Table 1 Replication of prior GWAS findings in pathways.

From: UACA locus is associated with breast cancer chemoresistance and survival

Publication ID (Year)

GWAS variants

Original GWAS

Replication in pathwaysξ

rsID

Chr

Position

Alleles (Ref/Alt)

Patient population

Events

Ntotal

Nevent

P-value¥

HR

Effect allele

EAF

Ntotal

Nevent

P-value

HR

Effect allele

EAF§

Rsq

31949161 (2020)

rs6990375

8

70,571,531

G/A

EUR, ER+

BCSD (censored at 10 years)

55,701

2854

6.35E−09

   

2404

107

0.76

0.96

A

0.294

Genotyped

31904872 (2020) €

rs1401069

3

116,279,888

T/G

EAS, ER+

Death, recurrence

953

159

5.29E−07

>1

T

 

372

55

0.61

1.23

G

0.931

0.99456

rs76462307

1

168,539,377

G/A

1.17E−06

2.01

A

 

0.17

1.5

A

0.155

0.92452

rs1560409

11

121,160,060

C/G

2.17E−06

>1

C

 

0.34

0.83

G

0.614

0.98566

rs2178052

6

46,541,231

G/A

5.47E−06

>1

A

 

2.69E−02

0.55

A

0.219

0.99824

rs1024176†

1

168,526,103

G/A

2.43E−05

1.67

G

 

0.72

0.93

G

0.373

0.99947

30787463 (2019)

rs4717568

7

70,400,700

T/C

EUR, ER+

BCSD (censored at 15 years)

64,171

4116

1.28E−07

0.88

T

0.62

2404

113

0.29

0.86

T

0.412

0.99081

rs67918676

7

27,445,956

A/AT

EUR, ER−

16,172

2125

1.38E−07

1.27

A

0.12

Absent in pathways

rs370332736

6

50,395,136

AACTT/A

EUR

96,661

7697

2.48E−07

1.16

A

0.09

Absent in pathways

29158497 (2017)

rs715212

9

18,786,181

A/C

EUR, ≤40 years at diagnosis

Death, recurrence

2172

642

5.37E−08

1.38

C

0.27

67

12

0.16

2.03

C

0.258

0.98589

25890600 (2015)

rs2059614

11

125,259,424

A/G

EUR, ER-

BCSD (censored at 10 years)

6881

920

1.30E−09

1.90

G

0.06

393

48

0.53

1.26

G

0.073

Genotyped

rs148760487

2

163,778,613

A/G

EUR

37,954

2900

1.50E−08

1.88

G

0.01

2798

155

0.92

0.95

G

0.013

0.97587

rs7149859

14

68,066,489

G/T

EUR, ER+

23,059

1333

7.00E−07

1.22

  

2404

107

0.50

1.10

T

0.444

0.98762

25964295 (2015)

rs8113308

19

52,445,386

T/C

EUR, ER+ with endocrine treatment

BCSD (censored at 10 years)

3682

 

6.34E−07

1.69

C

0.152

2117

95

0.06

0.62

C

0.139

0.9974

25867717 (2015)

rs166870

15

80,069,762

T/C

EAS, HR+ HER2−

Recurrence, 2nd cancer

1902

159

2.88E−07

2.3

T

0.13, 0.87

306

59

0.11

1.45

T

0.165

0.97658

rs10825036

10

55,266,231

T/G

EAS, HR− HER2−

554

100

3.54E−07

2.26

G

0.32, 0.29

37

3

NA

NA

G

0.298

0.98285

25526632 (2014)

rs421379

5

91,275,313

T/C

EUR

BCSD (censored at 10 years)

2756

758

1.10E−06

1.49

T

0.08

2797

155

0.92

1.02

T

0.069

Genotyped

rs12358475

10

11,848,792

G/A

1.80E−06

0.75

A

0.23

0.85

1.02

A

0.241

Genotyped

rs1728400

16

86,434,446

C/A

5.60E−06

1.25

 

0.38‡

0.38

0.90

A

0.451

Genotyped

23319801 (2013)

rs421379

5

91,275,313

T/C

EUR, ≤40 years at diagnosis

BCSD

2052

704

9.50E−07

1.61

T

0.05‡

109

9

1.45E−02

5.93

T

0.069

0.99962

rs1387389

1

164,689,762

G/A

3.80E−06

1.28

 

0.36‡

0.85

0.91

A

0.313

Genotyped

rs3884558

15

61,702,779

A/G

3.90E−06

1.46

 

0.07‡

NA

NA

G

0.910

Genotyped

rs2774307

1

114,670,969

A/G

7.90E−06

1.30

 

0.26‡

0.17

2.36

G

0.742

0.93071

rs3785982

17

9,090,224

C/T

7.90E−06

1.40

 

0.12‡

0.92

1.07

T

0.099

Genotyped

22232737 (2012)

rs3784099

14

68,749,927

G/A

EAS

Death

6110

719

1.17E−07

1.49

A

0.13

449

40

0.37

0.65

A

0.092

Genotyped

rs9934948

16

73,439,355

C/T

EAS

5.75E−06

1.29

C

0.46

0.10

0.68

C

0.464

Genotyped

EUR

1145

229

6.00E−03

3.27

C

0.84

2798

464

0.83

0.98

C

0.852

Genotyped

  1. One GWAS study (PubMed ID: 20332263) was not included as no significant variant was identified in the study.
  2. ¥P-values at or close to genome-wide significance (\(P < 5 \times 10^{ - 8}\)) were in bold.
  3. ξReplication in Pathways matched the setting reported in the original GWAS, including survival outcomes, patient population, and adjusted covariates.
  4. §The EAF was calculated in the whole Pathways EAS or EUR cohort.
  5. €Although the risk alleles of the four GWAS variants were not given in the publication, we were able to identify them using the accompanying genotyping and clinical data provided by the publication (see "Methods" section).
  6. †The causal variant claimed in the study for the chromosome 1 locus where the lead GWAS variant is rs76462307.
  7. ‡Only MAF was reported in the corresponding paper.
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