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Table 3 Comparison of summary statistics imputation performance across each linkage disequilibrium panels, that PRED-LD utilizes. These results were obtained using an \(r^{2}\) threshold of 0.5 for TOP-LD and HapMap LD panels and the \({ }r^{2}\) threshold of 0.8 for Pheno Scanner, as its data inherently provide information using this \(r^{2}\) threshold. When using the HapMap LD panel, we performed imputation for each subpopulation separately based on the respective GWAS population

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

LD Panel

GWAS

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)

TOP-LD

ADHD (EUR)

243,062

0.719

0.545

39.14

6 m 1 s

1.5

UACR (EUR)

64,371

0.866

0.748

6.15

5 m 13 s

4.9

GFR (EUR)

57,200

0.674

0.625

8.97

5 m 11 s

5.4

GFR (AFR)

41,834

0.851

0.592

7.15

3 m 9 s

4.5

Epilepsy (EUR)

440,870

0.924

0.860

91.82

9 m 50 s

1.3

Colorectal Cancer (EAS)

378,395

0.823

0.772

62.68

7 m 7 s

1.1

Double Eyelid (EAS)

274,356

0.628

0.427

47.27

6 m 8 s

1.3

CAD (EUR)

682,449

0.925

0.894

77.87

12 m 21 s

1.1

Pheno Scanner

ADHD (EUR)

277,745

0.913

0.859

23.13

2 m 44 s

0.6

UACR (EUR)

53,201

0.941

0.945

6.15

2 m 3 s

2.3

GFR (EUR)

52,243

0.857

0.789

9.05

1 m 57 s

2.2

GFR (AFR)

19,155

0.876

0.756

3.44

1 m 24 s

4.4

Epilepsy (EUR)

460,371

0.942

0.894

95.06

8 m 7 s

1.1

Colorectal Cancer (EAS)

339,280

0.917

0.876

61.25

3 m 40 s

0.6

Double Eyelid (EAS)

281,966

0.803

0.661

41.81

2 m 54 s

0.6

CAD (EUR)

589,504

0.960

0.938

77.65

10 m 13 s

1.0

HapMap (CEU)

ADHD (EUR)

44,510

0.568

0.472

30.22

1 m 20 s

1.8

HapMap (TSI)

43,810

0.662

0.509

29.62

1 m 51 s

2.5

HapMap (CEU)

UACR (EUR)

7,161

0.859

0.818

2.58

1 m 20 s

11.2

HapMap (TSI)

7,061

0.545

0.816

2.74

1 m 51 s

15.7

HapMap (CEU)

GFR (EUR)

7,200

0.530

0.490

3.93

1 m 9 s

9.6

HapMap (TSI)

7,076

0.725

0.605

4.01

1 m 32 s

13.0

HapMap (ASW)

GFR (AFR)

3,799

0.586

0.527

2.15

2 m 44 s

43.2

HapMap (LWK)

3,289

0.702

0.488

1.81

2 m 18 s

42.0

HapMap (MKK)

3,694

0.642

0.463

1.98

1 m 53 s

30.6

HapMap (YRI)

3,400

0.840

0.530

1.72

1 m 27 s

25.6

HapMap (CEU)

Epilepsy (EUR)

73,686

0.745

0.673

18.48

1 m 9 s

0.9

HapMap (TSI)

73,101

0.795

0.700

18.31

2 m 17 s

1.9

HapMap (CHB)

Colorectal Cancer (EAS)

40,336

0.760

0.732

9.54

1 m 14 s

1.8

HapMap (JPT)

40,609

0.772

0.761

9.43

2 m 26 s

3.6

HapMap (CHD)

39,193

0.820

0.790

9.00

2 m 56 s

4.5

HapMap (CHB)

Double Eyelid (EAS)

42,239

0.598

0.546

19.29

1 m 13 s

1.7

HapMap (JPT)

42,829

0.624

0.543

20.20

2 m 26 s

3.4

HapMap (CHD)

41,244

0.703

0.551

18.68

2 m 54 s

4.2

HapMap (CEU)

CAD (EUR)

82,190

0.836

0.806

11.73

1 m 42 s

1.2

HapMap (TSI)

82,278

0.795

0.799

11.75

2 m 30 s

1.8

Mean performance

TOP-LD

272,817

0.801

0.683

42.63

6 m 52 s

2.6

Pheno Scanner

259,183

0.901

0.840

39.69

4 m 7 s

1.6

HapMap

34,435

0.705

0.631

11.36

1 m 54 s

11.0

All panels combined

338,803

0.817

0.728

49.90

20 m 12 s

8.2

  1. Bold values denote the average performance across the datasets
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BMC Bioinformatics

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