Table 1 Genome-wide significant B-ALL risk loci after meta-analysis identified among African American childrena

From: Genome-wide association study of childhood B-cell acute lymphoblastic leukemia reveals novel African ancestry-specific susceptibility loci

      

Meta-analysis (n = 4200, 840 cases)

Discovery (COG) n = 3280 (656 cases)

Replication (Non-COG) n = 920 (184 cases)

1000 Genomes EAFsb

rsid

CHR

BP

EA

NEA

Closest gene

OR (95% CI)

P

OR (95% CI)

P

OR (95% CI)

P

AFR

AMR

EAS

EUR

SAS

Known loci

 rs17133807

7

50409989

A

G

IKZF1 (+4.9 kb)

1.62 (1.49-1.74)

3.3 x 10−14

1.72 (1.50-1.98)

2.1 x 10−14

1.27 (0.96-1.67)

0.093

0.16

0.23

0.11

0.32

0.29

 rs62445869c

7

50409913

A

G

IKZF1 (+4.9 kb)

1.67 (1.53-1.81)

3.4 × 10−13

1.75 (1.50-2.05)

9.5 x 10−13

1.37 (1.00-1.87)

0.046

0.09

0.23

0.10

0.32

0.29

 rs7090445

10

61961417

C

T

ARID5B (0 kb)

1.72 (1.41-2.17)

3.1 x 10−18

1.82 (1.45-2.44)

1.1 x 10−17

1.37 (1.06-1.79)

0.016

0.19

0.47

0.36

0.33

0.52

Novel loci

 rs77632976

2

34828430

T

C

FAM98A (-1229.0 kb)

1.87 (1.66-2.09)

1.0 x 10−8

1.87 (1.47-2.39)

5.3 x 10−7

1.86 (1.20-2.90)

5.8 x 10−3

0.08

*

–

–

–

 rs112113758

3

2292232

T

G

CNTN4 (0 kb)

2.09 (1.88-2.31)

1.4 × 10−11

2.20 (1.73-2.81)

1.7 x 10−10

1.75 (1.10-2.77)

0.017

0.09

0.01

–

–

–

 rs183221417

5

100102043

C

T

FAM174A (-433.3 kb)

2.94 (2.68-3.21)

1.2 x 10−15

3.04 (2.26-4.08)

1.9 x 10−13

2.60 (1.44-4.68)

1.5 x 10−3

0.06

*

–

*

–

 rs867166159

9

191139

T

G

ZNG1A (-12.0 kb)

2.69 (2.36-3.02)

2.7 x 10−9

2.51 (1.73-3.65)

1.4 x 10−6

3.36 (1.72-6.55)

3.9 x 10−4

0.05

*

–

–

–

 rs76135126

11

119033074

C

T

SLC37A4 (-2.2 kb)

2.02 (1.78-2.26)

1.1 × 10−8

2.03 (1.55-2.66)

2.5 x 10−7

1.99 (1.15-3.44)

0.014

0.08

*

–

–

–

 rs113299167

12

129961841

T

C

TMEM132D (-57.8 kb)

1.99 (1.76-2.23)

1.1 x 10−8

2.00 (1.53-2.62)

5.2 x 10−7

1.96 (1.21-3.17)

6.1 x 10−3

0.07

*

–

–

–

 rs116677565

15

24174608

C

T

NDN (-487.3 kb)

2.39 (2.08-2.69)

2.1 x 10−8

2.33 (1.63-3.33)

3.0 x 10−6

2.54 (1.41-4.58)

1.9 x 10−3

0.05

*

–

–

–

  1. rsid genetic variant identifier using dbSNP build 151, CHR chromosome, BP base position, GRCh38 (hg38) build, EA effect (risk) allele, NEA non-effect (reference) allele, EAF effect allele frequency, COG Children’s Oncology Group, OR odds ratio, CI confidence interval, P p-value. Odds ratios are from logistic regression models adjusted for the first 3 African ancestry principal components; all presented p-values are two-sided and uncorrected for multiple testing.
  2. aIncludes loci with genome-wide significant p-values (GWS P < 5 x 10−8) after meta-analysis showing associations in both datasets (discovery P < 5 x 10−6 and replication P < 0.05).
  3. bAsterisks (*) represent EAFs ≥0.001 and <0.01 and dashes (-) represent EAFs <0.001.
  4. 1Variant within a 1-Mb window closest to index with high LD (R2 = 0.71).
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