Table 2 B-ALL risk variant associations in African American children, stratified by correspondent local African ancestry haplotypes

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

 

0 local African ancestry haplotypes

1 local African ancestry haplotype

2 local African ancestry haplotypes

rsid

EAF in cases (n)

EAF in controls (n)

OR

P

EAF in cases (n)

EAF in controls (n)

OR

P

EAF in cases (n)

EAF in controls (n)

OR

P

Known loci

 rs17133807

0.39 (69)

0.28 (275)

1.65 (1.11-2.46)

0.013

0.29 (332)

0.22 (1172)

1.46 (1.2-1.77)

1.4 x 10−4

0.25 (439)

0.16 (1913)

1.72 (1.44-2.06)

2.5 x 10−9

 rs7090445

0.46 (67)

0.38 (258)

1.47 (0.97-2.22)

0.070

0.40 (319)

0.26 (1227)

1.97 (1.62-2.39)

6.9 x 10−12

0.26 (454)

0.18 (1875)

1.59 (1.34-1.88)

1.2 x 10−7

Novel loci

 rs77632976

0 (71)

0 (311)

–

–

0.06 (327)

0.04 (1060)

1.79 (1.20-2.69)

4.7 x 10−3

0.10 (442)

0.05 (1989)

1.96 (1.51-2.53)

3.0 x 10−7

 rs112113758

0 (62)

<0.01 (368)

–

–

0.06 (322)

0.03 (1042)

1.95 (1.26-3.01)

2.6 × 10−3

0.11 (456)

0.06 (1950)

2.13 (1.66-2.73)

2.6 x 10−9

 rs183221417

0 (86)

0 (337)

–

–

0.03 (283)

0.02 (1102)

1.81 (0.99-3.32)

0.054

0.09 (471)

0.03 (1921)

3.36 (2.49-4.53)

2.1 x 10−15

 rs867166159

0 (70)

0 (233)

–

–

0.03 (283)

0.01 (1189)

4.28 (1.99-9.17)

1.9 x 10−4

0.05 (487)

0.02 (1938)

2.44 (1.7-3.51)

1.5 x 10−6

 rs76135126

0 (63)

0 (270)

–

–

0.04 (301)

0.03 (1032)

1.43 (0.85-2.40)

0.17

0.09 (476)

0.04 (2058)

2.28 (1.73-3.01)

6.5 x 10−9

 rs113299167

0 (77)

0 (292)

–

–

0.04 (252)

0.01 (1064)

3.70 (1.97-6.96)

4.7 x 10−5

0.09 (511)

0.05 (2004)

1.78 (1.37-2.30)

1.2 x 10−5

 rs116677565

0.01 (70)

<0.01 (323)

–

–

0.04 (343)

0.01 (1178)

3.18 (1.85-5.46)

2.8 × 10−5

0.05 (427)

0.02 (1859)

2.17 (1.49-3.15)

4.9 x 10−5

  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) allel, EAF effect allele frequency, COG Children’s Oncology Group, OR, odds ratio, CI confidence interval, P p-value. Subgroup 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.
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