Mapping long-read sequences to a complete reference genome reveals uncaptured variants across the β-Globin cluster in Africans with sickle cell disease

Abstract

Summary African genomes are marked by extensive complexity in the number and distribution of variants yet remain under-represented in genetic databases and the human reference genome. This gap in representation limits the broad application of genomic medicine. Sickle cell disease (SCD)—one of the most common monogenic diseases—has its highest prevalence in Africa, and variation in disease severity has consistently been linked to the β-globin locus, including levels of fetal hemoglobin (HbF). Modulation of HbF is central to current SCD gene therapies; however, the inherent complexity and variation at the locus in African genomes present a challenge to translating these advances to Africa. Here, we align single-molecule long-read sequencing (LRS) targeted to the β-globin region to the human genome build 38 (hg38) and telomere-to-telomere (T2T)-CHM13.v2 genome references in 40 individuals with SCD, predominantly recruited from three African countries. We demonstrate that the expanded T2T-CHM13.v2 reference sequence at this locus reduces structural variant (SV) calls by 70% and uncovers uncaptured single-nucleotide variants (SNVs). Across the cluster, we report 343 SVs and 196 SNVs that have not been previously reported, including in LRS data from the All of Us project. By including African populations from ethnolinguistic groups that have not been previously surveyed, we improve variant resolution and bolster evidence for observed variation. Finally, we identify a common ∼4 kb insertion locus overlapping the HBB promoter among individuals with high HbF. These results demonstrate the utility of combining a comprehensive reference genome with LRS in African populations to uncover genomic variation at disease-associated loci.