Table 1 Lead SNPs near SP4, 8q24, and IKZF3 reaching genome-wide significance in discovery analyses of CCRLP acute lymphoblastic leukemia patients, including replication analyses in the Children’s Oncology Group and the California Childhood Leukemia Study Latino Participants

From: GWAS in childhood acute lymphoblastic leukemia reveals novel genetic associations at chromosomes 17q12 and 8q24.21

 

SP4—rs2390536 risk allele Aa

8q24.1—rs4617118 risk allele Gb

IKZF3—rs2290400 risk allele Tc

 

RAFd

P value

OR (95% CI)

RAFa

P value

OR (95% CI)

RAFa

P value

OR (95% CI)

CCRLP meta-analysise

 

3.59 × 10 −8

1.20 (1.13–1.29)

 

3.05 × 10 −9

1.27 (1.17–1.38)

 

2.05 × 10 −8

1.18 (1.11–1.25)

 CCRLP Latinos

0.26

1.42 × 10−4

1.19 (1.09–1.31)

0.15

2.90 × 10−5

1.25 (1.12–1.38)

0.57

4.33 × 10−6

1.20 (1.11–1.30)

 CCRLP Whites

0.35

5.69 × 10−5

1.23 (1.11–1.35)

0.18

1.74 × 10−3

1.26 (1.09–1.45)

0.50

2.72 × 10−3

1.15 (1.05–1.26)

 CCRLP African Americans

0.22

0.73

1.07 (0.73–1.58)

0.23

1.55 × 10−3

1.54 (1.18–2.01)

0.52

0.18

1.19 (0.92–1.53)

Replication meta-analysis

 

0.075

1.10 (0.99–1.23)

 

1.29 × 10 −4

1.30 (1.14–1.49)

 

0.013

1.14 (1.03–1.26)

 COG Replication (European)

0.36

0.025

1.15 (1.018–1.31)

0.17

0.011

1.22 (1.05–1.43)

0.45

0.13

1.10 (0.97–1.25)

 CCLS Replication (Hispanic)

0.2133

0.74

0.96 (0.77–1.20)

0.1069

1.03 × 10−3

1.58 (1.20–2.07)

0.6135

0.030

1.22 (1.02–1.46)

Combined datasets

 

1.77 × 10 −8

1.18 (1.11–1.24)

 

1.76 × 10 −12

1.28 (1.19–1.37)

 

1.06 × 10 −9

1.17 (1.11–1.23)

  1. RAF risk allele frequency, CCLS California Childhood Leukemia Study, CCRLP California Cancer Records Linkage Project, COG Children’s Oncology Group.
  2. Bold values indicate P values lower than genome-wide significance (P<5 × 10−8) for CCRLP GWAS and combined datasets, and nominal significance (P<0.05) for replication meta-analysis.
  3. a Rs2390536 was genotyped “on array” for all sample sets apart from COG Replication (Imputed INFO score = 0.99)
  4. b rs4617118 was genotyped “on array for CCRLP datasets, and imputed for COG Replication (INFO = 0.96) and CCLS Replication (INFO = 0.88)
  5. c rs2290400 was genotyped “on array” for all sample sets apart from COG replication (INFO = 0.88)
  6. d RAF calculated among ethnicity-matched controls
  7. e Sample sizes for all analyses: CCRLP Latinos: 1949 cases, 8584 controls; CCRLP whites: 1184 cases, 3551 controls; CCRLP African Americans: 130 cases, 3842 controls. For the replication: COG: 959 cases, 2624 controls; CCLS: 530 cases and 511 controls
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