. 2022 Aug 24;14(17):4090. doi: 10.3390/cancers14174090

Table 1.

Overview of genomic and epigenomic analyses of PDOs.

Cancer Type	Ref.	Species	Method	Sample No.	Major Subtypes /Classifications	Correlation with Drugs
Breast cancer	[7]	Human	WGS	101	PAM50, SCMGENE/SCMOD1, ER−/HER2−, HER+	Afatinib, Gefitinib, Pictilisib, GDC-0068, AZD8055, Everolimus, and Tamoxifen
Breast cancer	[7]	Human	RNA-seq	22	PAM50, SCMGENE/SCMOD1, ER−/HER2−, HER+
Bladder cancer	[3]	Human	WES	24	Basal, luminal	26 chemicals
Bladder cancer	[3]	Human	RNA-seq	42	Basal, luminal	26 chemicals
Colorectal cancer	[5]	Human	WES	43	Adenoma, serrated, MSS, MSI, and NEC	A83-01, SB202190
	[5]	Human	Target-seq	19	Adenoma, serrated, MSS, MSI, and NEC	A83-01, SB202190
	[8]	Human	WES	41	Hypermutated, non-hypermutated	17-AAG, 5-FU, Cetuximab, GDC0941, Gemcitabine, MK-2206, Nutlin-3a, NVP-BEZ235, and SCH772984
	[8]	Human	RNA-seq	108	Hypermutated, non-hypermutated
	[9]	Human	WGS	3	-	5-FU
	[10]	Human	WGS	73	BRAF/ACVR2A, APC/TP53, KRAS/APC	Doxorubicin, SN38, 5-FU, Afatinib, Nutilin3a
			RNA-seq	76
			HM450K	70
	[11]	Human	WGS	30	WT and mutant MLH-1	Y-27632
	[12]	Mouse	Bisulfite Pyro-seq	8	BRAF^V600E	IWP-2, IWR-1-endo, and CCT031374
	[13]	Human	WGS	6	KRAS^G12D, APC^KO, P53^KO, SMAD4^KO	Gefitinib, Noggin, A83-01. and SB202190
Epithelial ovarian cancer	[14]	Human	WGS	36	HR-proficient, TP53, BRAF, KRAS, NRAS, XIAP, and CDKN2a	Alpelisib, Adavosertib, Afatinib, AZD8055, Carboplatin, Gemcitabine, MK-2206, Niraparib, Olaparib, Plitaxel, Pictilisib, Rucaparib, Vemurafenib, Flavopiridol, Cobimetinib
	[15]	Mouse	WGS	12	Trp53^−/−; Ccne1^OE; Akt2^OE; Kras^OE, Trp53^−/−; Brca1^−/−; Myc^OE, and Trp53^−/−; Pten^−/−; Nf1^−/−	Rucaprib, Niraparib, Olaparib, Gemcitabine, Doxorubicin, Paclitaxel, Carboplatin, Seliciclib, PHA767491, BAY1895344, Chloroquine
	[15]	Mouse	RNA-seq	12
	[16]	Human	WES	34	BRCA1/2	Carboplatin, Olaparib, Prexasertib, and VE-822
ESCC	[17]	Mouse	WES	58	-	ADAR1 inhibitor
			RNA-seq	14
			ChIP-seq	44
			ATAC-seq	8
Gastric cancer	[18]	Human	WGS	3	MSI- and EBV-type	YM-155
	[18]	Human	RNA-seq	6	MSI- and EBV-type	YM-155
	[19]	Human	WES	46	CIMP+, CIMP−, and normal/normal like	Y-27632, EGFR/ErbB-2/ErbB-4 inhibitor, Nutlin-3, Crizotinib, and C59
			GEM	62
			EPIC array	51
	[20]	Mouse	WES	6	WT and mutant TP53	AZD7762, Prexasertib
	[20]	Mouse	RNA-seq	20	WT and mutant TP53	AZD7762, Prexasertib
HNSCC	[6]	Human	WES	24	-	Cetuximab, Cisplatin, Alpelisib, Vemurafenib, Everolimus, Nutlin-3 and AZD4547
HNSCC	[6]	Human	RNA-seq	16	-
Pediatric kidney cancer	[1]	Human	WGS	59	Wilms tumor, malignant rhabdoid tumor, renal cell carcinoma, congenital mesoblastic nephromas	Vincristine, Actinomycin D, Doxorubicin, Etoposide, Panobinostat, Romidepsin, PD-0325901, Idasanutlin
			RNA-seq	51
			EPIC array	45
Pancreatic cancer	[21]	Human	WGS	35	Classical-like, basal-like, classical-progenitor, Glycomet	283 epigenetic-related chemicals, 5 chemotherapeutic drugs
			RNA-seq	87
			ATAC-seq	44
	[2]	Human	WGS	22	Classic, basal-like, or C1, C2	Afatinib, Gemcitabine, Paclitaxel, SN-38, 5-FU, and Oxaliplatin
			WES	69
			RNA-seq	49
	[22]	Human	WES	48	WNT−, WNT+, WRi	A83-01, SB202190, Nutlin-3, and C59
			GEM	18
			EPIC array	25
Prostate cancer	[23]	Human	WES	7	TMPRSS2-ERG fusion, SPOP mut, SPINK1 overexpression, and CDH1 Loss	Enzalutamide, Everolimus, and BKM-120
Prostate cancer	[23]	Human	RNA-seq	7		Enzalutamide, Everolimus, and BKM-120
RB	[24]	Human	RNA-seq	8	-	R406, Bay61-3606, and Rapamycin
RB	[24]	Human	WGBS	8	-	R406, Bay61-3606, and Rapamycin

ESCC, esophageal squamous cell carcinoma; GEM, gene expression microarray; HNSCC, head and neck squamous cell carcinomas; No, number; Ref, Reference; RB, retinoblastoma; WT, wild type; WRi, Wnt, and R-spondin-independent; CIMP, CpG island methylator phenotype; WGS, whole-genome sequencing; WES, whole-exome sequencing; WGBS, whole-genome bisulfate sequencing; HM450K, Infinium HumanMethylation450 BeadChip; EPIC array, Infinium MethylationEPIC Kit.