TWAS / FUSION

Models from The Cancer Genome Atlas

Table 1: Model heritability

Heritability estimates across all genes in each cancer type. Cis-locus was defined as +/-500kb of the gene boundary. Samples were restricted to Europeans by principal components analysis. All models were adjusted for 20 gene expression PCs, 2 genetic ancestry PCs, and local structural variation estimated from a SNP array in the tumor. Heritability was estimated using GCTA/REML.

N samples: number of samples; N genes: number of converged genes with heritabiliy estimates; hsq: mean heritability estimate; hsq (se): standard error of the mean heritability estimate; hsq P<0.01: number of genes with heritability p-value < 0.01 (computed by likelihood ratio test), representing nominally predictive models.

Label	Cancer	N samples	N genes	hsq	hsq (se)	hsq P<0.01
TCGA-BLCA.TUMOR	Bladder Urothelial Carcinoma	380	16249	0.0157	0.0003	1677
TCGA-BRCA.TUMOR	Breast Invasive Carcinoma	1049	16633	0.0188	0.0003	4464
TCGA-CESC.TUMOR	Cervical Squamous Cell Carcinoma	277	16224	0.0194	0.0004	1117
TCGA-COAD.TUMOR	Colon Adenocarcinoma	275	16253	0.0275	0.0005	2098
TCGA-ESCA.TUMOR	Esophageal Carcinoma	170	16468	0.0218	0.0007	697
TCGA-GBM.TUMOR	Glioblastoma Multiforme	125	16090	0.0317	0.0007	1039
TCGA-HNSC.TUMOR	Head and Neck Squamous Cell Carcinoma	499	16586	0.0190	0.0003	2763
TCGA-KIRC.TUMOR	Kidney Renal Clear Cell Carcinoma	506	16608	0.0297	0.0005	4139
TCGA-KIRP.TUMOR	Kidney Renal Papillary Cell Carcinoma	283	16098	0.0286	0.0005	2080
TCGA-LGG.TUMOR	Brain Lower Grade Glioma	483	16695	0.0316	0.0005	4347
TCGA-LIHC.TUMOR	Liver Hepatocellular Carcinoma	352	15593	0.0213	0.0005	1121
TCGA-LUAD.TUMOR	Lung Adenocarcinoma	500	16636	0.0195	0.0003	2973
TCGA-LUSC.TUMOR	Lung Squamous Cell Carcinoma	464	16781	0.0169	0.0003	2544
TCGA-OV.TUMOR	Ovarian Serous Cystadenocarcinoma	284	16671	0.0184	0.0004	1620
TCGA-PAAD.TUMOR	Pancreatic Adenocarcinoma	172	16532	0.0325	0.0006	1685
TCGA-PCPG.TUMOR	Pheochromocytoma and Paraganglioma	175	15962	0.0291	0.0006	1342
TCGA-PRAD.TUMOR	Prostate Adenocarcinoma	468	16634	0.0366	0.0005	4675
TCGA-READ.TUMOR	Rectum Adenocarcinoma	89	15954	0.0330	0.0009	707
TCGA-SARC.TUMOR	Soft Tissue Sarcoma	249	15966	0.0159	0.0004	1091
TCGA-SKCM.TUMOR	Skin Cutaneous Melanoma	103	15538	0.0231	0.0007	541
TCGA-STAD.TUMOR	Stomach Adenocarcinoma	387	16654	0.0182	0.0004	1718
TCGA-TGCT.TUMOR	Testicular Germ Cell Tumors	149	15675	0.0304	0.0007	1296
TCGA-THCA.TUMOR	Thyroid Carcinoma	484	16454	0.0456	0.0006	5211
TCGA-UCEC.TUMOR	Uterine Corpus Endometrial Carcinoma	171	15980	0.0197	0.0007	518