Full-length haplotype reconstruction of CD36 by long-read sequencing

Purpose: CD36 deficiency predisposes to fetal/neonatal alloimmune thrombocytopenia (FNAIT) and platelet transfusion refractoriness (PTR), yet its genetic architecture remains incompletely understood. In particular, the contribution of large structural variants has been difficult to assess using conventional genotyping approaches. This study aimed to reconstruct full-length CD36 haplotypes using long-read sequencing and to systematically characterize its genetic architecture.Methods: We developed a long-read sequencing approach to reconstruct full-length (~77 kb) CD36 haplotypes from four overlapping amplicons. Samples from 43 CD36-deficient individuals (14 type I, 29 type II) were analyzed. Structural variants were validated via PacBio whole-genome sequencing, platelet CD36 expression was quantified by flow cytometry, and a gap-PCR assay screened 600 blood donors for large deletions.Results: Full-length CD36 haplotypes were reconstructed for the first time using overlapping amplicons. All 28 haplotypes from type I deficiency samples harbored known or novel variations, including a novel structural variant (c.1-15966_c.120 + 3887delinsCCAATGCTAAGGTTGA, 19,971 bp deletion-insertion) spanning intron 1-3 that eliminates exons 2/3 and the canonical translation initiation site. Among 58 haplotypes from type II cases, pathogenic variants were identified in only 26/58 (44.8%) (including one haplotype carrying the novel structural variant), while 32/58 (55.2%) lacked detectable variations. Gap-PCR screening revealed a 0.50% carrier frequency for this structural variant in blood donors. All heterozygous carriers showed normal platelet CD36 expression, indicating absence of haploinsufficiency.