Whole exome sequencing and rare variant association study to identify genetic modifiers, <i>KLF1</i> mutations, and a novel double mutation in Thai patients with hemoglobin E/beta-thalassemia

Clinical manifestations of patients with Hemoglobin E/beta-thalassemia vary from mild to severe phenotypes despite exhibiting the same genotype. Studies have partially identified genetic modifiers. We aimed to study the association between rare variants in protein-coding regions and clinical severity in Thai patients. From April to November 2018, a case–control study was conducted based on clinical information and DNA samples collected from Thai patients with hemoglobin E/beta-thalassemia over the age of four years. Cases were patients with severe symptoms, while patients with mild symptoms acted as controls. Whole exome sequencing and rare variant association study were used to analyze the data. All 338 unrelated patients were classified into 165 severe and 173 mild cases. Genotypes comprised 81.4% of hemoglobin E/beta-thalassemia, 2.7% of homozygous or compound heterozygous beta-thalassemia, and 0.3% of (δβ)⁰ thalassemia Hb E while 15.7% of samples were not classified as beta-thalassemia. A novel cis heterozygotes of IVS I-7 (A &gt; T) and codon 26 (G &gt; A) was identified. Six genes (<i>COL4A3</i>, <i>DLK1</i>, <i>FAM186A</i>, <i>PZP</i>, <i>THPO</i>, and <i>TRIM51</i>) showed the strongest associations with severity (observed <i>p</i>-values of &lt;0.05; significance lost after correction for multiplicity). Among known modifiers, <i>KLF1</i> variants were found in four mild patients and one severe patient. No rare variants were identified as contributors to the clinical heterogeneity of hemoglobin E/beta-thalassemia. <i>KLF1</i> mutations are potential genetic modifiers. Studies to identify genetic factors are still important and helpful for predicting severity and developing targeted therapy.