A Case-Only Genome-wide Association Study of Gender- and Age-specific Risk Markers for Childhood Leukemia

Authors

Sandeep Kumar SinghFollow

Document Type

Dissertation

Degree

Doctor of Philosophy (PhD)

Major/Program

Public Health

First Advisor's Name

Stanislaw F. Wnuk

First Advisor's Committee Title

Committee Co-Chair

Second Advisor's Name

Mehmet T. Dorak

Second Advisor's Committee Title

Committee Co-Chair

Third Advisor's Name

Wasim Maziak

Third Advisor's Committee Title

Committee Member

Fourth Advisor's Name

Helen Tempest

Fourth Advisor's Committee Title

Committee Member

Fifth Advisor's Name

Boubakari Ibrahimou

Fifth Advisor's Committee Title

Committee Member

Keywords

Genome-wide association study, Single nucleotide polymorphism, Acute lymphoblastic leukemia, Childhood Leukemia, Gender-specific, Age-specific, Case-only, Time-to-event analysis, Bioinformatics

Date of Defense

3-26-2015

Abstract

Males and age group 1 to 5 years show a much higher risk for childhood acute lymphoblastic leukemia (ALL). We performed a case-only genome-wide association study (GWAS), using the Illumina Infinium HumanCoreExome Chip, to unmask gender- and age-specific risk variants in 240 non-Hispanic white children with ALL recruited at Texas Children’s Cancer Center, Houston, Texas. Besides statistically most significant results, we also considered results that yielded the highest effect sizes. Existing experimental data and bioinformatic predictions were used to complement results, and to examine the biological significance of statistical results.

Our study identified novel risk variants for childhood ALL. The SNP, rs4813720 (RASSF2), showed the statistically most significant gender-specific associations (P < 2 x 10^-6). Likewise, rs10505918 (SOX5) yielded the lowest P value (P < 1 x 10^-5) for age-specific associations, and also showed the statistically most significant association with age-at-onset (P < 1 x 10^-4). Two SNPs, rs12722042 and 12722039, from the HLA-DQA1 region yielded the highest effect sizes (odds ratio (OR) = 15.7; P = 0.002) for gender-specific results, and the SNP, rs17109582 (OR = 12.5; P = 0.006), showed the highest effect size for age-specific results. Sex chromosome variants did not appear to be involved in gender-specific associations.

The HLA-DQA1 SNPs belong to DQA1*01:07and confirmed previously reported male-specific association with DQA1*01:07. Twenty one of the SNPs identified as risk markers for gender- or age-specific associations were located in the transcription factor binding sites and 56 SNPs were non-synonymous variants, likely to alter protein function. Although bioinformatic analysis did not implicate a particular mechanism for gender- and age-specific associations, RASSF2 has an estrogen receptor-alpha binding site in its promoter. The unknown mechanisms may be due to lack of interest in gender- and age-specificity in associations. These results provide a foundation for further studies to examine the gender- and age-differential in childhood ALL risk. Following replication and mechanistic studies, risk factors for one gender or age group may have a potential to be used as biomarkers for targeted intervention for prevention and maybe also for treatment.

Identifier

FI15032162

Recommended Citation

Singh, Sandeep Kumar, "A Case-Only Genome-wide Association Study of Gender- and Age-specific Risk Markers for Childhood Leukemia" (2015). FIU Electronic Theses and Dissertations. 1832.
https://digitalcommons.fiu.edu/etd/1832