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
P10	PDAC (NSCLC, cT1bN0, Colon Ca with peritoneal carcinomatosis)	4	75	20.3	Male	188.11

Mutation Profiles

Primary Tumor

ID	Gene	CHROM	POS	REF	ALT	Consequence	HGVSc	HGVSp	VAF
P10-Tissue	ZC3H12A	1	37948605	A	G	Missense_Mutation	ENST00000373087.6:c.1193A>G	ENSP00000362179.5:p.Tyr398Cys	0.01385041
P10-Tissue	TRIM17	1	228596209	C	T	Missense_Mutation	ENST00000366698.2:c.1127G>A	ENSP00000355659.2:p.Arg376Gln	0.01335877
P10-Tissue	ALS2CL	3	46713669	T	G	Missense_Mutation	ENST00000415953.1:c.2495A>C	ENSP00000413223.1:p.Lys832Thr	0.02976190
P10-Tissue	TRPC7	5	135692663	G	A	Missense_Mutation	ENST00000513104.1:c.413C>T	ENSP00000426070.1:p.Thr138Met	0.01346801
P10-Tissue	SYNE1	6	152847214	C	T	Splice_Site	ENST00000341594.5:c.225+1G>A		0.04444444
P10-Tissue	SLC35G5	8	11189184	C	T	Missense_Mutation	ENST00000382435.4:c.569C>T	ENSP00000371872.4:p.Thr190Ile	0.08135593
P10-Tissue	GNAQ	9	80537112	T	A	Missense_Mutation	ENST00000286548.4:c.286A>T	ENSP00000286548.4:p.Thr96Ser	0.08870967
P10-Tissue	MUC6	11	1027417	GCTGTGGTGGCACTCGGTGGCACGGTCC	G	In_Frame_Del	ENST00000421673.2:c.2055_2081del	ENSP00000406861.2:p.Asp686_Ser694del	0.00764818
P10-Tissue	SETD8	12	123875223	C	T	Missense_Mutation	ENST00000402868.3:c.179C>T	ENSP00000384629.3:p.Pro60Leu	0.03891050
P10-Tissue	MTMR6	13	25861369	G	A	Missense_Mutation	ENST00000540661.1:c.17C>T	ENSP00000443161.1:p.Thr6Met	0.01257861
P10-Tissue	EMR2	19	14877820	G	A	Missense_Mutation	ENST00000601345.1:c.457C>T	ENSP00000471297.1:p.Leu153Phe	0.08125
P10-Tissue	ZNF536	19	31039479	G	T	Missense_Mutation	ENST00000355537.3:c.2953G>T	ENSP00000347730.1:p.Ala985Ser	0.03171641
P10-Tissue	DHX34	19	47856633	C	CCG	Frame_Shift_Ins	ENST00000328771.4:c.346_347insCG	ENSP00000331907.4:p.Arg116ProfsTer61	0.00940070
P10-Tissue	SIGLEC10	19	51917716	C	T	Missense_Mutation	ENST00000525998.1:c.1114G>A	ENSP00000431444.1:p.Gly372Ser	0.04067796
P10-Tissue	KRTAP10-6	21	46012231	G	GCT	Frame_Shift_Ins	ENST00000400368.1:c.134_135insAG	ENSP00000383219.1:p.Cys46AlafsTer9	0.00459770
P10-Tissue	ESX1	X	103495171	G	C	Missense_Mutation	ENST00000372588.4:c.959C>G	ENSP00000361669.4:p.Pro320Arg	0.18840579
P10-Tissue	BRCC3	X	154299812	C	T	Nonsense_Mutation	ENST00000399042.1:c.10C>T	ENSP00000381998.1:p.Gln4Ter	0.03669724

Organoid

ID	Gene	CHROM	POS	REF	ALT	Consequence	HGVSc	HGVSp	VAF
P10-Organoid	CEP104	1	3754070	A	G	Missense_Mutation	ENST00000378230.3:c.905T>C	ENSP00000367476.3:NA	0.49137931
P10-Organoid	CATSPER4	1	26517899	G	A	Missense_Mutation	ENST00000456354.2:c.335G>A	ENSP00000390423.2:NA	0.48201438
P10-Organoid	ASH1L	1	155308000	T	C	Missense_Mutation	ENST00000392403.3:c.8683A>G	ENSP00000376204.3:p.Thr2895Ala	0.04390243
P10-Organoid	SMG5	1	156242115	G	A	Missense_Mutation	ENST00000368267.5:c.709C>T	ENSP00000357250.4:p.Arg237Cys	0.032
P10-Organoid	CACNA1S	1	201081373	A	T	Missense_Mutation	ENST00000367338.3:c.95T>A	ENSP00000356307.3:p.Phe32Tyr	0.03947368
P10-Organoid	OR14K1	1	247902100	C	T	Nonsense_Mutation	ENST00000283225.2:c.184C>T	ENSP00000283225.2:p.Arg62Ter	0.02839116
P10-Organoid	ASAP2	2	9347277	A	T	Missense_Mutation	ENST00000315273.4:c.44A>T	ENSP00000316404.4:p.His15Leu	0.07352941
P10-Organoid	TEKT4	2	95542476	C	T	Missense_Mutation	ENST00000295201.4:c.1270C>T	ENSP00000295201.4:p.Arg424Cys	0.02894736
P10-Organoid	TTN	2	179639033	G	A	Missense_Mutation	ENST00000591111.1:c.6958C>T	ENSP00000465570.1:p.Arg2320Cys	0.03301886
P10-Organoid	PARD3B	2	206305254	G	A	Missense_Mutation	ENST00000406610.2:c.2902G>A	ENSP00000385848.2:p.Val968Ile	0.02622950
P10-Organoid	IQCF3	3	51864572	C	A	Missense_Mutation	ENST00000444293.1:c.110C>A	ENSP00000402530.1:p.Thr37Lys	0.41747572
P10-Organoid	LRRC66	4	52860862	GT	G	Frame_Shift_Del	ENST00000343457.3:c.2325del	ENSP00000341944.3:p.Lys775AsnfsTer40	0.40514469
P10-Organoid	FRAS1	4	79205620	A	C	Missense_Mutation	ENST00000325942.6:c.1317A>C	ENSP00000326330.6:p.Gln439His	0.03041825
P10-Organoid	NLN	5	65105883	G	C	Missense_Mutation	ENST00000502464.1:c.1422G>C	ENSP00000423214.1:p.Gln474His	0.02659574
P10-Organoid	CMYA5	5	79034640	G	A	Missense_Mutation	ENST00000446378.2:c.10052G>A	ENSP00000394770.2:p.Arg3351His	0.44493392
P10-Organoid	PCDH12	5	141336818	T	G	Missense_Mutation	ENST00000231484.3:c.599A>C	ENSP00000231484.3:p.Lys200Thr	0.42028985
P10-Organoid	SLC29A1	6	44197363	C	T	Missense_Mutation	ENST00000427851.2:c.149C>T	ENSP00000392668.2:p.Ser50Phe	0.02359882
P10-Organoid	PREP	6	105726047	C	T	Missense_Mutation	ENST00000369110.3:c.2105G>A	ENSP00000358106.3:p.Arg702Gln	0.03716216
P10-Organoid	GRM1	6	146755216	G	A	Missense_Mutation	ENST00000361719.2:c.2869G>A	ENSP00000354896.2:p.Val957Ile	0.39426523
P10-Organoid	AUTS2	7	70231133	G	A	Missense_Mutation	ENST00000406775.2:c.1502G>A	ENSP00000385263.2:p.Arg501His	0.01907356
P10-Organoid	POM121	7	72413723	T	TCTC	In_Frame_Ins	ENST00000446813.1:c.2398_2399insCCT	ENSP00000393020.1:p.Phe799_Phe800insSer	0.04562737
P10-Organoid	GJC3	7	99527179	C	A	Missense_Mutation	ENST00000312891.2:c.65G>T	ENSP00000325775.2:p.Arg22Leu	0.05932203
P10-Organoid	ZNF3	7	99669202	T	C	Missense_Mutation	ENST00000424697.1:c.905A>G	ENSP00000415358.1:p.His302Arg	0.46818181
P10-Organoid	CTTNBP2	7	117513457	C	T	Missense_Mutation	ENST00000160373.3:c.13G>A	ENSP00000160373.3:p.Gly5Ser	0.04395604
P10-Organoid	GIMAP6	7	150325441	C	T	Missense_Mutation	ENST00000328902.5:c.245G>A	ENSP00000330374.5:p.Arg82Gln	0.02310231
P10-Organoid	ZFHX4	8	77763746	C	T	Missense_Mutation	ENST00000521891.2:c.4589C>T	ENSP00000430497.2:p.Thr1530Met	0.03225806
P10-Organoid	GLIS3	9	4118236	CT	C	Frame_Shift_Del	ENST00000381971.3:c.1241del	ENSP00000371398.3:p.Gln414ArgfsTer28	0.01851851
P10-Organoid	TAF1L	9	32632543	G	T	Missense_Mutation	ENST00000242310.4:c.3035C>A	ENSP00000418379.1:p.Ala1012Glu	0.03950617
P10-Organoid	COL15A1	9	101748020	G	A	Missense_Mutation	ENST00000375001.3:c.274G>A	ENSP00000364140.3:p.Ala92Thr	0.36904761
P10-Organoid	GRIN1	9	140040199	C	T	Missense_Mutation	ENST00000371561.3:c.415C>T	ENSP00000360616.3:p.Arg139Cys	0.34265734
P10-Organoid	ADARB2	10	1284350	C	T	Missense_Mutation	ENST00000381312.1:c.1205G>A	ENSP00000370713.1:p.Arg402Gln	0.04375
P10-Organoid	FRMD4A	10	13708300	C	T	Missense_Mutation	ENST00000378503.1:c.1400G>A	ENSP00000367764.1:p.Arg467Gln	0.47682119
P10-Organoid	ZNF503	10	77158605	C	T	Missense_Mutation	ENST00000535216.1:c.1843G>A	ENSP00000438988.1:p.Ala615Thr	0.04424778
P10-Organoid	OR5F1	11	55762069	C	A	Missense_Mutation	ENST00000278409.1:c.33G>T	ENSP00000278409.1:p.Glu11Asp	0.53846153
P10-Organoid	PCNXL3	11	65387314	TGCTCACCCGG	T	Frame_Shift_Del	ENST00000355703.3:c.1922_1931del	ENSP00000347931.3:p.Leu641ProfsTer45	0.23529411
P10-Organoid	KRAS	12	25398284	C	T	Missense_Mutation	ENST00000557334.1:c.35G>A	ENSP00000452512.1:p.Gly12Asp	0.44444444
P10-Organoid	ADAMTS20	12	43828109	A	G	Missense_Mutation	ENST00000553158.1:c.2659T>C	ENSP00000448341.1:p.Cys887Arg	0.45751634
P10-Organoid	RAPGEF3	12	48151822	C	G	Missense_Mutation	ENST00000449771.2:c.46G>C	ENSP00000395708.2:p.Ala16Pro	0.50549450
P10-Organoid	ADCY6	12	49171426	T	A	Missense_Mutation	ENST00000550422.1:c.1108A>T	ENSP00000446730.1:p.Ile370Phe	0.38031914
P10-Organoid	TMEM132D	12	130184839	C	T	Missense_Mutation	ENST00000422113.2:c.484G>A	ENSP00000408581.2:p.Gly162Arg	0.02747252
P10-Organoid	AKAP6	14	33291275	G	A	Missense_Mutation	ENST00000280979.4:c.4256G>A	ENSP00000280979.4:p.Ser1419Asn	0.04838709
P10-Organoid	ATP6V1D	14	67807202	T	C	Missense_Mutation	ENST00000555474.1:c.260A>G	ENSP00000450885.1:p.Tyr87Cys	0.53658536
P10-Organoid	SAMD15	14	77845271	T	A	Missense_Mutation	ENST00000216471.4:c.1510T>A	ENSP00000216471.4:p.Leu504Ile	0.06875
P10-Organoid	NPAP1	15	24921511	C	T	Missense_Mutation	ENST00000329468.2:c.497C>T	ENSP00000333735.2:p.Pro166Leu	0.40425531
P10-Organoid	MGA	15	41988341	A	G	Missense_Mutation	ENST00000570161.1:c.1133A>G	ENSP00000457035.1:p.Asn378Ser	0.03181818
P10-Organoid	HERC1	15	63986583	C	A	Missense_Mutation	ENST00000443617.2:c.5408G>T	ENSP00000390158.2:p.Gly1803Val	0.04347826
P10-Organoid	ZSCAN32	16	3433651	A	G	Missense_Mutation	ENST00000439568.2:c.428T>C	ENSP00000391787.2:p.Val143Ala	0.43103448
P10-Organoid	ZP2	16	21213466	G	A	Missense_Mutation	ENST00000574091.1:c.1246C>T	ENSP00000458991.1:p.Arg416Trp	0.08374384
P10-Organoid	OTOA	16	21698755	G	A	Missense_Mutation	ENST00000388958.3:c.421G>A	ENSP00000373610.3:p.Asp141Asn	0.5
P10-Organoid	CNGB1	16	57996879	T	A	Missense_Mutation	ENST00000564448.1:c.380A>T	ENSP00000454633.1:p.Gln127Leu	0.37593985
P10-Organoid	RNF43	17	56436026	G	A	Nonsense_Mutation	ENST00000584437.1:c.1111C>T	ENSP00000463069.1:p.Arg371Ter	0.42391304
P10-Organoid	RNF43	17	56492894	C	T	Nonsense_Mutation	ENST00000584437.1:c.45G>A	ENSP00000463069.1:p.Trp15Ter	0.36
P10-Organoid	TANC2	17	61315295	C	G	Missense_Mutation	ENST00000424789.2:c.668C>G	ENSP00000387593.2:p.Ser223Cys	0.5
P10-Organoid	RPTOR	17	78866552	C	G	Missense_Mutation	ENST00000544334.2:c.1651C>G	ENSP00000442479.2:p.Arg551Gly	0.04347826
P10-Organoid	COLEC12	18	480713	G	A	Missense_Mutation	ENST00000400256.3:c.52C>T	ENSP00000383115.3:p.Arg18Trp	0.45725646
P10-Organoid	STARD6	18	51851163	T	C	Missense_Mutation	ENST00000581310.1:c.562A>G	ENSP00000462349.1:p.Met188Val	0.42477876
P10-Organoid	ELANE	19	856061	C	T	Missense_Mutation	ENST00000590230.1:c.701C>T	ENSP00000466090.1:p.Pro234Leu	0.42679900
P10-Organoid	DNM2	19	10940937	T	C	Missense_Mutation	ENST00000585892.1:c.2426T>C	ENSP00000468734.1:p.Ile809Thr	0.50115473
P10-Organoid	ABHD8	19	17412043	T	A	Missense_Mutation	ENST00000247706.3:c.383A>T	ENSP00000247706.2:p.Asp128Val	0.02197802
P10-Organoid	HAS1	19	52216816	C	T	Missense_Mutation	ENST00000601714.1:c.1622G>A	ENSP00000472821.1:p.Arg541His	0.40372670
P10-Organoid	LILRB1	19	55147987	GA	CC	Missense_Mutation	ENST00000434867.2:c.1690_1691delinsCC	ENSP00000405243.2:p.Glu564Pro	0.11864406
P10-Organoid	ZNFX1	20	47887343	T	C	Missense_Mutation	ENST00000396105.1:c.1006A>G	ENSP00000379412.1:p.Met336Val	0.35260115
P10-Organoid	GNAS	20	57484421	G	A	Missense_Mutation	ENST00000371102.4:c.2489G>A	ENSP00000360143.4:p.Arg830His	0.46857142
P10-Organoid	HRH3	20	60791235	C	T	Missense_Mutation	ENST00000340177.5:c.1165G>A	ENSP00000342560.5:p.Val389Ile	0.02402402
P10-Organoid	KRTAP10-6	21	46012231	G	GCT	Frame_Shift_Ins	ENST00000400368.1:c.134_135insAG	ENSP00000383219.1:p.Cys46AlafsTer9	0.00934579
P10-Organoid	MICAL3	22	18300558	C	T	Missense_Mutation	ENST00000441493.2:c.4869G>A	ENSP00000416015.2:p.Met1623Ile	0.56129032
P10-Organoid	PKDREJ	22	46657950	T	TA	Frame_Shift_Ins	ENST00000253255.5:c.1269dup	ENSP00000253255.5:p.Lys424Ter	0.47945205
P10-Organoid	PKDREJ	22	46657953	G	A	Missense_Mutation	ENST00000253255.5:c.1267C>T	ENSP00000253255.5:p.Leu423Phe	0.5
P10-Organoid	PLXNB2	22	50728527	C	T	Missense_Mutation	ENST00000449103.1:c.487G>A	ENSP00000409171.1:p.Gly163Ser	0.41922290
P10-Organoid	TBL1X	X	9656079	G	A	Missense_Mutation	ENST00000536365.1:c.227G>A	ENSP00000445317.1:p.Arg76His	0.98173516
P10-Organoid	SHROOM2	X	9905361	C	T	Missense_Mutation	ENST00000418909.2:c.280C>T	ENSP00000415229.2:p.Arg94Cys	0.06727828
P10-Organoid	RBM10	X	47045136	C	T	Nonsense_Mutation	ENST00000377604.3:c.2377C>T	ENSP00000366829.3:p.Arg793Ter	0.05166051
P10-Organoid	BRCC3	X	154299812	C	T	Nonsense_Mutation	ENST00000399042.1:c.10C>T	ENSP00000381998.1:p.Gln4Ter	1

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
P10	AZD2014	3083
P10	AZD3759	557
P10	AZD4547	~ 990709
P10	AZD5363	2469
P10	AZD6738	4181
P10	AZD9291	862.1
P10	I.BET.762	~ 1147
P10	Rapamycin..Sirolimus.	~ 8729930242763
P10	AZD1775..MK.1775.	905.9
P10	Triptolide..PG490.	1.341
P10	Simvastatin	11813
P10	Temozolomide	4.436E-66
P10	Imatinib.Mesylate..STI571.	~ 38489
P10	Pazopanib..GW786034.	~ 6232
P10	Sunitinib.Malate	~ 4393
P10	Olaparib..AZD2281..KU0059436.	~ 278.5
P10	Regorafenib..BAY.73.4506.	~ 1250
P10	Erlotinib	332.3
P10	Gefitinib	66.57
P10	Afatinib	~ 8.681e-015
P10	OTX.015	93.4
P10	BKM120..NVP.BKM120.	1981
P10	BYL719	1599
P10	Cediranib..AZD2171.	2844
P10	Ceritinib.LDK378.	1172
P10	Crizotinib...PF.02341066.	1240
P10	Dabrafenib	~ 0.000
P10	Dacomitinib	~ 5.510e-008
P10	Everolimus..RAD001.	~ 19.49
P10	Ibrutinib..PCI.32765.	1288
P10	Lapatinib	1883
P10	LY2835219	287.3
P10	Brivanib..BMS.582664.	12.04
P10	Panobinostat	~ 75.46
P10	Selumetinib..AZD6244.	400.3
P10	Sorafenib	~ 19.91
P10	Trametinib	31.08
P10	Vandetanib..ZD6474.	496
P10	Vemurafenib	~ 4668
P10	AZD5153	10.11
P10	ABT.199..GDC.0199..	~ 2.333
P10	ABT.888..Veliparib..NSC.737664.	2392
P10	Avagacestat..BMS.708163.	~ 44622608
P10	Axitinib...AG.013736.	~ 3.039e+019
P10	Bosutinib..SKI.606.	848.4
P10	Cabozantinib..XL184.	3451
P10	Dasatinib..BMS.354825.	~ 2.971e-016
P10	decitabine	2487
P10	defactinib	~ 1455
P10	Dovitinib..TKI258.CHIR258.	909.9
P10	Fluorouracil..5.Fluoracil..5.FU.	2765
P10	Foretinib..XL880.	468.8
P10	Tivantinib..ARQ.197.	421.6
P10	Abraxane	6.564
P10	AZD2461.olaparib.analog.	~ 2.302
P10	Olaparib.	887.6
P10	Idelalisib	~ 5360
P10	Irinotecan	447.5
P10	Nilotinib..AMN.107.	273106
P10	NVP.AEW541	905.7
P10	Oxaliplatin	19106
P10	PLX3397	17930
P10	Quizartinib..AC220.	11862
P10	Saracatinib..AZD0530.	1004
P10	Semagacestat..LY450139.	~ 1.135e+122
P10	TGX.221	~ 302.3
P10	tozasertib	~ 11418802317346
P10	Vorinostat..SAHA..MK0683.	3872
P10	XAV939	3884
P10	gemcitabine	916.2
P10	palbociclib	~ 17664
P10	Neratinib..HKI.272.	202.6