Detection of maternal carriers of common α-thalassemia deletions from cell-free DNA

α-Thalassemia is a common inherited blood disorder manifested mainly by the deletions of α-globin genes. In geographical areas with high carrier frequencies, screening of α-thalassemia carrier state is therefore of vital importance. This study presents a novel method for identifying female carriers of common α-thalassemia deletions using samples routinely taken for non-invasive prenatal tests for screening of fetal chromosomal aneuploidies. A total of 68,885 Vietnamese pregnant women were recruited and α-thalassemia statuses were determined by gap-PCR, revealing 5344 women (7.76%) carried deletions including αα/−−(SEA) (4.066%), αα/−α(3.7) (2.934%), αα/−α(4.2) (0.656%), and rare genotypes (0.102%). A two-stage model was built to predict these α-thalassemia deletions from targeted sequencing of the HBA gene cluster on maternal cfDNA. Our method achieved F1-scores of 97.14–99.55% for detecting the three common genotypes and 94.74% for detecting rare genotypes (−α(3.7)/−α(4.2), αα/−−(THAI), −α(3.7)/−−(SEA), −α(4.2)/−−(SEA)). Additionally, the positive predictive values were 100.00% for αα/αα, 99.29% for αα/−−(SEA), 94.87% for αα/−α(3.7), and 96.51% for αα/−α(4.2); and the negative predictive values were 97.63%, 99.99%, 99.99%, and 100.00%, respectively. As NIPT is increasingly adopted for pregnant women, utilizing cfDNA from NIPT to detect maternal carriers of common α-thalassemia deletions will be cost-effective and expand the benefits of NIPT.