American Association for Cancer Research

Table 2.

Description of the prognostic germline variants identified in this study

A^a
Variant	Chrom	Pos	Ref	Alt	Population frequency	Sample size	Number of heterozygotes	Number of homozygotes	Gene name	Median expression (FPKM)	P	HR
rs61757955	17	75318086	A	G	5.01%	291	21	0	GRB2	42.2	7.08E-10	20.4
rs28672782	11	1446622	C	T	16.27%	50	15	5	BRSK2	7.29	<1E-16	1.15E-10
B^b
Variant	Chrom	Pos	Ref	Alt	Population frequency	CADD Score	PhyloP Score	Gene name	Dataset	Sample size	Number of heterozygotes	Number of homozygotes	P	HR
rs34988193	15	64943580	A	G	30.90%	32	8.42	ANKDD1a	TCGA	450	199	52	0.00113	1.73
									CGGA	76	18	2	0.0743	1.79

A^a
Variant	Chrom	Pos	Ref	Alt	Population frequency	Sample size	Number of heterozygotes	Number of homozygotes	Gene name	Median expression (FPKM)	P	HR
rs61757955	17	75318086	A	G	5.01%	291	21	0	GRB2	42.2	7.08E-10	20.4
rs28672782	11	1446622	C	T	16.27%	50	15	5	BRSK2	7.29	<1E-16	1.15E-10
B^b
Variant	Chrom	Pos	Ref	Alt	Population frequency	CADD Score	PhyloP Score	Gene name	Dataset	Sample size	Number of heterozygotes	Number of homozygotes	P	HR
rs34988193	15	64943580	A	G	30.90%	32	8.42	ANKDD1a	TCGA	450	199	52	0.00113	1.73
									CGGA	76	18	2	0.0743	1.79

^aA description of the two prognostic germline variants (FDR < 0.10) in the TCGA dataset identified when testing all 196,022 germline variants.

^bA description of the prognostic germline variant (FDR < 0.10) rs34988193 in ANKDD1a identified when the analysis was restricted to only germline variants with a combined annotation dependent depletion (CADD) score greater than 30 in the TCGA and CGGA datasets.

View Large

This Feature Is Available To Subscribers Only