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
P1	PDAC	4	70	15.7	Female	4931.76

Mutation Profiles

Primary Tumor

ID	Gene	CHROM	POS	REF	ALT	Consequence	HGVSc	HGVSp	VAF
P1-Tissue	ATAD3B	1	1431060	T	C	Missense_Mutation	ENST00000308647.7:c.1810T>C	ENSP00000311766.7:p.Tyr604His	0.19298245
P1-Tissue	CSF1	1	110466222	A	T	Missense_Mutation	ENST00000369802.3:c.979A>T	ENSP00000358817.3:p.Arg327Trp	0.04026845
P1-Tissue	ANAPC1	2	112614429	G	A	Nonsense_Mutation	ENST00000341068.3:c.1393C>T	ENSP00000339109.3:p.Gln465Ter	0.10502283
P1-Tissue	COL7A1	3	48629354	C	T	Missense_Mutation	ENST00000454817.1:c.1334G>A	ENSP00000412569.1:p.Arg445Gln	0.02439024
P1-Tissue	MAEA	4	1332266	G	A	Missense_Mutation	ENST00000514708.1:c.752G>A	ENSP00000427512.1:p.Arg251His	0.01990049
P1-Tissue	HTRA3	4	8307700	G	A	Missense_Mutation	ENST00000307358.2:c.1199G>A	ENSP00000303766.2:p.Gly400Asp	0.01587301
P1-Tissue	BBS7	4	122749622	T	G	Missense_Mutation	ENST00000506636.1:c.1825A>C	ENSP00000423626.1:p.Ile609Leu	0.00571428
P1-Tissue	AP3S1	5	115249078	C	T	Missense_Mutation	ENST00000316788.7:c.473C>T	ENSP00000325369.7:p.Pro158Leu	0.34177215
P1-Tissue	TMEM14B	6	10756712	C	T	Missense_Mutation	ENST00000473276.1:c.127C>T	ENSP00000420580.1:p.Arg43Cys	0.07432432
P1-Tissue	FIGNL1	7	50514478	G	A	Nonsense_Mutation	ENST00000433017.1:c.508C>T	ENSP00000399997.1:p.Arg170Ter	0.03813559
P1-Tissue	SLC35G5	8	11188922	T	C	Missense_Mutation	ENST00000382435.4:c.307T>C	ENSP00000371872.4:p.Trp103Arg	0.09507042
P1-Tissue	ANKRD20A2	9	42368614	A	G	Missense_Mutation	ENST00000377601.2:c.200A>G	ENSP00000366826.2:p.His67Arg	0.46282973
P1-Tissue	DGKZ	11	46369238	C	A	Missense_Mutation	ENST00000543978.1:c.29C>A	ENSP00000438417.1:p.Ala10Asp	0.17164179
P1-Tissue	KRT86	12	52699033	G	A	Missense_Mutation	ENST00000544024.1:c.745G>A	ENSP00000443169.1:p.Val249Ile	0.15346534
P1-Tissue	RP11-644F5.10	12	56112889	ACATGAAC	A	Frame_Shift_Del	ENST00000550412.1:c.236_242del	ENSP00000447650.1:p.Met79ArgfsTer8	0.01477832
P1-Tissue	AGAP2	12	58130876	A	G	Missense_Mutation	ENST00000547588.1:c.1154T>C	ENSP00000449241.1:p.Leu385Pro	0.02453987
P1-Tissue	C16orf58	16	31519193	CAAACGCCTGGAGAAGA	C	Splice_Site	ENST00000570164.1:c.301-10_306del		0.01612903
P1-Tissue	RPS15	19	1440068	G	C	Missense_Mutation	ENST00000593052.1:c.161G>C	ENSP00000466010.1:p.Arg54Pro	0.07782101
P1-Tissue	ABHD17A	19	1881526	AG	A	Frame_Shift_Del	ENST00000590661.1:c.39del	ENSP00000467638.1:p.Cys14AlafsTer43	0.00289017
P1-Tissue	ABHD17A	19	1881528	AAG	A	Frame_Shift_Del	ENST00000590661.1:c.36_37del	ENSP00000467638.1:p.Phe13LeufsTer27	0.13569321
P1-Tissue	CYP2A13	19	41595958	C	T	Missense_Mutation	ENST00000330436.3:c.350C>T	ENSP00000332679.1:p.Ala117Val	0.06424581
P1-Tissue	SIGLEC10	19	51920196	G	T	Missense_Mutation	ENST00000525998.1:c.430C>A	ENSP00000431444.1:p.Gln144Lys	0.11705685

Organoid

ID	Gene	CHROM	POS	REF	ALT	Consequence	HGVSc	HGVSp	VAF
P1-Organoid	ATAD3B	1	1431060	T	C	Missense_Mutation	ENST00000308647.7:c.1810T>C	ENSP00000311766.7:p.Tyr604His	0.25
P1-Organoid	ATAD3B	1	1431165	C	T	Missense_Mutation	ENST00000308647.7:c.1915C>T	ENSP00000311766.7:p.Pro639Ser	0.43035714
P1-Organoid	PRAMEF1	1	12855774	A	G	Missense_Mutation	ENST00000400814.3:c.319A>G	ENSP00000383616.3:p.Lys352Glu	0.10849056
P1-Organoid	CLCNKA	1	16354394	C	T	Missense_Mutation	ENST00000439316.2:c.731C>T	ENSP00000414445.2:p.Ala287Val	0.46101694
P1-Organoid	ADC	1	33563691	A	G	Missense_Mutation	ENST00000398167.1:c.1000A>G	ENSP00000381233.1:NA	0.39606741
P1-Organoid	HIVEP3	1	42049181	C	T	Missense_Mutation	ENST00000429157.2:c.1288G>A	ENSP00000410828.2:NA	0.24
P1-Organoid	LCE1D	1	152770503	G	A	Missense_Mutation	ENST00000326233.6:c.233G>A	ENSP00000316737.6:p.Arg78His	0.09282700
P1-Organoid	LCE1D	1	152770521	G	A	Missense_Mutation	ENST00000326233.6:c.251G>A	ENSP00000316737.6:p.Arg84His	0.17073170
P1-Organoid	AQP10	1	154294464	A	G	Missense_Mutation	ENST00000484864.1:c.161A>G	ENSP00000420341.1:p.Asn54Ser	0.19305019
P1-Organoid	DAP3	1	155699069	C	A	Missense_Mutation	ENST00000535183.1:c.632C>A	ENSP00000445003.1:p.Ser211Tyr	0.28767123
P1-Organoid	BLZF1	1	169347575	G	A	Missense_Mutation	ENST00000367808.3:c.476G>A	ENSP00000356782.3:p.Arg159His	0.53763440
P1-Organoid	BRE	2	28460164	A	G	Missense_Mutation	ENST00000379632.2:c.776A>G	ENSP00000368953.2:p.Asn259Ser	1
P1-Organoid	VWA3B	2	98779374	C	T	Missense_Mutation	ENST00000477737.1:c.1049C>T	ENSP00000417955.1:p.Thr350Met	0.43925233
P1-Organoid	ANAPC1	2	112614429	G	A	Nonsense_Mutation	ENST00000341068.3:c.1393C>T	ENSP00000339109.3:p.Gln465Ter	0.25130890
P1-Organoid	TUBA3E	2	130951894	G	T	Missense_Mutation	ENST00000312988.7:c.521C>A	ENSP00000318197.7:p.Ala174Asp	0.21052631
P1-Organoid	LRP1B	2	141079606	G	A	Missense_Mutation	ENST00000389484.3:c.12566C>T	ENSP00000374135.3:p.Pro4189Leu	0.17263843
P1-Organoid	BAZ2B	2	160205653	A	G	Missense_Mutation	ENST00000392783.2:c.5002T>C	ENSP00000376534.2:p.Phe1668Leu	0.456
P1-Organoid	VILL	3	38043268	G	A	Missense_Mutation	ENST00000465644.1:c.550G>A	ENSP00000422096.1:p.Val184Ile	0.03333333
P1-Organoid	COL7A1	3	48629354	C	T	Missense_Mutation	ENST00000454817.1:c.1334G>A	ENSP00000412569.1:p.Arg445Gln	0.64102564
P1-Organoid	MST1	3	49722905	T	TGG	Frame_Shift_Ins	ENST00000449682.2:c.1420_1421dup	ENSP00000414287.2:p.Asp475GlnfsTer52	0.09240924
P1-Organoid	SLC33A1	3	155571270	TTC	T	Frame_Shift_Del	ENST00000392845.3:c.515_516del	ENSP00000376587.2:p.Arg172AsnfsTer15	0.58139534
P1-Organoid	MYOZ2	4	120107249	G	T	Missense_Mutation	ENST00000307128.5:c.689G>T	ENSP00000306997.5:p.Arg230Leu	0.03157894
P1-Organoid	WDR17	4	177067184	G	A	Missense_Mutation	ENST00000508596.1:c.1568G>A	ENSP00000422763.1:p.Arg523His	0.39316239
P1-Organoid	ARSB	5	78135181	G	A	Missense_Mutation	ENST00000565165.1:c.1211C>T	ENSP00000456339.1:p.Pro404Leu	0.24679487
P1-Organoid	AP3S1	5	115249078	C	T	Missense_Mutation	ENST00000316788.7:c.473C>T	ENSP00000325369.7:p.Pro158Leu	0.35793357
P1-Organoid	TMEM14B	6	10756712	C	T	Missense_Mutation	ENST00000473276.1:c.127C>T	ENSP00000420580.1:p.Arg43Cys	0.05821917
P1-Organoid	TNXB	6	32035705	C	T	Missense_Mutation	ENST00000375247.2:c.6277G>A	ENSP00000364396.2:p.Ala2093Thr	0.41689373
P1-Organoid	BRD2	6	32943223	CAAT	C	In_Frame_Del	ENST00000449085.2:c.256_258del	ENSP00000409145.2:p.Asn86del	0.66666666
P1-Organoid	GNA12	7	2802374	C	T	Missense_Mutation	ENST00000407653.1:c.149G>A	ENSP00000386054.1:p.Arg50Gln	0.29927007
P1-Organoid	RADIL	7	4917673	C	T	Missense_Mutation	ENST00000536091.1:c.98G>A	ENSP00000442533.1:p.Ser33Asn	0.24489795
P1-Organoid	USP42	7	6194003	G	T	Nonsense_Mutation	ENST00000306177.5:c.2818G>T	ENSP00000301962.5:p.Glu940Ter	0.04255319
P1-Organoid	TNS3	7	47317793	G	A	Nonsense_Mutation	ENST00000398879.1:c.4219C>T	ENSP00000381854.1:p.Gln1407Ter	0.27559055
P1-Organoid	FIGNL1	7	50514478	G	A	Nonsense_Mutation	ENST00000433017.1:c.508C>T	ENSP00000399997.1:p.Arg170Ter	0.29333333
P1-Organoid	SLC12A9	7	100463991	G	A	Missense_Mutation	ENST00000354161.3:c.2509G>A	ENSP00000275730.4:p.Ala837Thr	0.45161290
P1-Organoid	SLC35G5	8	11188922	T	C	Missense_Mutation	ENST00000382435.4:c.307T>C	ENSP00000371872.4:p.Trp103Arg	0.08637873
P1-Organoid	GRHL2	8	102589721	CGGCGAAGCAGA	C	Frame_Shift_Del	ENST00000395927.1:c.932_942del	ENSP00000379260.1:p.Ala311GlyfsTer3	0.63636363
P1-Organoid	GLIS3	9	4118415	G	A	Missense_Mutation	ENST00000381971.3:c.1063C>T	ENSP00000371398.3:p.Arg355Cys	0.30769230
P1-Organoid	ANKRD20A2	9	42368614	A	G	Missense_Mutation	ENST00000377601.2:c.200A>G	ENSP00000366826.2:p.His67Arg	0.47982062
P1-Organoid	PTCH1	9	98270531	C	G	Missense_Mutation	ENST00000331920.6:c.113G>C	ENSP00000332353.6:p.Gly38Ala	0.45098039
P1-Organoid	TRIM32	9	119461721	ACTT	A	In_Frame_Del	ENST00000450136.1:c.1706_1708del	ENSP00000408292.1:p.Phe569del	0.58646616
P1-Organoid	RALGPS1	9	129812376	G	C	Missense_Mutation	ENST00000424082.2:c.355G>C	ENSP00000415630.2:p.Ala119Pro	0.13714285
P1-Organoid	LOXL4	10	100015394	C	T	Missense_Mutation	ENST00000260702.3:c.1531G>A	ENSP00000260702.3:p.Gly511Arg	0.34408602
P1-Organoid	TMEM138	11	61131879	A	G	Missense_Mutation	ENST00000542946.1:c.17A>G	ENSP00000445792.1:p.Asn6Ser	0.01734104
P1-Organoid	KRAS	12	25398284	C	T	Missense_Mutation	ENST00000557334.1:c.35G>A	ENSP00000452512.1:p.Gly12Asp	0.44
P1-Organoid	DDX11	12	31237978	C	T	Missense_Mutation	ENST00000545668.1:c.556C>T	ENSP00000440402.1:p.Arg186Trp	0.17760617
P1-Organoid	DDX11	12	31250875	G	C	Missense_Mutation	ENST00000545668.1:c.1819G>C	ENSP00000440402.1:p.Ala607Pro	0.18119266
P1-Organoid	PABPC3	13	25671585	TA	CC	Missense_Mutation	ENST00000281589.3:c.1249_1250delinsCC	ENSP00000281589.3:p.Tyr417Pro	0.04467354
P1-Organoid	PCCA	13	101020827	C	T	Missense_Mutation	ENST00000376286.4:c.1667C>T	ENSP00000365463.4:p.Ser556Leu	0.43697479
P1-Organoid	NOP9	14	24769311	C	T	Missense_Mutation	ENST00000396802.3:c.151C>T	ENSP00000380020.3:p.Pro51Ser	0.67407407
P1-Organoid	GZMH	14	25076877	G	C	Missense_Mutation	ENST00000382548.4:c.280C>G	ENSP00000371988.4:p.Pro94Ala	0.13839285
P1-Organoid	RP11-176H8.1	14	31926584	G	A	Missense_Mutation	ENST00000547378.1:c.16C>T	ENSP00000447056.1:p.Arg6Trp	0.35
P1-Organoid	YLPM1	14	75248907	G	A	Missense_Mutation	ENST00000552421.1:c.2161G>A	ENSP00000447921.1:p.Gly721Arg	0.73275862
P1-Organoid	DYNC1H1	14	102445804	A	AT	Frame_Shift_Ins	ENST00000360184.4:c.495dup	ENSP00000348965.4:p.Arg166Ter	0.39442231
P1-Organoid	TECPR2	14	102918775	G	A	Missense_Mutation	ENST00000558678.1:c.3451G>A	ENSP00000453671.1:p.Val1151Ile	0.27325581
P1-Organoid	WDR24	16	739642	G	A	Missense_Mutation	ENST00000248142.6:c.185C>T	ENSP00000248142.6:p.Ala62Val	0.55555555
P1-Organoid	HAGHL	16	778956	G	T	Missense_Mutation	ENST00000341413.4:c.661G>T	ENSP00000341952.4:p.Gly221Trp	0.0625
P1-Organoid	HAGHL	16	778962	G	T	Missense_Mutation	ENST00000341413.4:c.667G>T	ENSP00000341952.4:p.Ala223Ser	0.06666666
P1-Organoid	C16orf58	16	31519193	CAAACGCCTGGAGAAGA	C	Splice_Site	ENST00000570164.1:c.301-10_306del		0.23622047
P1-Organoid	IRX5	16	54967174	G	A	Missense_Mutation	ENST00000558597.1:c.643G>A	ENSP00000453725.1:p.Ala215Thr	0.40384615
P1-Organoid	MARVELD3	16	71668212	T	C	Missense_Mutation	ENST00000567501.1:c.152T>C	ENSP00000455814.1:p.Leu51Pro	0.47142857
P1-Organoid	TP53	17	7578406	C	T	Missense_Mutation	ENST00000455263.2:c.524G>A	ENSP00000398846.2:p.Arg175His	1
P1-Organoid	NCOR1	17	15952173	C	A	Missense_Mutation	ENST00000395857.3:c.2274G>T	ENSP00000379198.3:p.Glu758Asp	0.02684563
P1-Organoid	TBC1D29	17	28890301	G	A	Missense_Mutation	ENST00000580161.1:c.311G>A	ENSP00000462799.1:p.Ser104Asn	0.09022556
P1-Organoid	CCL4L2	17	34641494	A	C	Missense_Mutation	ENST00000394465.2:c.236A>C	ENSP00000377978.2:p.Glu79Ala	0.05882352
P1-Organoid	EVPL	17	74005146	C	A	Missense_Mutation	ENST00000586740.1:c.4206G>T	ENSP00000465630.1:p.Lys1402Asn	0.01724137
P1-Organoid	SMAD4	18	48573649	TG	T	Frame_Shift_Del	ENST00000588745.1:c.235del	ENSP00000464901.1:p.Asp79MetfsTer15	0.88888888
P1-Organoid	RPS15	19	1440068	G	C	Missense_Mutation	ENST00000593052.1:c.161G>C	ENSP00000466010.1:p.Arg54Pro	0.14814814
P1-Organoid	ZNF441	19	11891163	C	T	Missense_Mutation	ENST00000454339.2:c.323C>T	ENSP00000403738.2:p.Ala108Val	0.04705882
P1-Organoid	CCDC105	19	15121794	G	A	Missense_Mutation	ENST00000292574.3:c.157G>A	ENSP00000292574.2:p.Val53Met	0.68421052
P1-Organoid	PDCD2L	19	34900211	G	A	Missense_Mutation	ENST00000246535.3:c.482G>A	ENSP00000246535.1:p.Arg161Gln	0.13175675
P1-Organoid	PRX	19	40901570	G	A	Nonsense_Mutation	ENST00000324001.7:c.2689C>T	ENSP00000326018.6:p.Arg897Ter	0.11519607
P1-Organoid	NLRP12	19	54312910	G	A	Missense_Mutation	ENST00000535162.1:c.2003C>T	ENSP00000438030.1:p.Ala668Val	0.63928571
P1-Organoid	ZNF580	19	56154275	A	C	Missense_Mutation	ENST00000545125.1:c.401A>C	ENSP00000446126.1:p.His134Pro	0.72777777
P1-Organoid	SYNDIG1	20	24524031	C	T	Missense_Mutation	ENST00000376862.3:c.298C>T	ENSP00000366058.3:p.Arg100Cys	0.09803921
P1-Organoid	TTLL9	20	30530746	A	G	Splice_Site	ENST00000535842.1:c.1244-2A>G		0.51785714
P1-Organoid	PPDPF	20	62152689	C	T	Missense_Mutation	ENST00000370179.3:c.28C>T	ENSP00000359198.3:p.Leu10Phe	0.46909090
P1-Organoid	CBR3	21	37518742	C	A	Missense_Mutation	ENST00000290354.5:c.766C>A	ENSP00000290354.5:p.Leu256Ile	0.01875
P1-Organoid	RIPK4	21	43176822	A	AT	Frame_Shift_Ins	ENST00000544709.1:c.147dup	ENSP00000441754.1:p.Leu50IlefsTer49	0.875
P1-Organoid	MXRA5	X	3236044	C	G	Missense_Mutation	ENST00000217939.6:c.5678G>C	ENSP00000217939.5:p.Gly1893Ala	0.68316831
P1-Organoid	CLCN4	X	10176601	G	A	Missense_Mutation	ENST00000421085.2:c.1078G>A	ENSP00000405754.2:p.Val360Ile	0.64359861
P1-Organoid	ATP6AP2	X	40464996	C	T	Nonsense_Mutation	ENST00000544975.1:c.814C>T	ENSP00000440459.1:p.Arg272Ter	0.06072874
P1-Organoid	MED14	X	40542109	C	CATTAAGTG	Frame_Shift_Ins	ENST00000324817.1:c.2189_2196dup	ENSP00000323720.1:p.Gly733HisfsTer18	0.43730886
P1-Organoid	DLG3	X	69665197	C	T	Missense_Mutation	ENST00000374360.3:c.146C>T	ENSP00000363480.3:p.Ala49Val	0.325
P1-Organoid	LONRF3	X	118124436	C	T	Missense_Mutation	ENST00000422289.2:c.560C>T	ENSP00000408894.2:p.Pro187Leu	0.33079847

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
P1	AZD2014	10651
P1	AZD3759	443.7
P1	AZD4547	~ 5330
P1	AZD5363	4642
P1	AZD6738	3285
P1	AZD9291	~ 1.961e+016
P1	I.BET.762	845.1
P1	Rapamycin..Sirolimus.	30213
P1	AZD1775..MK.1775.	1448
P1	Triptolide..PG490.	~ 0.009898
P1	Simvastatin	746.2
P1	Temozolomide	~ 745060817
P1	Imatinib.Mesylate..STI571.	14091
P1	Pazopanib..GW786034.	4855
P1	Sunitinib.Malate	~ 731123507461
P1	Olaparib..AZD2281..KU0059436.	~ 4342079171
P1	Regorafenib..BAY.73.4506.	4898
P1	Erlotinib	487.3
P1	Gefitinib	~ 2.053e-047
P1	Afatinib	~ 1.289e+040
P1	OTX.015	97.13
P1	BKM120..NVP.BKM120.	1696
P1	BYL719	14307
P1	Cediranib..AZD2171.	7219
P1	Ceritinib.LDK378.	1323
P1	Crizotinib...PF.02341066.	3835
P1	Dabrafenib	~ 355.2
P1	Dacomitinib	~ 2.454e+019
P1	Everolimus..RAD001.	~ 16743
P1	Ibrutinib..PCI.32765.	270230
P1	Lapatinib	4320
P1	LY2835219	670.7
P1	Brivanib..BMS.582664.	~ 19250
P1	Panobinostat	41.97
P1	Selumetinib..AZD6244.	3010
P1	Sorafenib	~ 7732477860
P1	Trametinib	93.25
P1	Vandetanib..ZD6474.	1020
P1	Vemurafenib	~ 1934
P1	AZD5153	59.14
P1	ABT.199..GDC.0199..	~ 54425868
P1	ABT.888..Veliparib..NSC.737664.	~ 5589
P1	Avagacestat..BMS.708163.	66128
P1	Axitinib...AG.013736.	1073
P1	Bosutinib..SKI.606.	1210
P1	Cabozantinib..XL184.	8902
P1	Dasatinib..BMS.354825.	~ 2.524e-010
P1	decitabine	~ 4.348e+021
P1	defactinib	4831
P1	Dovitinib..TKI258.CHIR258.	2456
P1	Fluorouracil..5.Fluoracil..5.FU.	5520
P1	Foretinib..XL880.	695.6
P1	Tivantinib..ARQ.197.	193.4
P1	Abraxane	7.098
P1	AZD2461.olaparib.analog.	~ 5.990e-013
P1	Olaparib.	~ 5135
P1	Idelalisib	15024
P1	Irinotecan	1105
P1	Nilotinib..AMN.107.	~ 1194
P1	NVP.AEW541	6663
P1	Oxaliplatin	~ 17473
P1	PLX3397	17140
P1	Quizartinib..AC220.	~ 355.5
P1	Saracatinib..AZD0530.	1071
P1	Semagacestat..LY450139.	~ 8.036e-005
P1	TGX.221	~ 7333
P1	tozasertib	~ 71.49
P1	Vorinostat..SAHA..MK0683.	2474
P1	XAV939	4296
P1	gemcitabine	874.2
P1	palbociclib	~ 1.947e+018
P1	Neratinib..HKI.272.	534.5