A 3-bp deletion in the HBS1L-MYB intergenic region on chromosome 6q23 is associated with HbF expression

• Published in: Blood 2011-05, Vol.117 (18), p.4935-4945
• Main Authors: Farrell, John J., Sherva, Richard M., Chen, Zhi-yi, Luo, Hong-yuan, Chu, Benjamin F., Ha, Shau Yin, Li, Chi Kong, Lee, Anselm C.W., Li, Rever C.H., Li, Chi Keung, Yuen, Hui Leung, So, Jason C.C., Ma, Edmond S.K., Chan, Li Chong, Chan, Vivian, Sebastiani, Paola, Farrer, Lindsay A., Baldwin, Clinton T., Steinberg, Martin H., Chui, David H.K.
• Format: Article
• Language: English
• Subjects: Adult; Asian Continental Ancestry Group - genetics; Base Sequence; beta-Thalassemia - blood; beta-Thalassemia - genetics; Biological and medical sciences; Chromosomes, Human, Pair 6 - genetics; Cohort Studies; DNA Mutational Analysis; DNA Primers - genetics; DNA, Intergenic; Enhancer Elements, Genetic; Female; Fetal Hemoglobin - genetics; Gene Expression; Genes, myb; Genome-Wide Association Study; Hematologic and hematopoietic diseases; Heterozygote; Hong Kong; Humans; K562 Cells; Linkage Disequilibrium; Male; Medical sciences; Molecular Sequence Data; Polymorphism, Single Nucleotide; Quantitative Trait Loci; Red Cells, Iron, and Erythropoiesis; Sequence Deletion
• ISSN: 0006-4971; 1528-0020
• DOI: 10.1182/blood-2010-11-317081

Fetal hemoglobin (HbF) is regulated as a multigenic trait. By genome-wide association study, we confirmed that HBS1L-MYB intergenic polymorphisms (HMIP) and BCL11A polymorphisms are highly associated with HbF in Chinese β-thalassemia heterozygotes. In this population, the variance in HbF resulting from the HMIP is 13.5%; that resulting from the BCL11A polymorphism is 6.4%. To identify the functional variant in HMIP, we used 1000 Genomes Project data, single nucleotide polymorphism imputation, comparisons of association results across populations, potential transcription factor binding sites, and analysis of phylogenetic conservation. Based on these studies, a hitherto unreported association between HbF expression and a 3-bp deletion, between 135 460 326 and 135 460 328 bp on chromosome 6q23 was found. This 3-bp deletion is in complete linkage disequilibrium with rs9399137, which is the single nucleotide polymorphism in HMIP most significantly associated with HbF among Chinese, Europeans, and Africans. Chromatin immunoprecipitation assays confirmed erythropoiesis-related transcription factors binding to this region in K562 cells. Based on transient expression of a luciferase reporter plasmid, the DNA fragment encompassing the 3-bp deletion polymorphism has enhancer-like activity that is further augmented by the introduction of the 3-bp deletion. This 3-bp deletion polymorphism is probably the most significant functional motif accounting for HMIP modulation of HbF in all 3 populations.