Long-read Sequences Mapped to a Complete Reference Genome Uncover Uncaptured Structural Variants across the Beta-globin Cluster in Africans with Sickle Cell Disease

HBB

Resolution of the beta-globin cluster by long-read sequencing aligned to the complete T2T-CHM13v2 reference, uncovering structural variants missed on hg38

Forty individuals with sickle cell disease, recruited mainly from three African countries, underwent long-read sequencing targeted to the beta-globin region and aligned to both hg38 and the complete T2T-CHM13v2 reference. Using the T2T reference reduced structural variant calls at this locus by 70% and uncovered previously masked single nucleotide variants. In total, 343 structural variants and 196 single nucleotide variants not previously reported were described, including relative to All of Us long-read data. Including African ethnolinguistic groups never previously surveyed improved variant resolution. A common ~4 kb insertion overlapping the HBB promoter was found among individuals with high fetal haemoglobin.

Synthesis written by Geno'X. For the full original abstract, please refer to the source publication.

The number to remember is that 70% reduction in structural variant calls: much of what hg38 makes callable at this locus is a reference artefact, which should make anyone cautious about structural variants interpreted in complex regions without T2T. The link between the ~4 kb insertion at the HBB promoter and fetal haemoglobin remains an association in a small sample, but it bears directly on the target of current sickle cell gene therapies. Above all, this work is a reminder that under-representation of African genomes is a concrete technical problem, not only a question of equity.

Analysis by Dr Thibaut Benquey