Crizotinib...PF.02341066.	~ 6176
P2	Dabrafenib	~ 1233
P2	Dacomitinib	~ 19.47
P2	Everolimus..RAD001.	~ 1049
P2	Ibrutinib..PCI.32765.	~
P2	Lapatinib	120.8
P2	LY2835219	18.85
P2	Brivanib..BMS.582664.	~ 17432
P2	Panobinostat	52.12
P2	Selumetinib..AZD6244.	43.9
P2	Sorafenib	18.25
P2	Trametinib	33.84
P2	Vandetanib..ZD6474.	15669
P2	Vemurafenib	105
P2	AZD5153	2574
P2	ABT.199..GDC.0199..	~ 599.5
P2	ABT.888..Veliparib..NSC.737664.	822.8
P2	Avagacestat..BMS.708163.	~ 0.4067
P2	Axitinib...AG.013736.	1947
P2	Bosutinib..SKI.606.	1908
P2	Cabozantinib..XL184.
P2	Dasatinib..BMS.354825.	3646
P2	decitabine	~ 4800
P2	defactinib	~ 386.1
P2	Dovitinib..TKI258.CHIR258.	~ 4314
P2	Fluorouracil..5.Fluoracil..5.FU.	~ 5005
P2	Foretinib..XL880.	~ 5684641
P2	Tivantinib..ARQ.197.	~ 1.557e+019
P2	Abraxane	16.95
P2	AZD2461.olaparib.analog.	~
P2	Olaparib.	~ 0.000
P2	Idelalisib	3967
P2	Irinotecan	2937
P2	Nilotinib..AMN.107.	15.71
P2	NVP.AEW541	~ 18577
P2	Oxaliplatin	3.56E-17
P2	PLX3397	~ 5268
P2	Quizartinib..AC220.	~ 0.000
P2	Saracatinib..AZD0530.	~ 5001
P2	Semagacestat..LY450139.	~ 79.51
P2	TGX.221	~ 359.8
P2	tozasertib	~ 5619
P2	Vorinostat..SAHA..MK0683.	~ 5015
P2	XAV939	~ 307.1
P2	gemcitabine	~ 38216531
P2	palbociclib	~ 18427
P2	Neratinib..HKI.272.	~ 307.5