Long-read sequencing identifies single nucleotide variant patterns of (TG)n repeats linked to CD36 deficiency phenotypes

Abstract

CD36 plays a distinct role in immune regulation, lipid transport, and hemostasis. CD36 antigen deficiency has been observed in certain populations, yet its underlying genetic mechanisms remain unclear. Traditional sequencing methods face challenges in haplotype determination, emphasizing the need for advanced technologies like long-read sequencing. In this study, we collected 100 blood samples from donors with type Ⅰ and type Ⅱ CD36 deficiencies as well as from healthy controls, and employed long-read sequencing technology to analyze the haplotype of CD36 gene. All haplotypes harbored (TG) n repeats in intron 3, with repeat numbers of 11–20. These repeats were tightly linked to three distinct downstream SNV patterns (Patterns A, B, and C) after the c.748 + 757 A > G site. Notably, the haplotype combination (TG) n -B was predominant in type Ⅰ CD36 deficiency; in contrast, (TG) n -C was significantly dominant in type Ⅱ cases. These findings suggest the regulatory role of intronic (TG) n repeats and their associated haplotypes in manifesting CD36 deficiency, particularly for type Ⅱ deficiency, which lacks known mutations in the coding region. Our study presents new insights into the noncoding genetic architecture of CD36 and highlights the application of long-read sequencing in resolving complex haplotypes, thereby challenging traditional single-nucleotide variant-based classification methods.