Abstract A079: The impact of Indigenous American ancestry on the risk of acute lymphoblastic leukemia and the implications for future study designs
Authors: Langie Jalen , Morimoto Libby , Ma Xiaomei , Metayer Catherine , Wiemels Joseph L. , de Smith Adam J. , Chiang Charleston W.K. 
Published: September 2024

Acute lymphoblastic leukemia (ALL) is the most common childhood cancer, with Hispanic/Latino (H/L) children having up to 1.4 times the rate of ALL compared to their non-Hispanic White counterparts. This disparity has not been fully explained by environmental factors, suggesting the role of understudied genetic variants, particularly ones found in Indigenous American (IA) ancestry inherited by Latinos. In this study, we characterized the impact of IA ancestry on the frequency and effect size of known ALL risk alleles. We found that elevated risk of ALL in Latinos may be conferred by increased frequency of risk alleles due to IA ancestry. For instance, in an analysis of Latinos from the California Cancer Linkage Project (CCRLP; 1,930 cases, 2,103 controls) and the California Childhood Leukemia Study (CCLS; N = 605 cases, 515 controls), we found that, across independent known ALL loci (N=21), more loci than expected by chance showed a significant association between IA ancestry and increasing risk (p = 0.015). Compared to randomly-sampled, frequency-matched alleles from the genome, the risk alleles at all known ALL loci also showed a significant association with IA ancestry (46.9 % for known risk alleles vs. 43.5 % for matched alleles; ). The IA haplotype had 1.39 times the odds (95% CI: 1.35 – 1.43; ) of harboring the risk allele compared to the non-IA haplotype. Conversely, in a combined Latino sample of 2,535 cases and 9,035 controls, we found no evidence of GxAncestry interaction on ALL risk across all known loci (min P = 0.0026, prior to adjusting for multiple testing), suggesting that ALL risk alleles do not have increased effects on the IA ancestry background. This lack of synergism between local ancestry and genotype in ALL has methodological implications for gene discovery in admixed populations. To explore this, we implemented Tractor, a method that models genotype effects by ancestry, and thus is best powered in the presence of effect size heterogeneity by ancestry. Across known loci, we found that Tractor had 36.1% decreased power compared to standard GWAS. Taken together, our results suggest that the disproportionate burden of ALL in Latino populations may arise from the enrichment of risk alleles within the IA ancestry component, possibly driven by immunity- related selective pressures. Finally, future genetic studies of ALL in Latino patients may benefit from methods that incorporate contributions from ancestry to increase the statistical power in identifying associations, rather than leverage effect size heterogeneity across ancestries.

Citation Format: Jalen Langie, Libby Morimoto, Xiaomei Ma, Catherine Metayer, Joseph L. Wiemels, Adam J. de Smith, Charleston W.K. Chiang. The impact of Indigenous American ancestry on the risk of acute lymphoblastic leukemia and the implications for future study designs [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr A079.