PRED-LD: efficient imputation of GWAS summary statistics

Manios, Georgios A.; Michailidi, Aikaterini; Kontou, Panagiota I.; Bagos, Pantelis G.

doi:10.1186/s12859-025-06119-y

BMC Bioinformatics

Table 4 Comparison of the performance of the summary statistics imputation methods across the GWAS datasets

From: PRED-LD: efficient imputation of GWAS summary statistics

GWAS	Tool	Imputed SNPs	\(R^{2}\)(z)	\(R^{2}\left( { - \log_{10} \left( p \right)} \right)\)	Imputation percentage in masked SNPs	Time	Time per 1000 SNPs imputed (s)
ADHD (EUR)	PRED-LD	345,047	0.701	0.583	1,894/3,791 = 49.96%	21 m 37 s	3.8
	RAISS	213,003	0.576	0.366	1,504/3,791 = 39.67%	7 m 57 s	2.2
	DIST	737,618	0.558	0.402	3,784/3,791 = 99.81%	33 m 6 s	2.7
	SSIMP	1,875,319	0.614	0.452	3,763/3,791 = 99.26%	126 m 6 s	4.0
	FAPI	262,431	–	0.761	949/3,791 = 25.03%	146 m 45 s	33.5
UACR (EUR)	PRED-LD	91,989	0.885	0.874	166/1,819 = 9.12%	14 m 56 s	9.7
	RAISS	30,052	0.836	0.853	80/1,819 = 4.39%	7 m 24 s	14.7
	DIST	742,568	0.245	0.348	620/1,819 = 34.08%	25 m 1 s	2.0
	SSIMP	1,879,310	0.198	0.195	1,256/1,819 = 69.04%	117 m 54 s	3.8
	FAPI	47,068	–	0.947	90/1,819 = 4.94%	139 m 10 s	177.4
GFR (EUR)	PRED-LD	84,689	0.723	0.683	165/1,270 = 12.99%	14 m 20 s	10.2
	RAISS	24,284	0.853	0.826	69/1,270 = 5.43%	7 m 15 s	17.9
	DIST	742,593	0.185	0.171	639/1,270 = 50.31%	25 m 5 s	2.0
	SSIMP	1,879,896	0.145	0.070	1,111/1,270 = 87.48%	116 m 38 s	3.7
	FAPI	44,498	–	0.899	84/1,270 = 6.61%	139 m 10 s	187.6
GFR (AFR)	PRED-LD	51,633	0.838	0.585	98/1,160 = 8.44%	29 m 16 s	34.0
	RAISS	6,465	0.405	0.121	18/1,160 = 1.55%	9 m 27 s	87.7
	DIST	743,044	0.068	0.022	527/1,160 = 45.43%	9 m 17 s	0.8
	SSIMP	3,245,785	0.210	0.070	1,139/1,160 = 98.18%	153 m 50 s	2.8
	FAPI	47,232	–	0.514	83/1,160 = 7.15%	164 m 44 s	209.3
Epilepsy (EUR)	PRED-LD	516,837	0.927	0.873	72,589/73,759 = 98.41%	15 m 24 s	1.8
	RAISS	148,826	0.872	0.737	54,835/73,759 = 74.34%	60 m 22 s	24.3
	DIST	451,355	0.943	0.889	71,503/73,759 = 96.94%	232 m 28 s	30.9
	SSIMP	1,627,415	0.945	0.892	73,109/73,759 = 99.11%	1,096 m 24 s	40.4
	FAPI	182,768	–	0.922	66,251/73,759 = 89.82%	131 m 21 s	43.1
Colorectal Cancer (EAS)	PRED-LD	473,097	0.862	0.815	12,658/17,240 = 73.42%	9 m 15 s	1.2
	RAISS	240,299	0.877	0.770	8,839/17,240 = 51.27%	10 m 2 s	2.5
	DIST	689,032	0.759	0.506	14,028/17,240 = 81.36%	93 m 50 s	8.2
	SSIMP	1,783,481	0.850	0.787	16,512/17,240 = 95.77%	185 m 1 s	6.2
	FAPI	312,408	–	0.912	10,851/17,240 = 62.94%	92 m 6 s	17.7
Double Eyelid (EAS)	PRED-LD	367,707	0.664	0.499	4,709/7,820 = 60.21%	7 m 48 s	1.3
	RAISS	238,279	0.705	0.470	4,418/7,820 = 56.49%	7 m 53 s	2.0
	DIST	716,061	0.552	0.282	7,261/7,820 = 92.85%	64 m 20 s	5.4
	SSIMP	1,810,525	0.815	0.684	7,775/ 7,820 = 99.42%	183 m 27 s	6.1
	FAPI	279,728	–	0.760	3,437/7,820 = 43.95%	135 m 29 s	29.1
CAD (EUR)	PRED-LD	779,429	0.935	0.908	120,683/139,282 = 86.64%	49 m 2 s	3.8
	RAISS	139,507	0.892	0.812	74,897/139,282 = 53.77%	112 m 44 s	48.5
	DIST	251,662	0.905	0.872	112,862/139,282 = 81.03%	135 m 10 s	32.2
	SSIMP	1,450,754	0.867	0.835	136,174/139,282 = 97.76%	1,877 m 55 s	77.7
	FAPI	170,791	–	0.239	98,148/139,282 = 70.46%	142 m 7 s	49.9
Mean performance	PRED-LD	338,803	0.817	0.728	49.90%	20 m 12 s	8.2
	RAISS	130,089	0.752	0.619	35.86%	27 m 53 s	25.0
	DIST	634,241	0.527	0.436	72.72%	76 m 15 s	10.5
	SSIMP	1,944,061	0.581	0.498	93.25%	428 m 9 s	18.1
	FAPI	168,365	–	0.744	38.86%	136 m 21 s	93.5

Bold values denote the average performance across the datasets

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