Sickle cell disease (SCD) is a blood disorder caused by a point mutation on the beta globin gene resulting in the synthesis of abnormal hemoglobin. Fetal hemoglobin (HbF) reduces disease severity, but the levels vary from one individual to another. Most research has focused on common genetic variants which differ across populations and hence do not fully account for HbF variation. We investigated rare and common genetic variants that influence HbF levels in 14 SCD patients to elucidate variants and pathways in SCD patients with extreme HbF levels (≥7.7% for high HbF) and (≤2.5% for low HbF) in Tanzania. We performed targeted next generation sequencing (Illumina_Miseq) covering exonic and other significant fetal hemoglobin-associated loci, including BCL11A, MYB, HOXA9, HBB, HBG1, HBG2, CHD4, KLF1, MBD3, ZBTB7A and PGLYRP1. Results revealed a range of genetic variants, including bi-allelic and multi-allelic SNPs, frameshift insertions and deletions, some of which have functional importance. Notably, there were significantly more deletions in individuals with high HbF levels (11% vs 0.9%). We identified frameshift deletions in individuals with high HbF levels and frameshift insertions in individuals with low HbF. CHD4 and MBD3 genes, interacting in the same sub-network, were identified to have a significant number of pathogenic or non-synonymous mutations in individuals with low HbF levels, suggesting an important role of epigenetic pathways in the regulation of HbF synthesis. This study provides new insights in selecting essential variants and identifying potential biological pathways associated with extreme HbF levels in SCD interrogating multiple genomic variants associated with HbF in SCD.

中文翻译：

---

识别与坦桑尼亚镰状细胞病中胎儿血红蛋白极端水平相关的遗传变异和途径。

镰状细胞病（SCD）是一种血液疾病，由β珠蛋白基因上的点突变引起，导致合成异常的血红蛋白。胎儿血红蛋白（HbF）降低了疾病的严重程度，但水平因人而异。大多数研究都集中在不同人群之间常见的遗传变异上，因此不能完全说明HbF变异。我们调查了影响14名SCD患者HbF水平的罕见和常见遗传变异，以阐明坦桑尼亚极端HbF水平（高HbF≥7.7％）和低HbF≤2.5％的SCD患者的变异和途径。我们进行了靶向下一代测序（Illumina_Miseq），涵盖了外显子和其他与胎儿血红蛋白相关的基因座，包括BCL11A，MYB，HOXA9，HBB，HBG1，HBG2，CHD4，KLF1，MBD3，ZBTB7A和PGLYRP1。结果显示了一系列遗传变异，包括双等位基因和多等位基因SNP，移码插入和缺失，其中一些具有功能重要性。值得注意的是，高HbF水平的个体中有明显更多的缺失（11％比0.9％）。我们在高H​​bF水平的个体中发现了移码缺失，在低HbF个体中发现了移码插入。在低HbF水平的个体中，CHD4和MBD3基因在同一子网中相互作用，被发现具有大量致病性或非同义突变，表明表观遗传途径在HbF合成调控中具有重要作用。