Supplement Fig. S1. QQ-plot for Hispanic genome wide data
Quantile-quantile (Q-Q) plot comparing the distributing of the observed versus the expected –
log10 P values (log-additive model, adjusted for age and sex) of the 634,037 SNPs. The black
line indicates distribution expected under the null hypothesis of no association and the red line
indicates the inflation of the test statistics (λ=1.02)
1
Supplement Fig. S2: Association and recombination plots for IKZF1 (7p12.2 loci) associated
with childhood ALL risk in the Hispanic population, CCLS, 1995-2008
Genotyped SNPs are represented as diamonds and a larger diamond indicated the top-hit
association in each region. The strength of linkage disequilibrium between each SNPs and the
top hit is indicated by the color of the symbol. Recombination rates, plotted in light blue, are
based on HapMap3 MEX samples, and genomic coordinates are based on National Center for
Biotechnology Information (NCBI) Build 36 of the human genome (released in March 2006).
2
Supplement Fig. S3: Association and recombination plots for ARID5B (10q21.2 loci)
associated with childhood ALL risk in the Hispanic population, CCLS, 1995-2008
Genotyped SNPs are represented as diamonds and a larger diamond indicated the top-hit
association in each region. The strength of linkage disequilibrium between each SNPs and the
top hit is indicated by the color of the symbol. Recombination rates, plotted in light blue, are
based on HapMap3 MEX samples, and genomic coordinates are based on National Center for
Biotechnology Information (NCBI) Build 36 of the human genome (released in March 2006).
3
Supplement Fig. S4: Association and recombination plots for CEBPE (14q11.2 loci)
associated with childhood ALL risk in the Hispanic population, CCLS, 1995-2008
Genotyped SNPs are represented as diamonds and a larger diamond indicated the top-hit
association in each region. The strength of linkage disequilibrium between each SNPs and the
top hit is indicated by the color of the symbol. Recombination rates, plotted in light blue, are
based on HapMap3 MEX samples, and genomic coordinates are based on National Center for
Biotechnology Information (NCBI) Build 36 of the human genome (released in March 2006).
4
Supplement Table S1: P-values for gene by environment interaction of six candidate SNPs†
and daycare attendance by age of 6 months with the risk of ALL in Hispanic Children,
CCLS, 1995-2008
Gene
SNP
CEBPE
rs4982731
CEBPE
rs17794251
ARID5B
rs4506592
IKZF1
rs4132601
IKZF1
rs6964823
IKZF1
rs4917017
a.
Censored at
Age 6 months
No
Yes
No
Yes
No
Yes
No
Yes
No
Yes
No
Yes
Cases N‡
Controls N‡
OR (95%CI)a
Pinteraction
81/198
4/30
85/194
9/25
101/175
13/21
128/151
15/19
165/104
14/20
93/186
6/28
162/237
16/22
167/231
14/24
66/333
8/30
226/173
22/16
185/214
15/23
101/298
4/34
1.64 (1.17-2.29)
6.42 (1.56-26.48)
1.65 (1.17-2.31)
2.45 (0.64-9.42)
0.35 (0.24-0.51)
0.35 (0.09-1.31)
1.55 (1.14-2.13)
2.36 (0.69-8.03)
0.59 (0.43-0.82)
0.59 (0.17-2.09)
0.69 (0.49-0.97)
0.93 (0.18-4.73)
0.07
0.99
0.70
0.71
0.61
0.99
Odds ratios (OR) and 95% confidence intervals (CI) calculated using logistic regression model adjusting for
child’s age, gender, annual household income and 5 genetic principal components (PCs).
†
Six candidate SNPs were selected from all significant SNPs using a conditional haplotype analysis.
‡
Dominant models used to provide counts of cases with wild genotype versus having any copy of minor alleles
and counts of controls with wild genotype versus having any copy of minor alleles by daycare attendance by 6
months (yes/no).
5
Supplement Table S2. P-values for gene by environment interaction of six candidate
SNPs†and daycare attendance by age one with the risk of ALL in Hispanic Children,
CCLS, 1995-2008
Gene
SNP
CEBPE
rs4982731
rs17794251
ARID5B
rs4506592
IKZF1
rs4132601
rs6964823
rs4917017
a.
Censored at
Age one
No
Yes
No
Yes
No
Yes
No
Yes
No
Yes
No
Yes
Cases N‡
Controls N‡
OR (95%CI)a
Pinteraction
78/192
7/36
81/89
13/30
98/172
12/27
123/147
20/23
162/108
17/26
91/179
8/35
153/223
25/36
155/220
26/35
65/311
9/52
216/160
32/29
175/200
24/37
94/282
11/50
1.65 (1.17-2.33)
3.08 (1.07-8.85)
1.62 (1.15-2.29)
2.12 (0.78-5.76)
0.37 (0.25-0.53)
0.26 (0.08-0.82)
1.62 (1.17-2.23)
1.32 (0.52-3.33)
0.58 (0.42-0.81)
1.13 (0.42-3.02)
0.67 (0.47-0.96)
1.29 0.42-4.02)
0.15
0.78
0.70
0.74
0.35
0.65
Odds ratios (OR) and 95% confidence intervals (CI) calculated using logistic regression model adjusting for
child’s age, gender, annual household income and 5 genetic principal components (PCs).
†
Six candidate SNPs were selected from all significant SNPs using a conditional haplotype analysis.
‡
Dominant models used to provide counts of cases with wild genotype versus having any copy of minor alleles
and counts of controls with wild genotype versus having any copy of minor alleles by daycare attendance by
one year old (yes/no).
6