In this population-based case–control study, we examined the risk of childhood ALL associated with several genes within the xenobiotic transport and metabolism pathways, utilizing a haplotype-tagging approach to maximize capture of genetic variation. We identified haplotypes of several genes that were significantly associated with childhood ALL, including ABCB1, ARNT, CYP2C8, CYP1A2, CYP1B1, and IDH1. In addition, we observed significant interactions of identified risk haplotypes with a number of self-reported household chemical exposures, including use of paints and indoor insecticides. Although confirmation is required, our findings provide evidence that genes involved in the xenobiotic transport and metabolism pathway may play a role in mediating risk of childhood ALL, and that the childhood ALL risks associated with various household chemical exposures may be modified by these variation in these genes.
A haplotype of ABCB1
, which encodes a membrane transporter of lipophilic compounds, was significantly associated with childhood ALL risk and showed significant interaction with indoor insecticides, mirroring an earlier finding utilizing different genetic variants in the same gene [31
]. Our results indicate that the increased risk associated with use of indoor insecticides before birth is limited to subjects carrying the G–A–G–T haplotype. The SNPs in this risk haplotype are 21 kb from the nearest of the 3′ SNPs examined in our previous analysis, in which no significant haplotype main effect was observed [31
]. This is in agreement with the current analysis, which also shows no main effect of haplotypes at the 3′ end of the gene.
We also found significant childhood ALL associations with haplotypes in three genes in the CYP gene family: CYP2C8
, and CYP1B1
. The CYP2C8
gene product is involved in metabolism of numerous drugs and other compounds [32
]. In addition to a significant association with childhood ALL, the risk haplotype for CYP2C8
showed significant interaction with self-reported household paint use, with the increased risk associated with paint use being limited largely to those without the CYP2C8
G–G–T–G haplotype. For the common haplotype in CYP1A2
(31.5 % frequency among controls), we found an elevated risk of childhood ALL. The SNPs composing this haplotype are outside the CYP1A2
coding region, the nearest (rs11854147) being 5.4 kb from the 3′ end. The CYP1A2
gene product metabolizes polycyclic aromatic hydrocarbons (PAHs, found in tobacco smoke and vehicle exhaust); in utero exposures to PAHs have been linked to chromosomal aberrations [33
, for which we observed a significant haplotype association with childhood ALL risk, is also involved in metabolism of PAHs, as well as steroids [34
gene product is a key transporter of PAHs and other compounds, and a transcription inducer of xenobiotic metabolism genes including CYP1A1
] that metabolize PAHs. We identified a risk haplotype for ARNT
that showed a markedly higher risk of childhood ALL. We also observed a strong haplotype association for IDH1
; a somatic mutation in IDH1
has been linked to survival in adult glioblastoma and AML [36
]. The two SNPs we examined are downstream from and in strong LD with SNPs in the IDH1
In gauging these results, consideration must be given to several factors. First, despite this study’s relatively large sample size compared to those of most previous candidate gene studies, the presence of genetic heterogeneity due to the ethnic and racial diversity of the California population may have influenced our ability to detect associations. Our SNP selection strategy included elements designed to maximize capture of genetic variation in Hispanics. We examined Hispanics separately from non-Hispanics where there was significant heterogeneity in between-group effects of individual SNPs. Although this approach may have limited our ability to detect associations in the population as a whole, we believe it was necessary given that genetic susceptibility may be different in Hispanics versus non-Hispanics due to the Hispanic population’s relatively recent genetic admixture [22
]. Results that differ between Hispanics and non-Hispanics may be due to differences in allele frequency and/or haplotype structure or may reflect underlying differences in exposures that modulate the effects of genes. Regardless, if the results are not spurious, they represent potential risk loci, and we present them in either or both ethnic groups for replication and further followup. Whereas the entire study population yielded adequate power to detect modest effect sizes (81 % power for ORlog additive
= 1.40, minor allele frequency = 20 %), power was lower among Hispanics and non-Hispanics separately (44 and 59 %, respectively). In addition, the limited size of racial/ethnic sub-populations within the non-Hispanic group precluded further stratification of this group; as such, genetic heterogeneity among non-Hispanics might have obscured results. However, we found no evidence of strong confounding due to estimated genetic ancestry [23
], minimizing concerns about the impact of population stratification on the results.
Two large genome-wide association studies on childhood ALL have been published to date (with 907 cases and 2,398 adult and child controls, and 317 cases and 17,958 adult controls, respectively) [38
]. Although these studies have identified a number of novel loci, no significant associations were observed for genes in the pathways we studied here. Null findings for these genes in the genome-wide studies may be due to stringent multiple testing adjustment (at the p
≤ 1 × 10−7
level) to account for the large number of individual variants under study. In contrast to the agnostic approach to discovery used in genome-wide studies, our study focused on relatively few genes representing key elements of the xenobiotic transport and metabolism pathways. We concede that results of our study may be due to chance and therefore must be replicated. However, the haplotype-tagging approach we adopted maximizes capture of total variation within each candidate gene and the haplotype analysis increases statistical power to detect associations over analyses of individual variants. Furthermore, although the haplotype-tagging approach does not pinpoint potential causal SNPs, it does localize risk-associated regions for further investigation such as fine-mapping.
In this study, we examined potential interactions of xenobiotic transport and metabolism genes with self-reported household chemical exposures early in childhood in the modulation of childhood ALL risk, focusing on haplotype findings observed for both ethnicities (Hispanics and non-Hispanics) combined, as the sizes of the individual ethnic groups were considered too small to permit adequately powered examinations of gene–environment interactions. Our observation that the increased risk associated with paint and indoor insecticide use [5
] was limited to specific subgroups defined by haplotypes of specific genes is suggestive that these genes work in concert with chemical use to modulate risk. Although we focused on a limited number of biologically plausible interactions according to a rigorous a priori analysis plan, we acknowledge that this analysis might be considered exploratory. As such we report only those interactions that were significant after accounting for multiple hypothesis testing. We recognize that our total sample size (377 cases, 448 controls) may be insufficient to observe modest interaction effects with adequate statistical power. Furthermore, although the environmental chemical exposures we examined have been previously associated with childhood leukemia risk [5
], these measures are derived from maternal self-reports, which are prone to reporting errors and recall bias in that mothers of cases may recall exposures differently than mothers of controls. Since this study was population-based with participation rates of 86–87 % and biospecimen collection rates >95 % for interviewed subjects, it is unlikely the results presented here are driven by bias in selection or participation. Further studies with improved measures of chemical exposure are needed to confirm the interactions observed.
In summary, we set out to investigate the role of genes in the xenobiotic transport and metabolism pathway in risk of childhood ALL in greater depth and with larger sample size than previous candidate gene studies. We also sought to examine the putative joint effects of these genes with environmental chemical exposures for which we have observed significant main effects. Our results provide evidence that elements of the xenobiotic transport and metabolism pathway may be associated with childhood ALL, and that some of these elements interact with chemical exposures to modulate risk. This study does not address the potential effects of maternal genes, which may influence in utero susceptibility to chemical exposures. The associations and interactions identified should be considered targets for further study in additional studies, with larger sample sizes, high quality environmental exposure data, maternal genes, and finer coverage of SNPs in the identified associated regions.