A Multi-locus Approach to Characterization of Major Quantitative Trait Loci Influencing Hb F Regulation in Chinese β-thalassemia Carriers

Abstract

Genetic association studies showed that Hb F is under the influence of major quantitative trait loci (QTL) in β-thalassemia (β-thal) carriers. Single nucleotide polymorphisms (SNPs) at three major QTLs, BCL11A, HBS1L-MYB intergenic region and XmnI-HBG2 were individually validated in univariate models. However, their relative effect sizes on Hb F regulation are unknown. We genotyped 99 Chinese β-thal carriers for the three major QTLs and performed genetic association studies using three different statistical models, including mass univariate analysis, multivariate linear regression and partial least square regression structural equation modeling (PLS-SEM). Performances of the three models were compared and effect sizes of the three QTLs in a multivariate model were assessed. Traditional mass univariate analysis and multivariate linear regression showed limited statistical power in our small cohort and the latter was constrained by multicollinearity. Partial least structural equation modeling showed significant positive associations of each QTL (p <0.05) with Hb F regulation, together explained 34.4% of variance. The HBS1L-MYB intergenic region polymorphism (HMIP) demonstrated the highest effect on Hb F prediction with effect size f² 0.294. PLS-SEM offered a statistically powerful multivariate model for multi-locus genetic association studies. We reproduced findings of previous studies with a much smaller cohort and demonstrated HMIP as the strongest regulator of Hb F in Chinese β-thal carriers.

Keywords:

• β-Thalassemia (β-thal)
• fetal hemoglobin (Hb F)
• partial least square (PLS)
• quantitative trait loci (QTL)
• structural equation modeling (SEM)

Acknowledgments

We thank Ms. L.P. Chan and Ms. Connie M.L. Wong (Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, Hong Kong) for sample collection. We also express our gratitude to Dr. Radha Raghupathy and Dr. Frankie K.F. Mo (Department of Clinical Oncology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong), for advice on statistical analysis. NCC wrote the article and performed the statistical analysis. KML and KCC performed molecular analysis. NPC and MHN criticized and improved the article. MHN was the principal investigator.

Disclosure statement

The authors report no conflicts of interest. The authors alone are responsible for the content and writing of this article.

Funding

This study was supported by a donation from the Children’s Thalassemia Foundation, Hong Kong [2009/01].