Unmasking rare thalassemia variants through whole-exome sequencing in Huadu District, China: An observational study

In regions with a high prevalence of thalassemia, conventional diagnostic methods may fail to detect atypical or complex genetic variants. Whole-exome sequencing (WES) provides a comprehensive strategy to identify such variants, allowing more accurate genotype-phenotype correlation. Nevertheless, its optimal integration into clinical workflows and its incremental value over standard diagnostic approaches remain uncertain. This study aimed to evaluate the clinical utility of WES in a heterogeneous patient cohort and to propose a framework for its rational use in endemic settings. WES was performed on 21 patients with clinically suspected thalassemia from Huadu District, Guangzhou, stratified by severity. Variant analysis encompassed both coding and noncoding regions. On average, 5440.7 ± 94.3 insertions/deletions and 49,719.3 ± 492.5 single-nucleotide variants per individual were detected. Frameshift insertions/deletions were predominantly localized to the HBB gene. Noncoding single-nucleotide variants in 3' untranslated regions were associated with reduced mean corpuscular hemoglobin (HGB) concentration (301 ± 25 g/L in patients with vs 321 ± 18 g/L in those without 3' untranslated region variants, P = .008). Compound heterozygosity involving classical β-thalassemia mutations (CD41/42(-TTCT) β0 and IVS-II-654(C>T) β+) accounted for 85.7% of severe cases. Three rare non-β-globin variants were identified: MYB c.107G>A (p.R36H) in 1 case, a variant of uncertain significance potentially linked to fetal HGB regulation; HBD c.440A>T (p.H147L) in another, which produced an artificially normalized HbA2 value (3.1%), creating a risk of β-thalassemia misdiagnosis; and HBG1 c.364G>T (p.E122*) in a third case, co-occurring with α-thalassemia and iron deficiency. HGB levels declined significantly with increasing clinical severity (mild: 99.7 ± 2.5 g/L; very severe: 31.0 ± 26.1 g/L, P < .05). WES proved to be a powerful diagnostic tool, identifying causative or contributing genetic variants in all patients in this cohort, including those with complex or atypical presentations. Although it may not yet be feasible as a first-tier screening approach due to cost constraints, our findings strongly support the selective integration of WES into existing thalassemia diagnostic workflows in endemic regions. Such an approach enhances diagnostic precision, clarifies complex genotypes, and can guide more individualized management strategies.