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
P3	PDAC	4	75	23.6	Male	14988.7

Mutation Profiles

Primary Tumor

ID	Gene	CHROM	POS	REF	ALT	Consequence	HGVSc	HGVSp	VAF
P3-Tissue	CELA3A	1	22329523	A	G	Missense_Mutation	ENST00000374663.1:c.71A>G	ENSP00000363795.1:p.His24Arg	0.05660377
P3-Tissue	CELA3A	1	22329525	T	C	Missense_Mutation	ENST00000374663.1:c.73T>C	ENSP00000363795.1:p.Ser25Pro	0.04477611
P3-Tissue	RBM15	1	110882980	C	A	Missense_Mutation	ENST00000602849.1:c.953C>A	ENSP00000473638.1:p.Pro318Gln	0.04081632
P3-Tissue	LCE1C	1	152777707	C	T	Missense_Mutation	ENST00000607093.1:c.248G>A	ENSP00000475270.1:p.Arg83His	0.04324324
P3-Tissue	FCRLB	1	161696729	A	G	Missense_Mutation	ENST00000392158.1:c.811A>G	ENSP00000375999.1:p.Thr271Ala	0.01826484
P3-Tissue	OR6F1	1	247875319	C	T	Missense_Mutation	ENST00000302084.2:c.739G>A	ENSP00000305640.2:p.Val247Met	0.05913978
P3-Tissue	MAT2A	2	85766481	C	T	Missense_Mutation	ENST00000306434.3:c.71C>T	ENSP00000303147.3:p.Ser24Leu	0.03726708
P3-Tissue	CD200	3	112054863	A	G	Missense_Mutation	ENST00000473539.1:c.86A>G	ENSP00000420298.1:p.Gln29Arg	0.09493670
P3-Tissue	EPHB1	3	134960039	G	A	Missense_Mutation	ENST00000493838.1:c.1079G>A	ENSP00000419574.1:p.Arg360His	0.06278026
P3-Tissue	NKX2-5	5	172659685	C	T	Missense_Mutation	ENST00000329198.4:c.862G>A	ENSP00000327758.4:p.Ala288Thr	0.01840490
P3-Tissue	RING1	6	33177715	G	T	Missense_Mutation	ENST00000374656.4:c.263G>T	ENSP00000363787.4:p.Arg88Leu	0.05128205
P3-Tissue	MDFI	6	41621204	ACTGCGACCTGCC	A	In_Frame_Del	ENST00000373050.4:c.460_471del	ENSP00000362141.4:p.Pro154_Leu157del	0.02640264
P3-Tissue	TTBK1	6	43214466	T	G	Missense_Mutation	ENST00000259750.4:c.68T>G	ENSP00000259750.4:p.Ile23Ser	0.02790697
P3-Tissue	FOXD4	9	117371	C	G	Missense_Mutation	ENST00000382500.2:c.749G>C	ENSP00000371940.2:p.Gly250Ala	0.53030303
P3-Tissue	CDKN2A	9	21971120	G	A	Nonsense_Mutation	ENST00000579122.1:c.238C>T	ENSP00000464202.1:p.Arg80Ter	0.03886925
P3-Tissue	FANK1	10	127585221	C	T	Nonsense_Mutation	ENST00000368693.1:c.10C>T	ENSP00000357682.1:p.Gln4Ter	0.09375
P3-Tissue	MUC2	11	1093057	A	G	Missense_Mutation	ENST00000441003.2:c.4876A>G	ENSP00000415183.2:p.Thr1626Ala	0.23076923
P3-Tissue	KRTAP5-5	11	1651120	G	T	Missense_Mutation	ENST00000399676.2:c.50G>T	ENSP00000382584.2:p.Arg17Leu	0.38690476
P3-Tissue	NAV2	11	20066793	G	A	Missense_Mutation	ENST00000540292.1:c.3341G>A	ENSP00000443489.1:p.Ser1114Asn	0.04634146
P3-Tissue	OR9G1	11	56468212	G	A	Missense_Mutation	ENST00000312153.1:c.349G>A	ENSP00000309012.1:p.Val117Met	0.07633587
P3-Tissue	OR9G4	11	56510657	C	T	Missense_Mutation	ENST00000302957.3:c.631G>A	ENSP00000307515.3:p.Glu211Lys	0.04864864
P3-Tissue	RASGRP2	11	64506875	C	T	Missense_Mutation	ENST00000394432.3:c.770G>A	ENSP00000377953.3:p.Arg257His	0.06338028
P3-Tissue	GUCY1A2	11	106681104	C	T	Missense_Mutation	ENST00000526355.2:c.1307G>A	ENSP00000431245.1:p.Arg436Gln	0.09375
P3-Tissue	SPERT	13	46287581	C	T	Missense_Mutation	ENST00000378966.3:c.313C>T	ENSP00000368249.3:p.Arg105Cys	0.04180064
P3-Tissue	SPTB	14	65259941	G	A	Missense_Mutation	ENST00000556626.1:c.2440C>T	ENSP00000451752.1:p.Arg814Trp	0.02708803
P3-Tissue	AKT1	14	105246533	G	A	Missense_Mutation	ENST00000555528.1:c.67C>T	ENSP00000450688.1:p.Arg23Trp	0.09047619
P3-Tissue	TP53	17	7577121	G	A	Missense_Mutation	ENST00000455263.2:c.817C>T	ENSP00000398846.2:p.Arg273Cys	0.06338028
P3-Tissue	RNF43	17	56448395	C	A	Splice_Site	ENST00000584437.1:c.253-1G>T		0.07317073
P3-Tissue	ACTG1	17	79478217	G	T	Missense_Mutation	ENST00000575842.1:c.799C>A	ENSP00000458162.1:p.Leu267Met	0.04237288
P3-Tissue	TBXA2R	19	3599929	C	T	Missense_Mutation	ENST00000411851.3:c.704G>A	ENSP00000393333.2:p.Arg235His	0.03636363
P3-Tissue	ZNF536	19	31039824	G	A	Missense_Mutation	ENST00000355537.3:c.3298G>A	ENSP00000347730.1:p.Val1100Met	0.08
P3-Tissue	IFNL3	19	39734787	C	T	Missense_Mutation	ENST00000413851.2:c.269G>A	ENSP00000409000.2:p.Arg90His	0.06862745
P3-Tissue	FCGBP	19	40412150	C	G	Missense_Mutation	ENST00000221347.6:c.3478G>C	ENSP00000221347.5:p.Gly1160Arg	0.01558441
P3-Tissue	RRAS	19	50140383	T	C	Missense_Mutation	ENST00000246792.3:c.158A>G	ENSP00000246792.2:p.Tyr53Cys	0.10740740
P3-Tissue	MYBPC2	19	50962189	C	T	Missense_Mutation	ENST00000357701.5:c.2521C>T	ENSP00000350332.4:p.Arg841Trp	0.05387205
P3-Tissue	RBPJL	20	43945216	T	A	Missense_Mutation	ENST00000372743.1:c.1276T>A	ENSP00000361828.1:p.Tyr426Asn	0.05882352

Organoid

ID	Gene	CHROM	POS	REF	ALT	Consequence	HGVSc	HGVSp	VAF
P3-Organoid	BAI2	1	32198577	C	T	Missense_Mutation	ENST00000527361.1:c.3521G>A	ENSP00000435397.1:NA	0.45263157
P3-Organoid	KIF2C	1	45216159	G	A	Missense_Mutation	ENST00000372224.4:c.362G>A	ENSP00000361298.4:p.Arg121His	0.27272727
P3-Organoid	DMRTA2	1	50887013	G	A	Missense_Mutation	ENST00000418121.1:c.196C>T	ENSP00000399370.1:NA	0.24479166
P3-Organoid	LRRIQ3	1	74506901	C	CT	Frame_Shift_Ins	ENST00000395089.1:c.1713dup	ENSP00000378524.1:NA	0.29629629
P3-Organoid	HS2ST1	1	87570165	A	G	Missense_Mutation	ENST00000370550.5:c.857A>G	ENSP00000359581.4:NA	0.21487603
P3-Organoid	RBM15	1	110882980	C	A	Missense_Mutation	ENST00000602849.1:c.953C>A	ENSP00000473638.1:p.Pro318Gln	0.50554323
P3-Organoid	PEX11B	1	145518256	G	T	Missense_Mutation	ENST00000537888.1:c.316G>T	ENSP00000437510.1:NA	0.56976744
P3-Organoid	LCE1C	1	152777707	C	T	Missense_Mutation	ENST00000607093.1:c.248G>A	ENSP00000475270.1:p.Arg83His	0.41904761
P3-Organoid	OR10X1	1	158549687	C	T	Translation_Start_Site	ENST00000368150.1:c.3G>A	ENSP00000357132.1:p.Met1?	0.47692307
P3-Organoid	FCRLB	1	161696729	A	G	Missense_Mutation	ENST00000392158.1:c.811A>G	ENSP00000375999.1:p.Thr271Ala	0.45045045
P3-Organoid	ATP1B1	1	169076157	CAGTTGGTGTA	C	Splice_Site	ENST00000367816.1:c.94_97+6del		0.125
P3-Organoid	USH2A	1	215799151	C	T	Missense_Mutation	ENST00000366943.2:c.15653G>A	ENSP00000355910.2:p.Arg5218His	0.14606741
P3-Organoid	OR6F1	1	247875319	C	T	Missense_Mutation	ENST00000302084.2:c.739G>A	ENSP00000305640.2:p.Val247Met	0.48849104
P3-Organoid	CCDC85A	2	56603013	C	A	Missense_Mutation	ENST00000407595.2:c.1515C>A	ENSP00000384040.2:p.Ser505Arg	0.44
P3-Organoid	MAT2A	2	85766481	C	T	Missense_Mutation	ENST00000306434.3:c.71C>T	ENSP00000303147.3:p.Ser24Leu	0.53186274
P3-Organoid	NEB	2	152512803	A	T	Missense_Mutation	ENST00000604864.1:c.6359T>A	ENSP00000474498.1:p.Leu2120His	0.01935483
P3-Organoid	GRM2	3	51746586	G	A	Missense_Mutation	ENST00000442933.2:c.548G>A	ENSP00000408906.2:p.Arg183His	0.29866666
P3-Organoid	CD200	3	112054863	A	G	Missense_Mutation	ENST00000473539.1:c.86A>G	ENSP00000420298.1:p.Gln29Arg	0.54385964
P3-Organoid	EPHB1	3	134960039	G	A	Missense_Mutation	ENST00000493838.1:c.1079G>A	ENSP00000419574.1:p.Arg360His	0.37201365
P3-Organoid	CAMK2D	4	114426173	C	T	Missense_Mutation	ENST00000511664.1:c.1003G>A	ENSP00000425824.1:p.Val335Met	0.62376237
P3-Organoid	AADAT	4	170988477	C	T	Splice_Site	ENST00000515480.1:c.962+1G>A		0.29670329
P3-Organoid	SGTB	5	65004322	C	A	Missense_Mutation	ENST00000381007.4:c.268G>T	ENSP00000370395.4:p.Asp90Tyr	0.17272727
P3-Organoid	PIK3R1	5	67589274	A	T	Missense_Mutation	ENST00000523872.1:c.173A>T	ENSP00000430098.1:p.Asp58Val	0.56756756
P3-Organoid	NKX2-5	5	172659685	C	T	Missense_Mutation	ENST00000329198.4:c.862G>A	ENSP00000327758.4:p.Ala288Thr	0.50282485
P3-Organoid	RING1	6	33177715	G	T	Missense_Mutation	ENST00000374656.4:c.263G>T	ENSP00000363787.4:p.Arg88Leu	0.59090909
P3-Organoid	MDFI	6	41621204	ACTGCGACCTGCC	A	In_Frame_Del	ENST00000373050.4:c.460_471del	ENSP00000362141.4:p.Pro154_Leu157del	0.46956521
P3-Organoid	TTBK1	6	43214466	T	G	Missense_Mutation	ENST00000259750.4:c.68T>G	ENSP00000259750.4:p.Ile23Ser	0.63529411
P3-Organoid	COL12A1	6	75816171	C	G	Missense_Mutation	ENST00000483888.2:c.8142G>C	ENSP00000421216.1:p.Trp2714Cys	0.65408805
P3-Organoid	MDN1	6	90359882	C	T	Missense_Mutation	ENST00000428876.1:c.16067G>A	ENSP00000413970.1:p.Arg5356Gln	0.07738095
P3-Organoid	NUP43	6	150063660	C	T	Missense_Mutation	ENST00000460354.2:c.368G>A	ENSP00000432401.2:p.Gly123Asp	0.37301587
P3-Organoid	SLC22A2	6	160670366	G	A	Nonsense_Mutation	ENST00000366953.3:c.724C>T	ENSP00000355920.3:p.Gln242Ter	0.66115702
P3-Organoid	UNC93A	6	167708152	G	A	Missense_Mutation	ENST00000366829.2:c.235G>A	ENSP00000355794.2:p.Val79Met	0.31617647
P3-Organoid	SDK1	7	4088988	G	A	Missense_Mutation	ENST00000404826.2:c.2611G>A	ENSP00000385899.2:p.Ala871Thr	0.22262773
P3-Organoid	MOGAT3	7	100841617	C	T	Missense_Mutation	ENST00000440203.2:c.523G>A	ENSP00000403756.2:p.Asp175Asn	0.49275362
P3-Organoid	KMT2C	7	151882672	C	A	Missense_Mutation	ENST00000355193.2:c.5053G>T	ENSP00000347325.2:p.Ala1685Ser	0.12903225
P3-Organoid	GRHL2	8	102643864	G	C	Splice_Site	ENST00000395927.1:c.1210-1G>C		0.62222222
P3-Organoid	FOXD4	9	117371	C	G	Missense_Mutation	ENST00000382500.2:c.749G>C	ENSP00000371940.2:p.Gly250Ala	1
P3-Organoid	CDKN2A	9	21971120	G	A	Nonsense_Mutation	ENST00000579122.1:c.238C>T	ENSP00000464202.1:p.Arg80Ter	0.99342105
P3-Organoid	APBA1	9	72131199	G	A	Missense_Mutation	ENST00000265381.4:c.928C>T	ENSP00000265381.3:p.Arg310Cys	0.45454545
P3-Organoid	SLC2A6	9	136340162	C	T	Missense_Mutation	ENST00000371899.4:c.848G>A	ENSP00000360966.4:p.Arg283His	0.3671875
P3-Organoid	MYO3A	10	26385322	T	A	Missense_Mutation	ENST00000543632.1:c.1575T>A	ENSP00000445909.1:p.Asn525Lys	0.51612903
P3-Organoid	DNHD1	11	6541027	G	T	Missense_Mutation	ENST00000527990.2:c.1590G>T	ENSP00000436180.2:p.Gln530His	0.01591511
P3-Organoid	NAV2	11	20066793	G	A	Missense_Mutation	ENST00000540292.1:c.3341G>A	ENSP00000443489.1:p.Ser1114Asn	0.39295393
P3-Organoid	ALX4	11	44331215	G	A	Missense_Mutation	ENST00000329255.3:c.398C>T	ENSP00000332744.3:p.Pro133Leu	0.10227272
P3-Organoid	OR8K1	11	56113669	T	A	Missense_Mutation	ENST00000279783.2:c.155T>A	ENSP00000279783.2:p.Val52Asp	0.32984293
P3-Organoid	OR9G1	11	56468212	G	A	Missense_Mutation	ENST00000312153.1:c.349G>A	ENSP00000309012.1:p.Val117Met	0.63194444
P3-Organoid	OR9G4	11	56510657	C	T	Missense_Mutation	ENST00000302957.3:c.631G>A	ENSP00000307515.3:p.Glu211Lys	0.62992126
P3-Organoid	FAM111A	11	58919557	A	G	Missense_Mutation	ENST00000533703.1:c.416A>G	ENSP00000433154.1:p.Asn139Ser	0.33613445
P3-Organoid	RASGRP2	11	64506875	C	T	Missense_Mutation	ENST00000394432.3:c.770G>A	ENSP00000377953.3:p.Arg257His	0.64233576
P3-Organoid	GUCY1A2	11	106681104	C	T	Missense_Mutation	ENST00000526355.2:c.1307G>A	ENSP00000431245.1:p.Arg436Gln	0.62857142
P3-Organoid	PDE3A	12	20522547	G	A	Missense_Mutation	ENST00000359062.3:c.329G>A	ENSP00000351957.3:p.Gly110Asp	0.98148148
P3-Organoid	KRAS	12	25398284	C	T	Missense_Mutation	ENST00000557334.1:c.35G>A	ENSP00000452512.1:p.Gly12Asp	1
P3-Organoid	SPERT	13	46287581	C	T	Missense_Mutation	ENST00000378966.3:c.313C>T	ENSP00000368249.3:p.Arg105Cys	0.30191458
P3-Organoid	SPTB	14	65259941	G	A	Missense_Mutation	ENST00000556626.1:c.2440C>T	ENSP00000451752.1:p.Arg814Trp	0.35645933
P3-Organoid	ZNF839	14	102793048	G	A	Missense_Mutation	ENST00000559185.1:c.667G>A	ENSP00000453109.1:p.Gly223Ser	0.31775700
P3-Organoid	AKT1	14	105246533	G	A	Missense_Mutation	ENST00000555528.1:c.67C>T	ENSP00000450688.1:p.Arg23Trp	0.70642201
P3-Organoid	LCTL	15	66853402	G	A	Missense_Mutation	ENST00000537670.1:c.128C>T	ENSP00000445419.1:p.Ala43Val	0.27979274
P3-Organoid	IL16	15	81589273	C	T	Missense_Mutation	ENST00000394660.2:c.1907C>T	ENSP00000378155.2:p.Ala636Val	0.67441860
P3-Organoid	TEKT5	16	10729724	A	C	Missense_Mutation	ENST00000283025.2:c.1138T>G	ENSP00000283025.2:p.Ser380Ala	0.05844155
P3-Organoid	TP53	17	7577121	G	A	Missense_Mutation	ENST00000455263.2:c.817C>T	ENSP00000398846.2:p.Arg273Cys	1
P3-Organoid	ARHGAP27	17	43481661	C	T	Missense_Mutation	ENST00000528384.1:c.349G>A	ENSP00000431591.1:p.Val117Ile	0.29770992
P3-Organoid	RNF43	17	56448395	C	A	Splice_Site	ENST00000584437.1:c.253-1G>T		0.57295373
P3-Organoid	ACTG1	17	79478217	G	T	Missense_Mutation	ENST00000575842.1:c.799C>A	ENSP00000458162.1:p.Leu267Met	0.41418764
P3-Organoid	STK11	19	1221226	C	T	Missense_Mutation	ENST00000326873.7:c.749C>T	ENSP00000324856.6:p.Thr250Met	0.43478260
P3-Organoid	TBXA2R	19	3599929	C	T	Missense_Mutation	ENST00000411851.3:c.704G>A	ENSP00000393333.2:p.Arg235His	0.42696629
P3-Organoid	PDE4A	19	10561287	C	T	Missense_Mutation	ENST00000592685.1:c.563C>T	ENSP00000468507.1:p.Pro188Leu	0.43055555
P3-Organoid	FKBP8	19	18643527	T	C	Missense_Mutation	ENST00000610101.1:c.622A>G	ENSP00000476586.1:p.Met208Val	0.34275618
P3-Organoid	ZNF91	19	23542902	TGAATTATCTTATGTGTA	T	Frame_Shift_Del	ENST00000397082.2:c.2766_2782del	ENSP00000380272.2:p.Thr923TyrfsTer9	0.18709677
P3-Organoid	ZNF536	19	31039824	G	A	Missense_Mutation	ENST00000355537.3:c.3298G>A	ENSP00000347730.1:p.Val1100Met	0.74520547
P3-Organoid	IFNL3	19	39734787	C	T	Missense_Mutation	ENST00000413851.2:c.269G>A	ENSP00000409000.2:p.Arg90His	0.43699187
P3-Organoid	PSG2	19	43579505	C	T	Splice_Site	ENST00000406487.1:c.709+1G>A		0.17915309
P3-Organoid	RRAS	19	50140383	T	C	Missense_Mutation	ENST00000246792.3:c.158A>G	ENSP00000246792.2:p.Tyr53Cys	0.76515151
P3-Organoid	MYBPC2	19	50962189	C	T	Missense_Mutation	ENST00000357701.5:c.2521C>T	ENSP00000350332.4:p.Arg841Trp	0.17277486
P3-Organoid	RP4-576H24.4	20	1559023	CCA	C	Frame_Shift_Del	ENST00000564763.1:c.392_393del	ENSP00000457944.1:p.Val131GlyfsTer3	0.01988636
P3-Organoid	MAGEB18	X	26157473	C	T	Missense_Mutation	ENST00000325250.1:c.371C>T	ENSP00000314543.1:p.Thr124Met	0.55056179

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
P3	AZD2014	2.247
P3	AZD3759	~ 80380168
P3	AZD4547	~ 5209
P3	AZD5363	~ 4.208e-008
P3	AZD6738	~ 3.339e+015
P3	AZD9291	~ 7.133e+015
P3	I.BET.762	773.3
P3	Rapamycin..Sirolimus.	3.213
P3	AZD1775..MK.1775.	9.613
P3	Triptolide..PG490.	0.6901
P3	Simvastatin	~ 2.638e-015
P3	Temozolomide	~ 5.966
P3	Imatinib.Mesylate..STI571.	~ 53260676
P3	Pazopanib..GW786034.	~ 5566
P3	Sunitinib.Malate	5785
P3	Olaparib..AZD2281..KU0059436.	~ 7.487e+045
P3	Regorafenib..BAY.73.4506.	573.8
P3	Erlotinib	~ 1096415975
P3	Gefitinib	~ 3.598e+033
P3	Afatinib	~ 341442
P3	OTX.015	214.9
P3	BKM120..NVP.BKM120.	~ 296272
P3	BYL719	15868
P3	Cediranib..AZD2171.	~ 2142479
P3	Ceritinib.LDK378.	560.7
P3	Crizotinib...PF.02341066.	3486
P3	Dabrafenib	1316
P3	Dacomitinib	~ 2.437e-006
P3	Everolimus..RAD001.	~ 5617
P3	Ibrutinib..PCI.32765.	~ 25458752
P3	Lapatinib	~ 418520
P3	LY2835219	613.7
P3	Brivanib..BMS.582664.	~ 21485
P3	Panobinostat	15.69
P3	Selumetinib..AZD6244.	~ 6.377e+016
P3	Sorafenib	~ 1022
P3	Trametinib	65.71
P3	Vandetanib..ZD6474.	~ 159733754
P3	Vemurafenib	8.084
P3	AZD5153	61.32
P3	ABT.199..GDC.0199..	~ 1.731
P3	ABT.888..Veliparib..NSC.737664.	~ 5608
P3	Avagacestat..BMS.708163.	~ 1.201e-010
P3	Axitinib...AG.013736.	2167
P3	Bosutinib..SKI.606.	2694
P3	Cabozantinib..XL184.	~ 17.91
P3	Dasatinib..BMS.354825.	~ 1.401e+030
P3	decitabine	~ 1.201e+015
P3	defactinib	~ 0.009024
P3	Dovitinib..TKI258.CHIR258.	1371
P3	Fluorouracil..5.Fluoracil..5.FU.	4655
P3	Foretinib..XL880.	2136
P3	Tivantinib..ARQ.197.	~ 287.9
P3	Abraxane	7.309
P3	AZD2461.olaparib.analog.	~ 6.494e-014
P3	Olaparib.	4312
P3	Idelalisib	~ 52295
P3	Irinotecan	4749
P3	Nilotinib..AMN.107.	~ 16951
P3	NVP.AEW541	2843
P3	Oxaliplatin	~ 6.146
P3	PLX3397	~ 7561846
P3	Quizartinib..AC220.	~ 0.000
P3	Saracatinib..AZD0530.	3680
P3	Semagacestat..LY450139.	~ 1.932e+036
P3	TGX.221
P3	tozasertib	~ 69.96
P3	Vorinostat..SAHA..MK0683.	1040
P3	XAV939	~ 1118
P3	gemcitabine	~ 4.309e-005
P3	palbociclib	~ 3.479e+026
P3	Neratinib..HKI.272.	~ 100976859854